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Chen R, Hao Z, Ye J, Zhao X, Hu S, Luo J, Li J, Wu H, Liang X, Shen C, Deng M, Zhang W, Zhu Z, Qin Y, Hu G, Zhang L, Cao F, Liu Y, Liu R, Sun Q, Wei H, Wang Z. Decoding post-mortem infection dynamics of SARS-CoV-2, IAV and RSV: New insights for public health and emerging infectious diseases management. J Infect 2025; 90:106489. [PMID: 40268146 DOI: 10.1016/j.jinf.2025.106489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Revised: 03/25/2025] [Accepted: 04/12/2025] [Indexed: 04/25/2025]
Abstract
OBJECTIVES The persistence and infectivity of respiratory viruses in cadavers remain poorly characterized, posing significant biosafety risks for forensic and healthcare professionals. This study systematically evaluates the post-mortem stability and transmission potential of SARS-CoV-2, influenza A virus (IAV), and respiratory syncytial virus (RSV) under varying environmental conditions, providing critical insights into viral kinetics. METHODS To assess the post-mortem stability of SARS-CoV-2, tissue samples were collected from infected cadavers at 4 ℃, room temperature (RT, 20-22 ℃), and 37 ℃ over a predetermined timeframe. Viral kinetics were analyzed using quantitative assays, while histopathology and immunohistochemistry characterized tissue-specific distribution. Additionally, comparative analyses were conducted both in vitro and in cadaveric tissues to characterize the survival dynamics of IAV and RSV under identical conditions. RESULTS SARS-CoV-2 exhibited prolonged post-mortem infectivity, persisting for up to 5 days at RT and 37 ℃ and over 7 days at 4 ℃, with the highest risk of transmission occurring within the first 72 h at RT and 24 h at 37 ℃. In contrast, RSV remained viable for 1-2 days, while IAV persisted for only a few hours post-mortem. Viral decay rates were temperature-dependent and varied across tissues, demonstrating distinct post-mortem survival kinetics. CONCLUSIONS This study presents the first comprehensive analysis of viral persistence in cadavers, revealing prolonged SARS-CoV-2 stability compared to IAV and RSV. These findings underscore the need for enhanced post-mortem biosafety protocols to mitigate occupational exposure risks in forensic and clinical settings. By elucidating viral decay dynamics across environmental conditions, this research establishes a critical foundation for infection control strategies, informing biosafety policies for emerging respiratory pathogens.
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Affiliation(s)
- Run Chen
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zeyi Hao
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Jian Ye
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Sheng Hu
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Jianliang Luo
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Junhua Li
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
| | - Hao Wu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - XingGong Liang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Chen Shen
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Mingyan Deng
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Wanqing Zhang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zhengyang Zhu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Yudong Qin
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Gengwang Hu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Letong Zhang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Fan Cao
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Yuzhao Liu
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Ruina Liu
- Center for Translational Medicine, Shaanxi Belt and Road Joint Laboratory of Precision Medicine in Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710061, China
| | - Qinru Sun
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Hongping Wei
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei 430023, China.
| | - Zhenyuan Wang
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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Spiteri S, Salamon I, Girolamini L, Pascale MR, Marino F, Derelitto C, Caligaris L, Paghera S, Ferracin M, Cristino S. Surfaces environmental monitoring of SARS-CoV-2: Loop mediated isothermal amplification (LAMP) and droplet digital PCR (ddPCR) in comparison with standard Reverse-Transcription quantitative polymerase chain reaction (RT-qPCR) techniques. PLoS One 2025; 20:e0317228. [PMID: 39899502 PMCID: PMC11790120 DOI: 10.1371/journal.pone.0317228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 12/24/2024] [Indexed: 02/05/2025] Open
Abstract
The persistence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on substrates, and the impact of fomites on Coronavirus Disease 19 (COVID-19) transmission, is until now, widely discussed. Consequently, further investigations are required for a correct risk assessment in high-risk facilities such as hospitals, healthcare facilities (HCFs), and long-term care facilities (LTCFs). Therefore, appropriate surveillance and disinfection programs represent the best approach to guarantee the safety of these communities. This study proposes an environmental SARS-CoV-2 surfaces routine monitoring approach in HCF and communities' settings, to provide rapid and effective evaluation of surface hygienic conditions and the effectiveness of applied sanitization measures. Surfaces samples (n = 118) were collected using the SRK® kit (Copan Italia) from 2020 to 2023. Three molecular techniques were compared: Reverse Transcription Loop mediated isothermal AMPlification (RT-LAMP, Enbiotech), Reverse-Transcription quantitative polymerase chain reaction (RT-qPCR) (RT-qPCR, Seegene) and droplet digital PCR (ddPCR, Bio-Rad). For ddPCR, two RNA extraction methods were compared: TRIzol LS (Invitrogen) versus QIAmp Viral Mini kit (QIAGEN), showing how the latter is more suitable for surfaces. Regarding the quantitative ddPCR results, the ROC analysis allowed to reduce the manufacturer cut-off for droplets number (from 3 to 1) for the positive samples. Moreover, a new cut-off for the viral RNA copies' number/μL for each target (N1 and N2) on environmental monitoring was fixed at 2,82. The results obtained using the QIAmp kit, suggested that the N2 target is more stable in the environment and could be most suitable for the virus environmental detection. The percentage of positive samples was similar among the techniques (26% for RT-LAMP, 36% for ddPCR and 23% for RT-qPCR). Using RT-qPCR as reference method, a sensitivity (SE) of 30% for RT-LAMP and 41% for ddPCR was observed. By contrast, specificity (SP) was higher for RT-LAMP (75%) respect to ddPCR (66%). Comparing the faster RT-LAMP with the sensitive ddPCR the 26% and 74% of SE and SP for RT-LAMP, were reported. The low sensitivity for RT-LAMP and ddPCR could be explained with the use of clinical rather than environmental kits, other than the changing in the virus prevalence during the sampling campaign. Although the RT-LAMP requires improvements in term of SE and SP, this research presents an innovative environmental monitoring and prevention method for SARS-CoV-2, that could be extended to other pathogens that are under environmental surveillance.
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Affiliation(s)
- Simona Spiteri
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Irene Salamon
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Luna Girolamini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Maria Rosaria Pascale
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federica Marino
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Carlo Derelitto
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Laura Caligaris
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Manuela Ferracin
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Sandra Cristino
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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Thompson C, Leal CV, da Silva Faustino R, Leomil L, Jagadeeshwari U, Sharma R, de Oliveira M, Tschoeke D, Felix T, Macedo L, Khouri R, Koolen H, Landuci F, de Rezende C, Strobel Í, de Moraes L, P Ramos PI, de Souza H, Motta F, Barral-Netto M, Aguiar-Oliveira MDL, de Siqueira M, Sasikala C, Thompson F. Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:178089. [PMID: 39705959 DOI: 10.1016/j.scitotenv.2024.178089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 12/10/2024] [Accepted: 12/10/2024] [Indexed: 12/23/2024]
Abstract
The genomic monitoring of SARS-CoV-2 variants of concern (VOCs) in riverine and sewage water has been widely used as an epidemiological tool worldwide. But its utility for epidemiological assessments still needs to be evaluated in some areas. Our study encompassed thirteen Brazilian rivers spanning a vast urban expanse across the states of Rio de Janeiro, São Paulo, and Paraná. The sampled rivers in Rio de Janeiro are heavily contaminated with sewage. Meanwhile, the Indian samples were all wastewater before joining the water bodies from urban regions (Andhra Pradesh and Telangana). The viral copies were quantified using quantitative polymerase chain reaction (qPCR) in all examined samples (N = 91). The abundance of viral particles varied from 567 to 85,700,000 copies/ml. Subsequently, Illumina CovidSeq was applied to identify the major variants. In Brazil, while a single SARS-CoV-2 VOC was identified for just a few samples (6/50, 12 %), most samples harbored multiple VOCs (44/50, 88 %). In India only one probed sample had a single variant identified. Gamma (2021) and Omicron (2021 and 2022) were the most abundant variants. Delta and Omicron genetic material were detected in Rio de Janeiro city rivers before Brazil's first cases of these variants. Several negative samples in the Real-Time RT-PCR (qPCR) turned out to have SARS-CoV-2 sequences suggesting CovidSeq was more sensitive than RT-PCR for virus detection in environmental samples. Sewage surveillance holds promise for early detection of emerging variants driving pandemic waves, exemplified by the Delta and Omicron variants, potentially offering a preemptive advantage over clinical sample reports.
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Affiliation(s)
- Cristiane Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Camille V Leal
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Luciana Leomil
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, JNTUH University College Of Engineering, Science & Technology Hyderabad (UCESTH), India
| | - Richa Sharma
- Bacterial Discovery Laboratory, Centre for Environment, JNTUH University College Of Engineering, Science & Technology Hyderabad (UCESTH), India
| | - Marcelo de Oliveira
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo Tschoeke
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thais Felix
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Larissa Macedo
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo Khouri
- Medicine and Precision Health Laboratory (MeSP2), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil
| | | | - Felipe Landuci
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos de Rezende
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), State University of Northern of Rio de Janeiro Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil
| | - Ícaro Strobel
- Medicine and Precision Health Laboratory (MeSP2), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil
| | - Laíse de Moraes
- Medicine and Precision Health Laboratory (MeSP2), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil
| | - Pablo Ivan P Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil
| | - Heitor de Souza
- Department of Clinical Medicine, Hospital Universitário Clementino Fraga Filho (HUCFF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fernando Motta
- Laboratory of Respiratory Viruses, Instituto Oswaldo Cruz -FIOCRUZ, Rio de Janeiro, Brazil
| | - Manoel Barral-Netto
- Medicine and Precision Health Laboratory (MeSP2), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil
| | | | - Marilda de Siqueira
- Laboratory of Respiratory Viruses, Instituto Oswaldo Cruz -FIOCRUZ, Rio de Janeiro, Brazil
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, JNTUH University College Of Engineering, Science & Technology Hyderabad (UCESTH), India; Smart Microbiological Services, 5-3-357, Rashtrapathi Road, Secunderabad 500003, India.
| | - Fabiano Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Davenport C, Arevalo-Rodriguez I, Mateos-Haro M, Berhane S, Dinnes J, Spijker R, Buitrago-Garcia D, Ciapponi A, Takwoingi Y, Deeks JJ, Emperador D, Leeflang MMG, Van den Bruel A. The effect of sample site and collection procedure on identification of SARS-CoV-2 infection. Cochrane Database Syst Rev 2024; 12:CD014780. [PMID: 39679851 PMCID: PMC11648846 DOI: 10.1002/14651858.cd014780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
BACKGROUND Sample collection is a key driver of accuracy in the diagnosis of SARS-CoV-2 infection. Viral load may vary at different anatomical sampling sites and accuracy may be compromised by difficulties obtaining specimens and the expertise of the person taking the sample. It is important to optimise sampling accuracy within cost, safety and accessibility constraints. OBJECTIVES To compare the sensitivity of different sampling collection sites and methods for the detection of current SARS-CoV-2 infection with any molecular or antigen-based test. SEARCH METHODS Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 22 February 2022. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions. SELECTION CRITERIA We included studies of symptomatic or asymptomatic people with suspected SARS-CoV-2 infection undergoing testing. We included studies of any design that compared results from different sample types (anatomical location, operator, collection device) collected from the same participant within a 24-hour period. DATA COLLECTION AND ANALYSIS Within a sample pair, we defined a reference sample and an index sample collected from the same participant within the same clinical encounter (within 24 hours). Where the sample comparison was different anatomical sites, the reference standard was defined as a nasopharyngeal or combined naso/oropharyngeal sample collected into the same sample container and the index sample as the alternative anatomical site. Where the sample comparison was concerned with differences in the sample collection method from the same site, we defined the reference sample as that closest to standard practice for that sample type. Where the sample pair comparison was concerned with differences in personnel collecting the sample, the more skilled or experienced operator was considered the reference sample. Two review authors independently assessed the risk of bias and applicability concerns using the QUADAS-2 and QUADAS-C checklists, tailored to this review. We present estimates of the difference in the sensitivity (reference sample (%) minus index sample sensitivity (%)) in a pair and as an average across studies for each index sampling method using forest plots and tables. We examined heterogeneity between studies according to population (age, symptom status) and index sample (time post-symptom onset, operator expertise, use of transport medium) characteristics. MAIN RESULTS This review includes 106 studies reporting 154 evaluations and 60,523 sample pair comparisons, of which 11,045 had SARS-CoV-2 infection. Ninety evaluations were of saliva samples, 37 nasal, seven oropharyngeal, six gargle, six oral and four combined nasal/oropharyngeal samples. Four evaluations were of the effect of operator expertise on the accuracy of three different sample types. The majority of included evaluations (146) used molecular tests, of which 140 used RT-PCR (reverse transcription polymerase chain reaction). Eight evaluations were of nasal samples used with Ag-RDTs (rapid antigen tests). The majority of studies were conducted in Europe (35/106, 33%) or the USA (27%) and conducted in dedicated COVID-19 testing clinics or in ambulatory hospital settings (53%). Targeted screening or contact tracing accounted for only 4% of evaluations. Where reported, the majority of evaluations were of adults (91/154, 59%), 28 (18%) were in mixed populations with only seven (4%) in children. The median prevalence of confirmed SARS-CoV-2 was 23% (interquartile (IQR) 13%-40%). Risk of bias and applicability assessment were hampered by poor reporting in 77% and 65% of included studies, respectively. Risk of bias was low across all domains in only 3% of evaluations due to inappropriate inclusion or exclusion criteria, unclear recruitment, lack of blinding, nonrandomised sampling order or differences in testing kit within a sample pair. Sixty-eight percent of evaluation cohorts were judged as being at high or unclear applicability concern either due to inflation of the prevalence of SARS-CoV-2 infection in study populations by selectively including individuals with confirmed PCR-positive samples or because there was insufficient detail to allow replication of sample collection. When used with RT-PCR • There was no evidence of a difference in sensitivity between gargle and nasopharyngeal samples (on average -1 percentage points, 95% CI -5 to +2, based on 6 evaluations, 2138 sample pairs, of which 389 had SARS-CoV-2). • There was no evidence of a difference in sensitivity between saliva collection from the deep throat and nasopharyngeal samples (on average +10 percentage points, 95% CI -1 to +21, based on 2192 sample pairs, of which 730 had SARS-CoV-2). • There was evidence that saliva collection using spitting, drooling or salivating was on average -12 percentage points less sensitive (95% CI -16 to -8, based on 27,253 sample pairs, of which 4636 had SARS-CoV-2) compared to nasopharyngeal samples. We did not find any evidence of a difference in the sensitivity of saliva collected using spitting, drooling or salivating (sensitivity difference: range from -13 percentage points (spit) to -21 percentage points (salivate)). • Nasal samples (anterior and mid-turbinate collection combined) were, on average, 12 percentage points less sensitive compared to nasopharyngeal samples (95% CI -17 to -7), based on 9291 sample pairs, of which 1485 had SARS-CoV-2. We did not find any evidence of a difference in sensitivity between nasal samples collected from the mid-turbinates (3942 sample pairs) or from the anterior nares (8272 sample pairs). • There was evidence that oropharyngeal samples were, on average, 17 percentage points less sensitive than nasopharyngeal samples (95% CI -29 to -5), based on seven evaluations, 2522 sample pairs, of which 511 had SARS-CoV-2. A much smaller volume of evidence was available for combined nasal/oropharyngeal samples and oral samples. Age, symptom status and use of transport media do not appear to affect the sensitivity of saliva samples and nasal samples. When used with Ag-RDTs • There was no evidence of a difference in sensitivity between nasal samples compared to nasopharyngeal samples (sensitivity, on average, 0 percentage points -0.2 to +0.2, based on 3688 sample pairs, of which 535 had SARS-CoV-2). AUTHORS' CONCLUSIONS When used with RT-PCR, there is no evidence for a difference in sensitivity of self-collected gargle or deep-throat saliva samples compared to nasopharyngeal samples collected by healthcare workers when used with RT-PCR. Use of these alternative, self-collected sample types has the potential to reduce cost and discomfort and improve the safety of sampling by reducing risk of transmission from aerosol spread which occurs as a result of coughing and gagging during the nasopharyngeal or oropharyngeal sample collection procedure. This may, in turn, improve access to and uptake of testing. Other types of saliva, nasal, oral and oropharyngeal samples are, on average, less sensitive compared to healthcare worker-collected nasopharyngeal samples, and it is unlikely that sensitivities of this magnitude would be acceptable for confirmation of SARS-CoV-2 infection with RT-PCR. When used with Ag-RDTs, there is no evidence of a difference in sensitivity between nasal samples and healthcare worker-collected nasopharyngeal samples for detecting SARS-CoV-2. The implications of this for self-testing are unclear as evaluations did not report whether nasal samples were self-collected or collected by healthcare workers. Further research is needed in asymptomatic individuals, children and in Ag-RDTs, and to investigate the effect of operator expertise on accuracy. Quality assessment of the evidence base underpinning these conclusions was restricted by poor reporting. There is a need for further high-quality studies, adhering to reporting standards for test accuracy studies.
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Affiliation(s)
- Clare Davenport
- Department of Applied Health Science, School of Health Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Miriam Mateos-Haro
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Clinical Medicine and Public Health Programme, Universidad de Granada, Granada, Spain
| | - Sarah Berhane
- Department of Applied Health Science, School of Health Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jacqueline Dinnes
- Department of Applied Health Science, School of Health Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - René Spijker
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Diana Buitrago-Garcia
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
- Hospital Universitario Mayor - Méderi. Universidad del Rosario, Bogotá, Colombia
| | - Agustín Ciapponi
- Argentine Cochrane Centre, Institute for Clinical Effectiveness and Health Policy (IECS-CONICET), Buenos Aires, Argentina
| | - Yemisi Takwoingi
- Department of Applied Health Science, School of Health Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Department of Applied Health Science, School of Health Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | - Mariska M G Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam, Netherlands
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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5
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Al-Momani H, Aolymat I, Al Haj Mahmoud S. Critical appraisal of how COVID-19 infection and imposed lockdowns have impacted gastroesophageal reflux: A review. Medicine (Baltimore) 2024; 103:e38074. [PMID: 38728518 PMCID: PMC11081575 DOI: 10.1097/md.0000000000038074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/10/2024] [Indexed: 05/12/2024] Open
Abstract
Previous literature has demonstrated that COronaVIrus Disease of 2019 (COVID-19) impacts an individual gastrointestinal tract (GIT), causing symptoms like nausea, diarrhea, and loss of appetite. Severe acute respiratory syndrome coronavirus RNA has been discovered in the stool of infected individuals in earlier research. It was discovered that severe acute respiratory syndrome coronavirus was significantly expressed in the GIT, indicating that the virus can also infect the digestive system. Angiotensin-converting enzyme 2 functions as the viral receptor. The chronic illness known as gastroesophageal reflux disease (GERD) is typified by frequent reflux of stomach acid into the esophagus. By triggering the sensitized esophageal-bronchial neuronal circuit or aspirating into the airways (microaspiration), GER exacerbates respiratory diseases. Aspiration is a well-known risk to be considered when treating patients in intensive care units. Strong genetic correlations have been identified between COVID-19 infection and GERD susceptibility, suggesting a shared genetic basis for both conditions. Nonetheless, even though GERD, extraesophageal reflex, and COVID-19 have a number of significant risk factors and exhibit similar symptoms, the relationship between these illnesses has not yet been examined in depth. This review is the first of its kind to critically examine the association between the COVID-19 epidemic and GER and its associated diseases. The key objective of this work is to promote the creation of prevention plans, treatment plans, and guidelines while also enhancing and optimizing our understanding of the relationship between COVID-19 and GERs.
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Affiliation(s)
- Hafez Al-Momani
- Department of Microbiology, Pathology and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Iman Aolymat
- Department of Anatomy, Physiology & Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Sameer Al Haj Mahmoud
- Department of Basic Medical Science, Faculty of Medicine, Al-Balqa’ Applied University, Al-Salt, Jordan
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6
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Sharma V, Takamura H, Biyani M, Honda R. Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies. BIOSENSORS 2024; 14:115. [PMID: 38534222 DOI: 10.3390/bios14030115] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/10/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Wastewater-based epidemiology (WBE) is an effective and efficient tool for the early detection of infectious disease outbreaks in a community. However, currently available methods are laborious, costly, and time-consuming due to the low concentration of viruses and the presence of matrix chemicals in wastewater that may interfere with molecular analyses. In the present study, we designed a highly sensitive "Quick Poop (wastewater with fecal waste) Sensor" (termed, QPsor) using a joint approach of Nanotrap microbiome particles and RICCA (RNA Isothermal Co-Assisted and Coupled Amplification). Using QPsor, the WBE study showed a strong correlation with standard PEG concentrations and the qPCR technique. Using a closed format for a paper-based lateral flow assay, we were able to demonstrate the potential of our assay as a real-time, point-of-care test by detecting the heat-inactivated SARS-CoV-2 virus in wastewater at concentrations of 100 copies/mL and within one hour. As a proof-of-concept demonstration, we analyzed the presence of viral RNA of the SARS-CoV-2 virus and PMMoV in raw wastewater samples from wastewater treatment plants on-site and within 60 min. The results show that the QPsor method can be an effective tool for disease outbreak detection by combining an AI-enabled case detection model with real-time on-site viral RNA extraction and amplification, especially in the absence of intensive clinical laboratory facilities. The lab-free, lab-quality test capabilities of QPsor for viral prevalence and transmission in the community can contribute to the efficient management of pandemic situations.
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Affiliation(s)
- Vishnu Sharma
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Hitomi Takamura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
| | - Manish Biyani
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
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7
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Yan C, Hu YN, Gui ZC, Lai TN, Ali W, Wan NH, He SS, Liu S, Li X, Jin TX, Nasir ZA, Alcega SG, Coulon F. Quantitative SARS-CoV-2 exposure assessment for workers in wastewater treatment plants using Monte-Carlo simulation. WATER RESEARCH 2024; 248:120845. [PMID: 37976948 DOI: 10.1016/j.watres.2023.120845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023]
Abstract
Several studies on COVID-19 pandemic have shown that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originating from human stool are detected in raw sewage for several days, leading to potential health risks for workers due to the production of bioaerosols and droplets during wastewater treatment process. In this study, data of SARS-CoV-2 concentrations in wastewater were gathered from literatures, and a quantitative microbial risk assessment with Monte Carlo simulation was used to estimate the daily probability of infection risk through exposure to viable infectious viral airborne particles of the workers during four seasons and under six environmental conditions. Inhalation of bioaerosols and direct ingestion of wastewater droplets were selected as exposure pathways. Spearman rank correlation coefficients were used for sensitivity analysis to identify the variables with the greatest influence on the infection risk probability. It was found that the daily probability of infection risk decreased with temperature (T) and relative humidity (RH) increase. The probability of direct droplet ingestion exposure pathway was higher than that of the bioaerosol inhalation pathway. The sensitivity analysis indicated that the most sensitive variable for both exposure pathways was the concentration of SARS-CoV-2 in stool. So, appropriate aeration systems, covering facilities, and effective ventilation are suggested to implement in wastewater treatment plants (WWTPs) to reduce emission concentration. Further to this, the exposure time (t) had a larger variance contribution than T and RH for the bioaerosol inhalation pathway. Implementing measures such as adding more work shifts, mandating personal protective equipment for all workers, and implementing coverage for treatment processes can significantly reduce the risk of infection among workers at WWTPs. These measures are particularly effective during environmental conditions with low temperatures and humidity levels.
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Affiliation(s)
- Cheng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China; Hubei Key Laboratory of Environmental Water Science in the Yangtze River Basin, China University of Geosciences, Wuhan 430074, PR China.
| | - Yi-Ning Hu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Zi-Cheng Gui
- CCDI (Suzhou) exploration and design consultant Co., Ltd., Suzhou 215123, PR China
| | - Tian-Nuo Lai
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Wajid Ali
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Nian-Hong Wan
- Central & Southern China Municipal Engineering Design and Research Institute Co, Ltd., Wuhan 430010, PR China
| | - Shan-Shan He
- Central & Southern China Municipal Engineering Design and Research Institute Co, Ltd., Wuhan 430010, PR China
| | - Sai Liu
- CITIC Treated Water into River Engineering Investment Co., Ltd., Wuhan 430200, PR China
| | - Xiang Li
- Three Gorges Base Development Co., Ltd., Yichang 443002, PR China
| | - Ting-Xu Jin
- Department of Toxicology, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou 215123, PR China; School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, PR China
| | - Zaheer Ahmad Nasir
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Sonia Garcia Alcega
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK6 7AA, UK
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
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8
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Zhao B, Fujita T, Nihei Y, Yu Z, Chen X, Tanaka H, Ihara M. Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166420. [PMID: 37611711 DOI: 10.1016/j.scitotenv.2023.166420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in regions of low prevalence, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Here, we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to December 2022 during the third, fourth, fifth, sixth, seventh, and eighth waves of the COVID-19 outbreak in Japan. Viral RNA was below the limit of detection in all samples during the third and fourth waves. However, by counting the number of positive replicates in qPCR of each sample, we found that the positive ratio to all replicates in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during the third, fourth, and fifth waves. Time-step analysis indicated that, for 2 days either side of symptom onset, COVID-19 patients excreted in their feces large amounts of virus that wastewater surveillance could detect. We also demonstrated that the viral genome copy number in wastewater, as estimated from the positive ratio of SARSA-CoV-2 RNA, was correlated with the number of clinically confirmed cases. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.
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Affiliation(s)
- Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Tomonori Fujita
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Yoshiaki Nihei
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Water Agency Inc., 3-25 Higashi-Goken-cho, Shinjuku-ku, Tokyo 162-0813, Japan
| | - Zaizhi Yu
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Xiaohan Chen
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe-Otsu, Nankoku city, Kochi 783-8502, Japan.
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9
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Wilhelm A, Schoth J, Meinert-Berning C, Bastian D, Blum H, Elsinga G, Graf A, Heijnen L, Ho J, Kluge M, Krebs S, Stange C, Uchaikina A, Dolny R, Wurzbacher C, Drewes JE, Medema G, Tiehm A, Ciesek S, Teichgräber B, Wintgens T, Weber FA, Widera M. Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166540. [PMID: 37634730 DOI: 10.1016/j.scitotenv.2023.166540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results. In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values. All PCR-laboratories reported SARS-CoV-2 genome copy equivalents (GCE) for all spiked samples with a mean intra- and inter-laboratory variability of 19 % and 104 %, respectively, largely reproducing the spike-in scheme. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/ml wastewater and had limited predictive value when analyzing at a genome coverage below 60 %. This interlaboratory test demonstrates that despite highly heterogeneous isolation and analysis procedures, overall SARS-CoV-2 GCE and mutations were determined accurately. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection.
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Affiliation(s)
- Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Johannes Ho
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Mariana Kluge
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Claudia Stange
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Anna Uchaikina
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Regina Dolny
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Andreas Tiehm
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Sandra Ciesek
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D 60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
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10
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Swain RK, Mohanty SS, Thakor M, Sharma AK. Assessment of thermal and temporal stability of SARS-CoV-2 samples using real-time qRT-PCR. Mol Biol Rep 2023; 50:8565-8573. [PMID: 37644371 DOI: 10.1007/s11033-023-08740-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND As per the guidelines of the Indian Council of Medical Research, nasopharyngeal and oropharyngeal swabs in viral transport medium (VTM) are to be stored at 4 °C for less than 5 days and for more than 5 days at -70 °C. Samples are not transported or stored as per prescribed conditions because of the limitations, resulting in an apprehensive diagnosis. The aim of the study was to test the stability of the SARS-CoV-2 sample stored in VTM at different temperatures. METHODS In this study, the stability of 21 positive and 9 negative samples for SARS-CoV-2 was evaluated in commercial VTM at different temperatures (-80 °C, -20 °C, 4 °C, and 25 to 30 °C). Stability was checked for up to 50 days in the above storage conditions at different intervals. PathoDetect™ and Hi-PCR® kits were used for the detection of the four genes of SARS-CoV-2. The Cycle Threshold (Ct) value for determining the positivity of samples for PathoDetect™ was < 40 and for Hi-PCR® was < 38. RESULTS The SARS-CoV-2 confirmatory genes (RdRp and E genes) and the internal housekeeping gene remained detectable even on the 50th day of the study. The Ct of the RdRp and E genes were found to increase with storage duration, but all positive samples remained positive till the end of the study, or the Ct value remained below the cut-off level. The negative samples gave consistent results until the end of the study. When the differences in Ct values were compared between the days in a set of experiments, they were not significantly different except in a few samples. CONCLUSION The SARS-CoV-2 genetic materials in commercial VTM were stable at room temperature to -80 °C for 50 days.
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Affiliation(s)
- Rohit Kumar Swain
- Department of Biological Sciences and Engineering, MANIT, Bhopal, India
| | - S S Mohanty
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India.
| | - Mahendra Thakor
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India
| | - A K Sharma
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India
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11
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Rabe A, Ravuri S, Burnor E, Steele JA, Kantor RS, Choi S, Forman S, Batjiaka R, Jain S, León TM, Vugia DJ, Yu AT. Correlation between wastewater and COVID-19 case incidence rates in major California sewersheds across three variant periods. JOURNAL OF WATER AND HEALTH 2023; 21:1303-1317. [PMID: 37756197 PMCID: wh_2023_173 DOI: 10.2166/wh.2023.173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Monitoring for COVID-19 through wastewater has been used for adjunctive public health surveillance, with SARS-CoV-2 viral concentrations in wastewater correlating with incident cases in the same sewershed. However, the generalizability of these findings across sewersheds, laboratory methods, and time periods with changing variants and underlying population immunity has not been well described. The California Department of Public Health partnered with six wastewater treatment plants starting in January 2021 to monitor wastewater for SARS-CoV-2, with analyses performed at four laboratories. Using reported PCR-confirmed COVID-19 cases within each sewershed, the relationship between case incidence rates and wastewater concentrations collected over 14 months was evaluated using Spearman's correlation and linear regression. Strong correlations were observed when wastewater concentrations and incidence rates were averaged (10- and 7-day moving window for wastewater and cases, respectively, ρ = 0.73-0.98 for N1 gene target). Correlations remained strong across three time periods with distinct circulating variants and vaccination rates (winter 2020-2021/Alpha, summer 2021/Delta, and winter 2021-2022/Omicron). Linear regression revealed that slopes of associations varied by the dominant variant of concern, sewershed, and laboratory (β = 0.45-1.94). These findings support wastewater surveillance as an adjunctive public health tool to monitor SARS-CoV-2 community trends.
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Affiliation(s)
- Angela Rabe
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA; These first authors contributed equally to this manuscript. E-mail:
| | - Sindhu Ravuri
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA; These first authors contributed equally to this manuscript
| | - Elisabeth Burnor
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project (SCCWRP), Department of Microbiology, Costa Mesa, CA, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Samuel Choi
- Orange County Sanitation District, Fountain Valley, CA, USA
| | - Stanislav Forman
- Zymo Research Corp. Department of Sample Collection and Nucleic Acid Purification, Zymo Research Corp., Irvine, CA, USA
| | - Ryan Batjiaka
- San Francisco Public Utilities Commission, San Francisco, CA, USA
| | - Seema Jain
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA
| | - Tomás M León
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA
| | - Duc J Vugia
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA
| | - Alexander T Yu
- California Department of Public Health COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond and Sacramento, CA, USA
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12
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Zippi M, Fiorino S, Hong W, de Biase D, Gallo CG, Grottesi A, Centorame A, Crispino P. Post-COVID-19 cholangiopathy: A systematic review. World J Meta-Anal 2023; 11:229-237. [DOI: 10.13105/wjma.v11.i5.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The recent and still ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entailed various long-term complications, including post-infectious cholangiopathy.
AIM To identify the available studies concerning post-coronavirus disease 2019 (COVID-19) cholangiopathy.
METHODS An extensive bibliographical search was carried out in PubMed and in Cochrane Library to identify the articles (retrospective and prospective studies, cohort studies, case series and case reports) published between January 1, 2020 and August 22, 2022, using both MeSH terms and free-language keywords: cholangiopathy; COVID-19; post-COVID-19 cholangiopathy; SARS-CoV-2.
RESULTS Thirteen studies fulfilled the inclusion criteria, which included 64 patients suffering from this condition. The patients were male in 82.8% of cases. Liver transplant was executed in 6 patients and scheduled in 7 patients, while 2 patients refused the surgical approach. Therefore in 23.4% of the cases, performing this procedure appeared to be necessary.
CONCLUSION This review has revealed that generally the involvement of the liver in the course of SARS-CoV-2 infection is mild and transient, inducing cholestasis of cholangiocytes but can also be severe enough to cause organ failure in some cases.
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Affiliation(s)
- Maddalena Zippi
- Unit of Gastroenterology and Digestive Endoscopy, Sandro Pertini Hospital, Rome 00157, Italy
| | - Sirio Fiorino
- Unit of Internal Medicine, Maggiore Hospital, Local Health Unit of Bologna, Bologna 40133, Italy
| | - Wandong Hong
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Alfonso Grottesi
- Unit of General Surgery, Sandro Pertini Hospital, Rome 00157, Italy
| | | | - Pietro Crispino
- Unit of Emergency Medicine, Santa Maria Goretti Hospital, Latina 04100, Italy
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13
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Kim DY, Lin MY, Jennings C, Li H, Jung JH, Moore NM, Ghinai I, Black SR, Zaccaro DJ, Brofman J, Hayden MK, for the CDC Prevention Epicenter Program. Duration of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Shedding Among Patients With Severe or Critical Coronavirus Disease 2019 (COVID-19). Clin Infect Dis 2023; 76:e416-e425. [PMID: 35607802 PMCID: PMC9213867 DOI: 10.1093/cid/ciac405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Patterns of shedding replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in severe or critical COVID-19 are not well characterized. We investigated the duration of replication-competent SARS-CoV-2 shedding in upper and lower airway specimens from patients with severe or critical coronavirus disease 2019 (COVID-19). METHODS We enrolled patients with active or recent severe or critical COVID-19 who were admitted to a tertiary care hospital intensive care unit (ICU) or long-term acute care hospital (LTACH) because of COVID-19. Respiratory specimens were collected at predefined intervals and tested for SARS-CoV-2 using viral culture and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Clinical and epidemiologic metadata were reviewed. RESULTS We collected 529 respiratory specimens from 78 patients. Replication-competent virus was detected in 4 of 11 (36.3%) immunocompromised patients up to 45 days after symptom onset and in 1 of 67 (1.5%) immunocompetent patients 10 days after symptom onset (P = .001). All culture-positive patients were in the ICU cohort and had persistent or recurrent symptoms of COVID-19. Median time from symptom onset to first specimen collection was 15 days (range, 6-45) for ICU patients and 58.5 days (range, 34-139) for LTACH patients. SARS-CoV-2 RNA was detected in 40 of 50 (80%) ICU patients and 7 of 28 (25%) LTACH patients. CONCLUSIONS Immunocompromise and persistent or recurrent symptoms were associated with shedding of replication-competent SARS-CoV-2, supporting the need for improving respiratory symptoms in addition to time as criteria for discontinuation of transmission-based precautions. Our results suggest that the period of potential infectiousness among immunocompetent patients with severe or critical COVID-19 may be similar to that reported for patients with milder disease.
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Affiliation(s)
- Do Young Kim
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Chicago Department of Public Health, Chicago, Illinois, USA
| | - Michael Y Lin
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Cheryl Jennings
- Rush Research Cores, Rush University Medical Center, Chicago, Illinois, USA
| | - Haiying Li
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Jae Hyung Jung
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Nicholas M Moore
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
- Department of Medical Laboratory Science, Rush University Medical Center, Chicago, Illinois, USA
| | - Isaac Ghinai
- Chicago Department of Public Health, Chicago, Illinois, USA
| | | | - Daniel J Zaccaro
- Social & Scientific Systems, Inc, a DLH Holdings Corporation, Durham, North Carolina, USA
| | | | - Mary K Hayden
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
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14
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Zippi M, Fiorino S, Hong W, de Biase D, Gallo CG, Grottesi A, Centorame A, Crispino P. Post-COVID-19 cholangiopathy: A systematic review. World J Meta-Anal 2023; 11:29-37. [DOI: 10.13105/wjma.v11.i1.29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/13/2022] [Accepted: 11/23/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The recent and still ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entailed various long-term complications, including post-infectious cholangiopathy.
AIM To identify the available studies concerning post-coronavirus disease 2019 (COVID-19) cholangiopathy.
METHODS An extensive bibliographical search was carried out in PubMed and in Cochrane Library to identify the articles (retrospective and prospective studies, cohort studies, case series and case reports) published between January 1, 2020 and August 22, 2022, using both MeSH terms and free-language keywords: cholangiopathy; COVID-19; post-COVID-19 cholangiopathy; SARS-CoV-2.
RESULTS Thirteen studies fulfilled the inclusion criteria, which included 64 patients suffering from this condition. The patients were male in 82.8% of cases. Liver transplant was executed in 6 patients and scheduled in 7 patients, while 2 patients refused the surgical approach. Therefore in 23.4% of the cases, performing this procedure appeared to be necessary.
CONCLUSION This review has revealed that generally the involvement of the liver in the course of SARS-CoV-2 infection is mild and transient, inducing cholestasis of cholangiocytes but can also be severe enough to cause organ failure in some cases.
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Affiliation(s)
- Maddalena Zippi
- Unit of Gastroenterology and Digestive Endoscopy, Sandro Pertini Hospital, Rome 00157, Italy
| | - Sirio Fiorino
- Unit of Internal Medicine, Maggiore Hospital, Local Health Unit of Bologna, Bologna 40133, Italy
| | - Wandong Hong
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Alfonso Grottesi
- Unit of General Surgery, Sandro Pertini Hospital, Rome 00157, Italy
| | | | - Pietro Crispino
- Unit of Emergency Medicine, Santa Maria Goretti Hospital, Latina 04100, Italy
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M. Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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Clinical and epidemiological investigation of a child with asymptomatic COVID-19 infection following reoccurrence. Health Inf Sci Syst 2022; 10:18. [PMID: 36016579 PMCID: PMC9399974 DOI: 10.1007/s13755-022-00188-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Objective To investigate the case of a child infected with coronavirus disease 2019 (COVID-19) who had subsequent viral reactivation. Methods We retrospectively analyzed the clinical manifestations, epidemiological data, laboratory and imaging examinations, treatment, and follow-up of the child. And then, we searched related literature using PubMed. Results The 9-year-old boy was exposed to COVID-19 in Malawi and tested positive for NAT in Haikou, China. He was asymptomatic and admitted to our hospital. After six negative NATs, he was discharged from the hospital and quarantined in a hotel. His infection was reactivated again after 22 days (interval between first and last positive NATs). The cycle threshold (Ct) values of positive tests were 25 and 31, and the gene sequencing viral loads were very low. The viral strain Kenya/P2601/2020, a variant of the hCoV-19/Wuhan/IVDC-HB-01/2019 genome (GISAID accession IL: EPI_ISL_402119), was found when polymerase chain reaction enrichment was used to sequence the virus. However, people around him tested negative for COVID-19. Conclusion First, we confirmed the reactivation of COVID-19 in a child. The risk of recurrent infection with SARS-CoV-2 was low, and the policy of strictly isolating patients carrying long-term viral ribonucleic acid should be reconsidered. The interval positivity was most likely due to incorrect sampling and/or testing methods. SGS and aB testing are recommended for children with viral reactivation. Second, SARS-CoV-2 viral reactivation cannot be ruled out. The possible mechanisms, such as prolonged infection and viral latent reactivation, need further investigation.
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Soh JH, Balleza E, Abdul Rahim MN, Chan HM, Mohd Ali S, Chuah JKC, Edris S, Atef A, Bahieldin A, Ying JY, Sabir JS. CRISPR-based systems for sensitive and rapid on-site COVID-19 diagnostics. Trends Biotechnol 2022; 40:1346-1360. [PMID: 35871983 PMCID: PMC9174145 DOI: 10.1016/j.tibtech.2022.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/15/2022] [Accepted: 06/02/2022] [Indexed: 01/21/2023]
Abstract
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions.
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Affiliation(s)
- Jun Hui Soh
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Enrique Balleza
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | | | - Hsi-Min Chan
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Siswand Mohd Ali
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | | | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Al-Borg Medical Laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jackie Y. Ying
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Institute of Materials Research and Engineering (IMRE), A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Correspondence:
| | - Jamal S.M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Correspondence:
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18
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Díaz LA, García-Salum T, Fuentes-López E, Reyes D, Ortiz J, Chahuan J, Levican J, Almonacid LI, Valenzuela GH, Serrano E, Budnik S, Gandara V, Gallardo A, Seydewitz MF, Ferrés M, Cofré C, Álvarez M, Pavez C, Candia R, Monrroy H, Espino A, Rada G, Ortiz L, Valderrama S, Salinas E, Toro A, Ortega M, Pizarro M, Medina RA, Riquelme A. High prevalence of SARS-CoV-2 detection and prolonged viral shedding in stools: A systematic review and cohort study. GASTROENTEROLOGIA Y HEPATOLOGIA 2022; 45:593-604. [PMID: 35077722 PMCID: PMC8783395 DOI: 10.1016/j.gastrohep.2021.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/02/2021] [Accepted: 12/29/2021] [Indexed: 10/25/2022]
Abstract
OBJECTIVES To: 1. Describe the frequency of viral RNA detection in stools in a cohort of patients infected with SARS-CoV-2, and 2. Perform a systematic review to assess the clearance time in stools of SARS-CoV-2. METHODS We conducted a prospective cohort study in two centers between March and May 2020. We included SARS-CoV-2 infected patients of any age and severity. We collected seriated nasopharyngeal swabs and stool samples to detect SARS-CoV-2. After, we performed a systematic review of the prevalence and clearance of SARS-CoV-2 in stools (PROSPERO-ID: CRD42020192490). We estimated prevalence using a random-effects model. We assessed clearance time by using Kaplan-Meier curves. RESULTS We included 32 patients; mean age was 43.7±17.7 years, 43.8% were female, and 40.6% reported gastrointestinal symptoms. Twenty-five percent (8/32) of patients had detectable viral RNA in stools. The median clearance time in stools of the cohort was 11[10-15] days. Systematic review included 30 studies (1392 patients) with stool samples. Six studies were performed in children and 55% were male. The pooled prevalence of viral detection in stools was 34.6% (twenty-four studies, 1393 patients; 95%CI:25.4-45.1); heterogeneity was high (I2:91.2%, Q:208.6; p≤0.001). A meta-regression demonstrates an association between female-gender and lower presence in stools (p=0.004). The median clearance time in stools was 22 days (nineteen studies, 140 patients; 95%CI:19-25). After 34 days, 19.9% (95%CI:11.3-29.7) of patients have a persistent detection in stools. CONCLUSIONS Detection of SARS-CoV-2 in stools is a frequent finding. The clearance of SARS-CoV-2 in stools is prolonged and it takes longer than nasopharyngeal secretions.
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Affiliation(s)
- Luis Antonio Díaz
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tamara García-Salum
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Fuentes-López
- Department of Health Sciences, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Diego Reyes
- Department of Internal Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Ortiz
- Department of Internal Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Chahuan
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Levican
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo I Almonacid
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo H Valenzuela
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eileen Serrano
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sigall Budnik
- School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vicente Gandara
- School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Gallardo
- School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Marcela Ferrés
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Colomba Cofré
- Department of Pediatric Gastroenterology and Nutrition, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Álvarez
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Pavez
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roberto Candia
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Hugo Monrroy
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Espino
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gabriel Rada
- Department of Internal Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile; Evidence Center, Cochrane Chile Associated Center, Pontificia Universidad Católica de Chile, Santiago, Chile; Epistemonikos Foundation, Santiago, Chile
| | - Luis Ortiz
- Evidence Center, Cochrane Chile Associated Center, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián Valderrama
- Department of Internal Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Erick Salinas
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Adriana Toro
- Pediatric Service, Clínica UC San Carlos, Red Salud UC Christus, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcos Ortega
- Department of Intensive Care Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Respiratory Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita Pizarro
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Arnoldo Riquelme
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Health Sciences, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
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High prevalence of SARS-CoV-2 detection and prolonged viral shedding in stools: A systematic review and cohort study. GASTROENTEROLOGÍA Y HEPATOLOGÍA (ENGLISH EDITION) 2022; 45:593-604. [PMCID: PMC9574026 DOI: 10.1016/j.gastre.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/29/2021] [Indexed: 11/01/2022]
Abstract
Objectives To: 1. Describe the frequency of viral RNA detection in stools in a cohort of patients infected with SARS-CoV-2, and 2. Perform a systematic review to assess the clearance time in stools of SARS-CoV-2. Methods We conducted a prospective cohort study in two centers between March and May 2020. We included SARS-CoV-2 infected patients of any age and severity. We collected seriated nasopharyngeal swabs and stool samples to detect SARS-CoV-2. After, we performed a systematic review of the prevalence and clearance of SARS-CoV-2 in stools (PROSPERO-ID: CRD42020192490). We estimated prevalence using a random-effects model. We assessed clearance time by using Kaplan–Meier curves. Results We included 32 patients; mean age was 43.7 ± 17.7 years, 43.8% were female, and 40.6% reported gastrointestinal symptoms. Twenty-five percent (8/32) of patients had detectable viral RNA in stools. The median clearance time in stools of the cohort was 11[10–15] days. Systematic review included 30 studies (1392 patients) with stool samples. Six studies were performed in children and 55% were male. The pooled prevalence of viral detection in stools was 34.6% (twenty-four studies, 1393 patients; 95%CI:25.4–45.1); heterogeneity was high (I 2:91.2%, Q:208.6; p ≤ 0.001). A meta-regression demonstrates an association between female-gender and lower presence in stools (p = 0.004). The median clearance time in stools was 22 days (nineteen studies, 140 patients; 95%CI:19–25). After 34 days, 19.9% (95%CI:11.3–29.7) of patients have a persistent detection in stools. Conclusions Detection of SARS-CoV-2 in stools is a frequent finding. The clearance of SARS-CoV-2 in stools is prolonged and it takes longer than nasopharyngeal secretions.
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20
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Mandal A, Nandi S, Chhebbi M, Basu A, Ray M. A Systematic Review on Tracheostomy in COVID-19 Patients: Current Guidelines and Safety Measures. Indian J Otolaryngol Head Neck Surg 2022; 74:2738-2742. [PMID: 33014752 PMCID: PMC7521770 DOI: 10.1007/s12070-020-02152-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/14/2020] [Indexed: 01/08/2023] Open
Abstract
At this moment the world is fighting with COVID-19 pandemic. Because of increasing number of critical cases, the ICU admissions are also increasing and overwhelming the hospital. These group of patients often required Tracheostomy for proper management and ventilation. As Surgeons we often required to examine and perform procedures in head and neck patients and are in high risk of exposure to aerosol and droplet contamination. We did a literature search for research regarding tracheostomy and its post procedure care during the ongoing COVID-19 pandemic. In this review various international guidelines and sources were put together, and we aim to summarize in a systematic way the available recommendations: indications, timing, technique and safety measures for tracheostomy for COVID-19 patients, from all over the world.
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Affiliation(s)
- Amitabha Mandal
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sourabh Nandi
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Madiwalesh Chhebbi
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Mukurdipi Ray
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
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21
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Alkhamis A, Alshamali Y, Chehadeh W, Jasem A, Omar AA, Alghounaim M, Elsaaran H, Al-Youha S, Almazeedi S, Alkhamis MA, Alsabah S. Predictors of intensive care unit admission and mortality in SARS-CoV-2 infection: A cross sectional study at a tertiary care hospital. Ann Med Surg (Lond) 2022; 80:104097. [PMID: 35818560 PMCID: PMC9259005 DOI: 10.1016/j.amsu.2022.104097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background The transmissibility and associated morbidity and mortality of severe acute respiratory syndrome-related coronavirus (SARS-Cov-2), have overwhelmed worldwide healthcare systems, resulting in an urgent need to understand this virus and its associated effects. The aim of our study was to identify patient symptoms, clinical characteristics, laboratory, and radiology findings that are associated with serious morbidity and mortality in COVID-19 patients. Methods A cross sectional study was conducted in Jaber Al Ahmad Hospital, the designated COVID-19 center in Kuwait between August 1st, 2020 and January 31st, 2021. The main outcomes measured in this study were to identify variables associated with intensive care unit (ICU) admission, as proxy for serious morbidity, and in hospital mortality. Results Two hundred and seventy-six patients were included in the study. Thirty-six (13%) patients were admitted to intensive care unit (ICU) and 33 (12%) patients expired. On multivariate analysis we found having elevated fibrinogen [OR 1.39, 95% CI 1.08–1.64, P = 0.04], low estimated glomerular filtration rate (eGFR) [OR 0.89, 95% CI 0.81–0.95, P = 0.02], and having bilateral patchy lung shadowing [OR 6.68, 95% CI 1.85–15.28, P < 0.01] to be significantly associated with increase odds of ICU admission. Elevated CRP [OR 1.25, 95% CI 1.10–1.98, P < 0.01], low eGFR [OR 0.95, 95% CI 0.90–0.99, P = 0.05] and having ischemic heart disease [OR 7.03, 95% CI 1.60–46.42, P = 0.04] were independently associated with increased odds of mortality. Conclusion Certain inflammatory and coagulopathy markers, and having certain lung radiological features, in addition to having medical comorbidities, specifically, ischemic heart disease and renal impairment are key predictors for serious morbidity and mortality in patients infected with COVID-19. These should be incorporated into medical institutes risk assessment tools used by physicians and policy makers to instigate, prioritize, and reprioritize care in patients with COVID-19 and instigate preventative strategy to reduce the impact of future outbreak.
Understanding risk factors associated with worse outcomes when infected with COVID-19 infection is important. A multifactorial model incorporating certain laboratory blood tests and patient clinical characteristics seems to be the best way to predict morbidity and mortality. Obesity, Cardiovascular and renal deficiencies are predictors of worse outcomes and so should be prioritized in managing COVID-19 patients.
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22
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Urdaneta F, Wardhan R, Wells G, White JD. Prevention of pulmonary complications in sedated patients undergoing interventional procedures in the nonoperating room anesthesia setting. Curr Opin Anaesthesiol 2022; 35:493-501. [PMID: 35787534 DOI: 10.1097/aco.0000000000001158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Nonoperating room anesthesia (NORA) procedures have expanded in number, variety, and complexity. NORA involves all age groups, including frail older adults and patients often considered too sick to tolerate traditional surgical interventions. Postoperative pulmonary complications are a significant source of adverse events in the perioperative setting. We present a review focused on preventing pulmonary complications in the interventional NORA setting. RECENT FINDINGS NORA locations should function as independent, autonomous ambulatory units. We discuss a strategic plan involving a thorough preoperative evaluation of patients, including recognizing high-risk patients and their anesthetic management. Finally, we offer guidance on the challenges of conducting sedation and anesthesia in patients with coronavirus disease 2019 (COVID-19) or a history of COVID-19. SUMMARY The demands on the interventional NORA anesthesia team are increasing. Strategic planning, checklists, consistent staffing assignments, and scheduled safety drills are valuable tools to improve patient safety. In addition, through quality improvement initiatives and reporting, NORA anesthetists can achieve reductions in periprocedural pulmonary complications.
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Affiliation(s)
- Felipe Urdaneta
- Department of Anesthesiology, University of Florida College of Medicine, Gainesville, Florida, USA
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Paoletti AM, Melilli MG, Vecchio I. Experimental Models of SARS-COV-2 Infection in the Central Nervous System. J Cent Nerv Syst Dis 2022; 14:11795735221102231. [PMID: 35783991 PMCID: PMC9247991 DOI: 10.1177/11795735221102231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/05/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has raised serious concerns worldwide due to
its great impact on human health and forced scientists racing to find effective
therapies to control the infection and a vaccine for the virus. To this end,
intense research efforts have focused on understanding the viral biology of
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for
COVID-19. The ever-expanding list of cases, reporting clinical neurological
complications in COVID-19 patients, strongly suggests the possibility of the
virus invading the nervous system. The pathophysiological processes responsible
for the neurological impact of COVID-19 are not fully understood. Some
neurodegenerative disorders sometimes take more than a decade to manifest, so
the long-term pathophysiological outcomes of SARS-CoV-2 neurotropism should be
regarded as a challenge for researchers in this field. There is no documentation
on the long-term impact of SARS-CoV-2 on the human central nervous system (CNS).
Most of the data relating to neurological damage during SARS-CoV-2 infection
have yet to be established experimentally. The purpose of this review is to
describe the knowledge gained, from experimental models, to date, on the
mechanisms of neuronal invasion and the effects produced by infection. The hope
is that, once the processes are understood, therapies can be implemented to
limit the damage produced. Long-term monitoring and the use of appropriate and
effective therapies could reduce the severity of symptoms and improve quality of
life of the most severely affected patients, with a special focus on those have
required hospital care and assisted respiration.
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Affiliation(s)
- Anna Maria Paoletti
- Institute for Biomedical Research and Innovation (IRIB), National Council of Research (CNR), Catanzaro, Italy
| | | | - Immacolata Vecchio
- Institute for Biomedical Research and Innovation (IRIB), National Council of Research (CNR), Catanzaro, Italy
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Farooq M, Khan AW, Ahmad B, Kim MS, Choi S. Therapeutic Targeting of Innate Immune Receptors Against SARS-CoV-2 Infection. Front Pharmacol 2022; 13:915565. [PMID: 35847031 PMCID: PMC9280161 DOI: 10.3389/fphar.2022.915565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
The innate immune system is the first line of host's defense against invading pathogens. Multiple cellular sensors that detect viral components can induce innate antiviral immune responses. As a result, interferons and pro-inflammatory cytokines are produced which help in the elimination of invading viruses. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to Coronaviridae family, and has a single-stranded, positive-sense RNA genome. It can infect multiple hosts; in humans, it is responsible for the novel coronavirus disease 2019 (COVID-19). Successful, timely, and appropriate detection of SARS-CoV-2 can be very important for the early generation of the immune response. Several drugs that target the innate immune receptors as well as other signaling molecules generated during the innate immune response are currently being investigated in clinical trials. In this review, we summarized the current knowledge of the mechanisms underlying host sensing and innate immune responses against SARS-CoV-2 infection, as well as the role of innate immune receptors in terms of their therapeutic potential against SARS-CoV-2. Moreover, we discussed the drugs undergoing clinical trials and the FDA approved drugs against SARS-CoV-2. This review will help in understanding the interactions between SARS-CoV-2 and innate immune receptors and thus will point towards new dimensions for the development of new therapeutics, which can be beneficial in the current pandemic.
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Affiliation(s)
- Mariya Farooq
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University, Suwon, South Korea
| | - Abdul Waheed Khan
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University, Suwon, South Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University, Suwon, South Korea
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Saleem SM, Bhattacharya S. Sputum Testing as the New Mass Screening Method for COVID-19 Patients in India - A Public Health Perspective. Int J Prev Med 2022; 13:86. [PMID: 35958371 PMCID: PMC9362747 DOI: 10.4103/ijpvm.ijpvm_323_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/29/2021] [Indexed: 11/04/2022] Open
Abstract
In December 2019, an unusual form of pneumonia of unknown origin was identified in Wuhan and soon expanded into an intercontinental pandemic that affected nations all over the world. The unusual pneumonia was subsequently named COVID-19. The management of COVID-19 disease has been highly dependent on the early identification of patients who are positive for SARS-CoV-2 infection. For detecting the SARS-CoV-2 virus in upper or lower respiratory tracts, the Centers for Disease Control and Prevention (CDC) recommend strategic sampling approaches. Most countries collect nasopharyngeal swabs and oropharyngeal swabs for rapid viral testing by experienced healthcare workers. Due to the increase in single-day cases, the high cost of RT-PCR, and the requirement for greater coverage in order to detect COVID-19 infections, the screening method has been changed to the Rapid Antigen Test during this phase of the pandemic in India. Considering the limited sensitivity of the fast antigen test compared to the sputum test, and the benefit of having additional resources available from an already established TB network, policymakers should consider implementing COVID-19 with sputum testing. For India, which has 1.3 billion people and limited resources, contemplating a community level sample collection of COVID-19 samples will be an effective decision if scientific data is used for this purpose will be an effective choice for the country with more than 1.3 billion population and limited resources.
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Affiliation(s)
| | - Sudip Bhattacharya
- Department of Community and Family Medicine, All India Institute of Medical Science, Mudurai, India,Address for correspondence: Dr. Sudip Bhattacharya, Assistant Professor, Department of Community and Family Medicine, All India Institute of Medical Science, Mudurai, India. E-mail:
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26
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Abstract
Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.
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Affiliation(s)
- Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Karen M Frank
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
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27
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Okita Y, Morita T, Kumanogoh A. Duration of SARS-CoV-2 RNA positivity from various specimens and clinical characteristics in patients with COVID-19: a systematic review and meta-analysis. Inflamm Regen 2022; 42:16. [PMID: 35642011 PMCID: PMC9156361 DOI: 10.1186/s41232-022-00205-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/10/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity will be important to prevent the spread of coronavirus disease 2019 (COVID-19). A systematic review and meta-analysis were conducted following PRISMA to determine the duration from several parts of the body and clinical characteristics affecting it. MAIN TEXT PubMed, Web of Science, Scopus, and CENTRAL were searched for original studies reporting the duration from COVID-19 onset to the disappearance of viral RNA. Of the 1682 studies identified, 100 met the selection criteria and 13,431 patients were included in this study. The duration of SARS-CoV-2 RNA positivity was 18.29 [95% confidence interval: 17.00-19.89] days in the upper respiratory tract samples, 23.79 [20.43-27.16] days in the sputum, 14.60 [12.16-17.05] days in the blood, and 22.38 [18.40-26.35] days in the stool. Sensitivity analysis revealed that the duration was positively correlated with age, comorbidities, severity, and usage of glucocorticoid. Subgroup analysis indicated that the presence or absence of complications had the greatest impact on the difference in DSRP. CONCLUSIONS The duration of SARS-CoV-2 RNA positivity was 18.29 days in the upper respiratory tract samples. The duration in the sputum and the stool was longer, while that in the blood was shorter. The duration in the upper respiratory tract samples was longer in older, with any comorbidities, severer, and treated with glucocorticoid. These results provide the basic data for the duration of SARS-CoV-2 RNA positivity, and in the future, the effect of vaccination against SARS-CoV-2 and the SARS-CoV-2 variants on the duration of RNA positivity should be assessed.
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Affiliation(s)
- Yasutaka Okita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Immunopathology, World Premier International Immunology Frontier Research Center (iFReC), Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
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28
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Wang S, Gao H, Wang X, Ma X, Zhang L, Xing Y, Jia Y, Wang Y. Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Vitamin D3 and COVID-19 as Potential Therapeutic Targets. Front Pharmacol 2022; 13:874637. [PMID: 35571107 PMCID: PMC9095980 DOI: 10.3389/fphar.2022.874637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: The persistent pandemic of coronavirus disease 2019 (COVID-19), the discovery of gastrointestinal transmission routes and the possible susceptibility of cancer patients to COVID-19 have forced us to search for effective pathways against stomach adenocarcinoma (STAD)/COVID-19. Vitamin D3 (VD3) is a steroid hormone with antiviral, anti-inflammatory and immunomodulatory properties. This study aimed to evaluate the possible functional role and potential mechanisms of action of VD3 as an anti-COVID-19 and anti- STAD. Methods: Clinicopathological analysis, enrichment analysis and protein interaction analysis using bioinformatics and network pharmacology methods. Validate the binding activity of VD3 to core pharmacological targets and viral crystal structures using molecular docking. Results: We revealed the clinical characteristics of STAD/COVID-19 patients. We also demonstrated that VD3 may be anti- STAD/COVID-19 through antiviral, anti-inflammatory, and immunomodulatory pathways. Molecular docking results showed that VD3 binds well to the relevant targets of COVID-19, including the spike RBD/ACE2 complex and main protease (Mpro, also known as 3CLpro). We also identified five core pharmacological targets of VD3 in anti-STAD/COVID-19 and validated the binding activity of VD3 to PAI1 by molecular docking. Conclusion: This study reveals for the first time that VD3 may act on disease target gene SERPINE1 through inflammatory and viral related signaling pathways and biological functions for the therapy of STAD/COVID-19. This may provide a new idea for the use of VD3 in the treatment of STAD/COVID-19.
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Affiliation(s)
- Shanglin Wang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Huayu Gao
- Department of Pediatric Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Xiaoru Wang
- Department of Traditional Chinese Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Xiaoli Ma
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Lulu Zhang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Yuanxin Xing
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Yanfei Jia
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Yunshan Wang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China.,Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, China
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29
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Wang Y, Liu P, Zhang H, Ibaraki M, VanTassell J, Geith K, Cavallo M, Kann R, Saber L, Kraft CS, Lane M, Shartar S, Moe C. Early warning of a COVID-19 surge on a university campus based on wastewater surveillance for SARS-CoV-2 at residence halls. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153291. [PMID: 35090922 PMCID: PMC8788089 DOI: 10.1016/j.scitotenv.2022.153291] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 05/05/2023]
Abstract
As COVID-19 continues to spread globally, monitoring the disease at different scales is critical to support public health decision making. Surveillance for SARS-CoV-2 RNA in wastewater can supplement surveillance based on diagnostic testing. In this paper, we report the results of wastewater-based COVID-19 surveillance on Emory University campus that included routine sampling of sewage from a hospital building, an isolation/quarantine building, and 21 student residence halls between July 13th, 2020 and March 14th, 2021. We examined the sensitivity of wastewater surveillance for detecting COVID-19 cases at building level and the relation between Ct values from RT-qPCR results of wastewater samples and the number of COVID-19 patients residing in the building. Our results show that weekly wastewater surveillance using Moore swab samples was not sensitive enough (6 of 63 times) to reliably detect one or two sporadic cases in a residence building. The Ct values of the wastewater samples over time from the same sampling location reflected the temporal trend in the number of COVID-19 patients in the isolation/quarantine building and hospital (Pearson's r < -0.8), but there is too much uncertainty to directly estimate the number of COVID-19 cases using Ct values. After students returned for the spring 2021 semester, SARS-CoV-2 RNA was detected in the wastewater samples from most of the student residence hall monitoring sites one to two weeks before COVID-19 cases surged on campus. This finding suggests that wastewater-based surveillance can be used to provide early warning of COVID-19 outbreaks at institutions.
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Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Haisu Zhang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Makoto Ibaraki
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie VanTassell
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Kelly Geith
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Matthew Cavallo
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rebecca Kann
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lindsay Saber
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Morgan Lane
- Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Samuel Shartar
- Emory University Office of Critical Event Preparedness and Response, Atlanta, GA, USA
| | - Christine Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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30
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Cao X, Hao G, Li YY, Wang M, Wang JX. On male urination and related environmental disease transmission in restrooms: From the perspectives of fluid dynamics. SUSTAINABLE CITIES AND SOCIETY 2022; 80:103753. [PMID: 35136716 PMCID: PMC8812150 DOI: 10.1016/j.scs.2022.103753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 05/02/2023]
Abstract
Indoor transmission of COVID-19 is highly probable. Multiple sources have verified that the SARS-CoV-2 can be detected within toilets, and people can be infected in restrooms. There is a huge gap in the coronavirus transmission mechanism in restrooms. Understanding it can help to flatten the curve of the infected cases as well as prevent other viruses transmitted through the sewage or human body fluid. Previous studies have shown how simple actions in daily life (coughing, sneezing, or toilet flushing) contribute to virus transmission. This paper visually and quantitatively demonstrates that male urination, which is also a daily action, can agitate virus particles within the toilet and raise them, which may be the main promoter of cross-infection of COVID-19 in restrooms. Adopting numerical and experimental methods, we demonstrate that male urination can cause strong turbulent flow with an averaged urine impinging velocity of 2.3 m/s, which can act as an agitator to raise the virus particles. The climbing velocity of the airflow can be 0.75-1.05 m/s. The observed upwards flow will disturb and spread any lurking virus particles (not limited to SARS-CoV-2). Experiments demonstrated that the concentration of the airborne particle could be tripled during male urination. Corresponding precautions are offered as well to prepare the public to act properly when and after using facilities in restrooms for preventing emerging and re-emerging pandemics not limited to the current COVID-19, contributing to the sustainability of human society.
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Affiliation(s)
- Xiang Cao
- College of Electrical, Energy and Power Engineering, Yangzhou University, Yangzhou 225009, China
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Guanqiu Hao
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yun-Yun Li
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Mengxiao Wang
- Department of Traditional Chinese Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ji-Xiang Wang
- College of Electrical, Energy and Power Engineering, Yangzhou University, Yangzhou 225009, China
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon Hong Kong, China
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31
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Žabka D, Konečná B, Celec P, Janíková M, Ivašková N, Tóthová Ľ, Tamáš M, Škulcová AB, Púček Belišová N, Horáková I, Bímová P, Híveš J, Ryba J, Klempa B, Sláviková M, Kopáček J, Krahulec J, Gál M, Mackuľak T. Ferrate (VI), Fenton Reaction and Its Modification: An Effective Method of Removing SARS-CoV-2 RNA from Hospital Wastewater. Pathogens 2022; 11:450. [PMID: 35456125 PMCID: PMC9027194 DOI: 10.3390/pathogens11040450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/28/2022] [Accepted: 04/07/2022] [Indexed: 12/15/2022] Open
Abstract
The outbreak of the coronavirus disease 2019 (COVID-19) raises questions about the effective inactivation of its causative agent, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in medical wastewater by disinfectants. For this reason, our study of wastewater from a selected hospital evaluated several different advanced oxidation methods (Fenton reaction and Fenton-like reaction and ferrate (VI)) capable of effectively removing SARS-CoV-2 RNA. The obtained results of all investigated oxidation processes, such as ferrates, Fenton reaction and its modifications achieved above 90% efficiency in degradation of SARS-CoV-2 RNA in model water. The efficiency of degradation of real SARS-CoV-2 from hospital wastewater declines in following order ferrate (VI) > Fenton reaction > Fenton-like reaction. Similarly, the decrease of chemical oxygen demand compared to effluent was observed. Therefore, all of these methods can be used as a replacement of chlorination at the wastewater effluent, which appeared to be insufficient in SARS-CoV-2 removal (60%), whereas using of ferrates showed efficiency of up to 99%.
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Affiliation(s)
- Dušan Žabka
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
| | - Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia; (B.K.); (P.C.); (M.J.); (N.I.); (Ľ.T.)
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia; (B.K.); (P.C.); (M.J.); (N.I.); (Ľ.T.)
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Monika Janíková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia; (B.K.); (P.C.); (M.J.); (N.I.); (Ľ.T.)
| | - Nadja Ivašková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia; (B.K.); (P.C.); (M.J.); (N.I.); (Ľ.T.)
| | - Ľubomíra Tóthová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia; (B.K.); (P.C.); (M.J.); (N.I.); (Ľ.T.)
| | - Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
| | - Andrea Butor Škulcová
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
| | - Noemi Púček Belišová
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
| | - Ivana Horáková
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
| | - Paula Bímová
- Department of Inorganic Technology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (P.B.); (J.H.)
| | - Ján Híveš
- Department of Inorganic Technology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (P.B.); (J.H.)
| | - Jozef Ryba
- Department of Polymer Processing, Institute of Natural and Synthetic Polymers, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia; (B.K.); (M.S.); (J.K.)
| | - Monika Sláviková
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia; (B.K.); (M.S.); (J.K.)
| | - Juraj Kopáček
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia; (B.K.); (M.S.); (J.K.)
| | - Ján Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Miroslav Gál
- Department of Inorganic Technology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (P.B.); (J.H.)
| | - Tomáš Mackuľak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.T.); (A.B.Š.); (N.P.B.); (I.H.)
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32
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Zhang X, Meng H, Liu H, Ye Q. Advances in laboratory detection methods and technology application of SARS-CoV-2. J Med Virol 2022; 94:1357-1365. [PMID: 34854101 PMCID: PMC9015480 DOI: 10.1002/jmv.27494] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
At present, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide, and the coronavirus disease 2019 outbreak caused by SARS-CoV-2 seriously threatens the life and health of all humankind. There is no specific medicine for novel coronavirus yet. So, laboratory diagnoses of novel coronavirus as soon as possible and isolation of the source of infection play a vital role in preventing and controlling the epidemic. Therefore, selecting appropriate detection techniques and methods is particularly important to improve the efficiency of disease diagnosis and treatment and to curb the outbreak of infectious diseases. In this paper, virus nucleic acid, protein, and serum immunology were reviewed to provide a reference for further developing virus detection technology to provide better prevention and treatment strategies and research ideas for clinicians and researchers.
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Affiliation(s)
- Xiucai Zhang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Hanyan Meng
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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33
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Monday HN, Li J, Nneji GU, Hossin MA, Nahar S, Jackson J, Chikwendu IA. WMR-DepthwiseNet: A Wavelet Multi-Resolution Depthwise Separable Convolutional Neural Network for COVID-19 Diagnosis. Diagnostics (Basel) 2022; 12:765. [PMID: 35328318 PMCID: PMC8947526 DOI: 10.3390/diagnostics12030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/07/2022] [Accepted: 03/18/2022] [Indexed: 11/17/2022] Open
Abstract
Timely discovery of COVID-19 could aid in formulating a suitable treatment plan for disease mitigation and containment decisions. The widely used COVID-19 test necessitates a regular method and has a low sensitivity value. Computed tomography and chest X-ray are also other methods utilized by numerous studies for detecting COVID-19. In this article, we propose a CNN called depthwise separable convolution network with wavelet multiresolution analysis module (WMR-DepthwiseNet) that is robust to automatically learn details from both spatialwise and channelwise for COVID-19 identification with a limited radiograph dataset, which is critical due to the rapid growth of COVID-19. This model utilizes an effective strategy to prevent loss of spatial details, which is a prevalent issue in traditional convolutional neural network, and second, the depthwise separable connectivity framework ensures reusability of feature maps by directly connecting previous layer to all subsequent layers for extracting feature representations from few datasets. We evaluate the proposed model by utilizing a public domain dataset of COVID-19 confirmed case and other pneumonia illness. The proposed method achieves 98.63% accuracy, 98.46% sensitivity, 97.99% specificity, and 98.69% precision on chest X-ray dataset, whereas using the computed tomography dataset, the model achieves 96.83% accuracy, 97.78% sensitivity, 96.22% specificity, and 97.02% precision. According to the results of our experiments, our model achieves up-to-date accuracy with only a few training cases available, which is useful for COVID-19 screening. This latest paradigm is expected to contribute significantly in the battle against COVID-19 and other life-threatening diseases.
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Affiliation(s)
- Happy Nkanta Monday
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Jianping Li
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Grace Ugochi Nneji
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China; (G.U.N.); (J.J.)
| | - Md Altab Hossin
- School of Management and Economics, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Saifun Nahar
- Department of Information System and Technology, University of Missouri-St. Louis, St. Louis, MO 63121, USA;
| | - Jehoiada Jackson
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China; (G.U.N.); (J.J.)
| | - Ijeoma Amuche Chikwendu
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China;
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34
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Monday HN, Li J, Nneji GU, Nahar S, Hossin MA, Jackson J, Ejiyi CJ. COVID-19 Diagnosis from Chest X-ray Images Using a Robust Multi-Resolution Analysis Siamese Neural Network with Super-Resolution Convolutional Neural Network. Diagnostics (Basel) 2022; 12:diagnostics12030741. [PMID: 35328294 PMCID: PMC8946937 DOI: 10.3390/diagnostics12030741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Chest X-ray (CXR) is becoming a useful method in the evaluation of coronavirus disease 19 (COVID-19). Despite the global spread of COVID-19, utilizing a computer-aided diagnosis approach for COVID-19 classification based on CXR images could significantly reduce the clinician burden. There is no doubt that low resolution, noise and irrelevant annotations in chest X-ray images are a major constraint to the performance of AI-based COVID-19 diagnosis. While a few studies have made huge progress, they underestimate these bottlenecks. In this study, we propose a super-resolution-based Siamese wavelet multi-resolution convolutional neural network called COVID-SRWCNN for COVID-19 classification using chest X-ray images. Concretely, we first reconstruct high-resolution (HR) counterparts from low-resolution (LR) CXR images in order to enhance the quality of the dataset for improved performance of our model by proposing a novel enhanced fast super-resolution convolutional neural network (EFSRCNN) to capture texture details in each given chest X-ray image. Exploiting a mutual learning approach, the HR images are passed to the proposed Siamese wavelet multi-resolution convolutional neural network to learn the high-level features for COVID-19 classification. We validate the proposed COVID-SRWCNN model on public-source datasets, achieving accuracy of 98.98%. Our screening technique achieves 98.96% AUC, 99.78% sensitivity, 98.53% precision, and 98.86% specificity. Owing to the fact that COVID-19 chest X-ray datasets are low in quality, experimental results show that our proposed algorithm obtains up-to-date performance that is useful for COVID-19 screening.
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Affiliation(s)
- Happy Nkanta Monday
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Jianping Li
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China;
- Correspondence:
| | - Grace Ugochi Nneji
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China; (G.U.N.); (J.J.); (C.J.E.)
| | - Saifun Nahar
- Department of Information System and Technology, University of Missouri-St. Louis, St. Louis, MO 63121, USA;
| | - Md Altab Hossin
- School of Management and Economics, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Jehoiada Jackson
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China; (G.U.N.); (J.J.); (C.J.E.)
| | - Chukwuebuka Joseph Ejiyi
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China; (G.U.N.); (J.J.); (C.J.E.)
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35
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Twigg C, Wenk J. Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater. CHEMBIOENG REVIEWS 2022. [PMCID: PMC9083821 DOI: 10.1002/cben.202100039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.
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Affiliation(s)
- Charlotte Twigg
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
| | - Jannis Wenk
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
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Zhou JQ, Liu GX, Huang XL, Gan HT. The importance of fecal nucleic acid detection in patients with coronavirus disease(COVID-19):a systematic review and meta-analysis. J Med Virol 2022; 94:2317-2330. [PMID: 35174515 PMCID: PMC9088624 DOI: 10.1002/jmv.27652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 02/05/2023]
Abstract
Pooled data from 2352 hospitalized coronavirus disease 2019 (COVID‐19) patients with viral RNA in feces across 46 studies were analyzed and the pooled prevalence of fecal RNA was 46.8% (95% confidence interval [CI]: 0.383–0.554). The pooled analysis showed that the occurrence of total gastrointestinal (GI) symptoms was 28.5% (95% CI: 0.125–0.44) in COVID‐19 patients with fecal RNA, that of both respiratory and GI symptoms was 21.9% (95% CI: 0.09–0.346), that of only GI symptoms was 19.8% (95% CI: 0.107–0.288), and that of only respiratory symptoms was 50.5%（95% CI: 0.267–0.744). The pooled data showed no significant difference in positive fecal RNA between severe and nonsevere cases (odds ratio = 2.009, p = 0.079, 95% CI: 0.922–4.378). During hospital admission, after samples from the respiratory system tested negative for viral RNA, 55.4% (95% CI: 0.418–0.669) of the patients with positive fecal RNA had persistent shedding of fecal RNA and pooled results from the other 4 studies including 848 discharged patients with nucleic acid‐negative stool samples indicated that the occurrence of repositive stool swabs was 18.1% (95% CI: 0.028–0.335), that of repositive respiratory swabs was 22.8% (95% CI: 0.003–0.452), that of both repositive stool and respiratory swabs was 19.1% (95% CI: 0.019–0.363), and that of only repositive stool swabs was 9.6% (95% CI: 0.010–0.203). The digestive tract may be an important organ involved in COVID‐19 infection and in the excretion of the virus. Because of the potential risk of fecal–oral transmission, giving emphasis on stool swab tests can help increase the detection rate of asymptomatic carriers and reduce missed diagnoses.
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Affiliation(s)
- Jin-Qiu Zhou
- Department of Geriatrics Medicine and the Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Geriatrics Medicine and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Gong-Xiang Liu
- Department of Geriatrics Medicine and the Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Geriatrics Medicine and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao-Li Huang
- Department of Geriatrics Medicine and the Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hua-Tian Gan
- Department of Geriatrics Medicine and the Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Benevides Lima L, Mesquita FP, Brasil de Oliveira LL, Andréa da Silva Oliveira F, Elisabete Amaral de Moraes M, Souza PFN, Montenegro RC. True or False: What are the factors that influence COVID-19 diagnosis by RT-qPCR? Expert Rev Mol Diagn 2022; 22:157-167. [PMID: 35130461 PMCID: PMC8862161 DOI: 10.1080/14737159.2022.2037425] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease has had a catastrophic impact on the world resulting in several deaths. Since World Health Organization declared the pandemic status of the disease, several molecular diagnostic kits have been developed to help the tracking of viruses spread. Areas Covered This review aims to describe and evaluate the currently reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) diagnosis kit. Several processes used in COVID-19 diagnostic procedures are detailed in further depth to demonstrate optimal practices. Therefore, we debate the main factors that influence the viral detection of SARS-COV-2 and how they can affect the diagnosis of patients. Expert Opinion Here is highlighted and discussed several factors that can interfere in the RT-PCR analysis, such as the viral load of the sample, collection site, collection methodology, sample storage, transport, primer, and probe mismatch/dimerization in different brand kits. This is a pioneer study to discuss the factor that could lead to the wrong interpretation of RT-qPCR diagnosis of SARS-CoV-2. This study aimed to help the readers to understand what very likely is behind a bad result of SARS-CoV-2 detection by RT-PCR and what could be done to reach a reliable diagnosis.
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Affiliation(s)
- Luina Benevides Lima
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Felipe Pantoja Mesquita
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Lais Lacerda Brasil de Oliveira
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Francisca Andréa da Silva Oliveira
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Maria Elisabete Amaral de Moraes
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology (DBBM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Raquel Carvalho Montenegro
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
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The Public Health Governance of the COVID-19 Pandemic: A Bibliometric Analysis. Healthcare (Basel) 2022; 10:healthcare10020299. [PMID: 35206913 PMCID: PMC8872432 DOI: 10.3390/healthcare10020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
The 2019 global outbreak of COVID-19 has had a huge impact on public health governance systems around the world. In response, numerous scholars have conducted research on public health governance in the context of the COVID-19 pandemic. This paper provides a bibliometric analysis of 1437 documents retrieved from the Web of Science (WoS) core collection database, with 49,695 references. It analyses the research directions, countries of publications, core journals, leading authors and institutions and important publications. The paper also summarises research trends by analysing the co-occurrence of keywords, frequently cited documents and co-cited references. It summarises the global responses to COVID-19, including public health interventions and a range of supporting policies based on the features and impacts of the COVID-19 pandemic. The paper provides comprehensive literary support and clear lines of research for future studies on the governance or regulation of public health emergencies.
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Gunawardena SA, Cordeiro C, Di Vella G, Fernando D, Rajapaksha S, Samaranayake R, Sapino A, Tennakoon A, Waduge S, Woodford N, Wijeratne S, Zoja R. Survey on postmortem screening and management of COVID-19 related deaths. Pathologica 2022; 113:413-420. [PMID: 34974546 PMCID: PMC8720393 DOI: 10.32074/1591-951x-254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/13/2021] [Indexed: 12/21/2022] Open
Abstract
The COVID-19 pandemic is associated with a high case fatality rate in some countries even thought the majority of cases are asymptomatic. Scientific studies on this novel virus is limited and there is uncertainty regarding the best practices for death investigations both in terms of detection of the disease as well as autopsy safety. An online survey was conducted to identify how different institutions responded to the screening and management of dead bodies during the early phase of the pandemic from January to May. A questionnaire was developed using Google Forms and data was collected from 14 different forensic and pathological institutions in 9 countries. None of the institutions had performed any screening prior to March. Four institutions stated that screening was done routinely. In total, 322 cases had been screened using RT-PCR, out of which 40 positive cases were detected among four institutions. The commonest types of samples obtained were nasopharyngeal and oropharyngeal swabs which also had the highest rates of positivity followed by tracheal swab. Blood, swabs from cut surfaces of lung and lung tissue also gave positive results in some cases. Majority of the positive cases were > 65 years with a history suggestive of respiratory infection and were clinically suspected to have COVID-19 before death. Except for one institution which performed limited dissections, standard autopsies were conducted on all positive cases. Disposal of bodies involved the use of sealed body bags and labelling as COVID positive. Funeral rites were restricted and none of the institutions advocated cremation. There were no reports of disease transmission to those who handled COVID positive bodies.
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Affiliation(s)
- Sameera A Gunawardena
- Department of Forensic Medicine and Toxicology, Faculty of Medicine, University of Colombo, Sri Lanka
| | - Cristina Cordeiro
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
| | | | - Dinesh Fernando
- Department of Forensic Medicine, University of Peradeniya, Sri Lanka
| | | | - Ravindra Samaranayake
- Department of Forensic Medicine and Toxicology, Faculty of Medicine, University of Colombo, Sri Lanka
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Italy on behalf of SIAPEC-IAP
| | - Ajith Tennakoon
- Institute of Forensic Medicine and Toxicology, Colombo, Sri Lanka
| | | | - Noel Woodford
- Department of Forensic Medicine, Monash University & Victorian Institute of Forensic Medicine, Southbank, Victoria, Australia
| | | | - Riccardo Zoja
- Institute of Legal and Forensic Medicine, University of Milan, Italy
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40
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Affiliation(s)
- Yufan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences Nankai University Tianjin China
| | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences Nankai University Tianjin China
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Abstract
PURPOSE OF REVIEW COVID-19 patients can present gastrointestinal symptoms, being diarrhoea one of the most frequent, suggesting intestinal health can be impacted by COVID-19. Here, we will discuss whether there is a correlation between the presence of SARS-CoV-2 RNA in faeces and diarrhoea, the relevance of gastrointestinal symptoms in disease diagnosis and transmission, and how COVID-19 can impact the gut microbial balance. RECENT FINDINGS SARS-CoV-2 RNA has been reported in faeces or rectal swabs of COVID-19 patients with and without diarrhoea, suggesting faecal shedding can occur independently of gastrointestinal symptoms. However, the presence of the virus in the intestine can persist beyond its presence in the respiratory tract, with some reports suggesting that SARS-CoV-2 in the faeces can be infectious.COVID-19 can impact the gut microbiota causing an enhancement of biosynthesis pathways that favour the expansion of bacterial pathogens in the inflamed gut, and causing a decline in commensals involved in the human immune response. SUMMARY Gastrointestinal symptoms may be the first indication of COVID-19. SARS-CoV-2 in faeces can potentiate routes of disease transmission, particularly as the high viral loads reported in patients with severe illness suggest virus replication in the intestine may be possible.
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Affiliation(s)
- Ines B. Moura
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Anthony M. Buckley
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
| | - Mark H. Wilcox
- Healthcare-Associated Infections Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds
- Microbiology, Leeds Teaching Hospital NHS Trust, Old Medical School, Leeds General Infirmary, Leeds, UK
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Lavania M, Potdar VA, Ranshing S, Vipat V, Saha U, Jadhav SM, Sawant PM, Padbidri V, Chaudhari PA, Patwardhan S. Whole-genome sequencing & mutational analysis of SARS-CoV-2 from patients' faecal samples reveal the possible role in faecal-oral transmission. Indian J Med Res 2022; 155:205-210. [PMID: 35859446 PMCID: PMC9552375 DOI: 10.4103/ijmr.ijmr_1045_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Varsha A Potdar
- National Influenza Centre, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sujata Ranshing
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Veena Vipat
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Ujjayni Saha
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Santosh M Jadhav
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Pradeep M Sawant
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Vikram Padbidri
- Department of Microbiology & Infection Control, Jehangir Hospital, Pune 411 001, Maharashtra, India
| | - Piyush A Chaudhari
- Department of Microbiology & Infection Control, Jehangir Hospital, Pune 411 001, Maharashtra, India
| | - Sampada Patwardhan
- Department of Microbiology and Hospital Infection Control, Deenanath Mangeshkar Hospital and Research Centre, Pune 411 004, Maharashtra, India
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Xie X, Sheng L, Han C, Jin Y, Bai T, Lin R, Ding Z, Hou X. Features of capsule endoscopy in COVID-19 patients with a six-month follow-up: A prospective observational study. J Med Virol 2022; 94:246-252. [PMID: 34460118 PMCID: PMC8662114 DOI: 10.1002/jmv.27308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023]
Abstract
Recently, the coronavirus disease 2019 (COVID-19) has caused a global pandemic. Several studies indicate that the digestive system can also be affected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, patients with digestive symptoms should have a capsule endoscopy (CE). COVID-19 patients with gastrointestinal (GI) symptoms who underwent CE were recruited from March 2020 to April 2020. We collected patients' data and performed a prospective follow-up study for 6 months. All 11 COVID-19 cases with GI symptoms who underwent CE presented gastritis. Eight cases (72.7%) had intestinal mucosa inflammation. Among them, two cases showed intestinal ulcers or erosions. Moreover, two cases displayed colonic mucositis. One case was lost during follow-up. At 3-6 months after hospital discharge, five patients underwent CE again, presenting gastrointestinal lesions. Five of the 10 cases had GI symptoms, such as abdominal pain, diarrhea, constipation, and others. Among these five cases, the GI symptoms of three patients disappeared at the last follow-up and two patients still presented diarrhea symptoms. Overall, we observed damaged digestive tract mucosa that could be caused by SARS-CoV-2. Moreover, after discharge, some patients still presented intestinal lesions and GI symptoms.
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Affiliation(s)
- Xiao‐Ping Xie
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Li‐Ping Sheng
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Chao‐Qun Han
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Yu Jin
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Tao Bai
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Zhen Ding
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Xiao‐Hua Hou
- Department of Gastroenterology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
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Juvekar M, Sarkar B. Guidelines for otorhinolaryngologists and head neck surgeons in coronavirus disease 2019 pandemic. THE EGYPTIAN JOURNAL OF OTOLARYNGOLOGY 2021. [PMCID: PMC7887715 DOI: 10.1186/s43163-021-00082-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 was first identified in Wuhan, the capital of China’s Hubei province, in December 2019. India has witnessed a massive surge of coronavirus cases. Main text This study details the measures to be taken by the clinicians involved in doing otorhinolaryngology and head neck surgery in light of the recent coronavirus disease 2019 pandemic. All COVID-positive patients should be admitted in a separate COVID ward, and patients should be screened for COVID-19 before admission. Only emergent ENT surgeries should be done in an operating room having a negative pressure environment with high-frequency air changes, and all staff must wear personal protective equipment. The anesthetist intubates the patient while the surgical team waits outside the operation theater post-intubation for 21 min. For otology surgery, double draping of the microscope should be done; for rhinology surgery, concept of negative-pressure otolaryngology viral isolation drape (NOVID) system should be used. Smoke evacuation system is set up inside the tent to evacuate any smoke produced during the surgery. Tracheostomy should be done at least after 10 days of mechanical ventilation with cuffed, non-fenestrated tracheal tube inserted through the tracheal window, and a separate closed suction system is used for suctioning. After the surgery is completed, disposal of PPE kit needs to be done according to local guidelines. After completion of the surgery, the full anesthesia unit should be disinfected for 2 h with 12 % hydrogen peroxide. Chlorine-containing disinfectant (2000 mg/L) is used to clean the floor of the operation theater and clean all the reusable medical equipment. Ultra-low volume 20 to 30 mL/m of 3% hydrogen peroxide is used to fumigate the OT for 2 h. Conclusions COVID-19 is a newly discovered infectious disease. Measures need to be taken to prevent transmission and attain a plateau and decline in the disease. Otorhinolaryngologists and head neck surgeons are at high risk of this infection. This review summarizes the protocol for otorhinolaryngologists and head neck surgeons caring for patients in this current scenario. Protocols need to be strictly followed to prevent the spread of this disease.
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McMahan CS, Self S, Rennert L, Kalbaugh C, Kriebel D, Graves D, Colby C, Deaver JA, Popat SC, Karanfil T, Freedman DL. COVID-19 wastewater epidemiology: a model to estimate infected populations. Lancet Planet Health 2021; 5:e874-e881. [PMID: 34895497 PMCID: PMC8654376 DOI: 10.1016/s2542-5196(21)00230-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND Wastewater-based epidemiology provides an opportunity for near real-time, cost-effective monitoring of community-level transmission of SARS-CoV-2. Detection of SARS-CoV-2 RNA in wastewater can identify the presence of COVID-19 in the community, but methods for estimating the numbers of infected individuals on the basis of wastewater RNA concentrations are inadequate. METHODS This is a wastewater-based epidemiology study using wastewater samples that were collected weekly or twice a week from three sewersheds in South Carolina, USA, between either May 27 or June 16, 2020, and Aug 25, 2020, and tested for SARS-CoV-2 RNA. We developed a susceptible-exposed-infectious-recovered (SEIR) model based on the mass rate of SARS-CoV-2 RNA in the wastewater to predict the number of infected individuals, and have also provided a simplified equation to predict this. Model predictions were compared with the number of confirmed cases identified by the Department of Health and Environmental Control, South Carolina, USA, for the same time period and geographical area. FINDINGS We plotted the model predictions for the relationship between mass rate of virus release and numbers of infected individuals, and we validated this prediction on the basis of estimated prevalence from individual testing. A simplified equation to estimate the number of infected individuals fell within the 95% confidence limits of the model. The rate of unreported COVID-19 cases, as estimated by the model, was approximately 11 times that of confirmed cases (ie, ratio of estimated infections for every confirmed case of 10·9, 95% CI 4·2-17·5). This rate aligned well with an independent estimate of 15 infections for every confirmed case in the US state of South Carolina. INTERPRETATION The SEIR model provides a robust method to estimate the total number of infected individuals in a sewershed on the basis of the mass rate of RNA copies released per day. This approach overcomes some of the limitations associated with individual testing campaigns and thereby provides an additional tool that can be used to inform policy decisions. FUNDING Clemson University, USA.
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Affiliation(s)
- Christopher S McMahan
- School of Mathematics and Statistical Sciences, Clemson University, Clemson, SC, USA
| | - Stella Self
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC, USA
| | - Corey Kalbaugh
- Department of Public Health Sciences, Clemson University, Clemson, SC, USA
| | - David Kriebel
- Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts, Lowell, MA, USA
| | | | | | - Jessica A Deaver
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - Sudeep C Popat
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - Tanju Karanfil
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - David L Freedman
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA.
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McMahan CS, Self S, Rennert L, Kalbaugh C, Kriebel D, Graves D, Colby C, Deaver JA, Popat SC, Karanfil T, Freedman DL. COVID-19 wastewater epidemiology: a model to estimate infected populations. Lancet Planet Health 2021; 5:e874-e881. [PMID: 34895497 DOI: 10.1101/2020.11.05.20226738v1.abstract] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Wastewater-based epidemiology provides an opportunity for near real-time, cost-effective monitoring of community-level transmission of SARS-CoV-2. Detection of SARS-CoV-2 RNA in wastewater can identify the presence of COVID-19 in the community, but methods for estimating the numbers of infected individuals on the basis of wastewater RNA concentrations are inadequate. METHODS This is a wastewater-based epidemiology study using wastewater samples that were collected weekly or twice a week from three sewersheds in South Carolina, USA, between either May 27 or June 16, 2020, and Aug 25, 2020, and tested for SARS-CoV-2 RNA. We developed a susceptible-exposed-infectious-recovered (SEIR) model based on the mass rate of SARS-CoV-2 RNA in the wastewater to predict the number of infected individuals, and have also provided a simplified equation to predict this. Model predictions were compared with the number of confirmed cases identified by the Department of Health and Environmental Control, South Carolina, USA, for the same time period and geographical area. FINDINGS We plotted the model predictions for the relationship between mass rate of virus release and numbers of infected individuals, and we validated this prediction on the basis of estimated prevalence from individual testing. A simplified equation to estimate the number of infected individuals fell within the 95% confidence limits of the model. The rate of unreported COVID-19 cases, as estimated by the model, was approximately 11 times that of confirmed cases (ie, ratio of estimated infections for every confirmed case of 10·9, 95% CI 4·2-17·5). This rate aligned well with an independent estimate of 15 infections for every confirmed case in the US state of South Carolina. INTERPRETATION The SEIR model provides a robust method to estimate the total number of infected individuals in a sewershed on the basis of the mass rate of RNA copies released per day. This approach overcomes some of the limitations associated with individual testing campaigns and thereby provides an additional tool that can be used to inform policy decisions. FUNDING Clemson University, USA.
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Affiliation(s)
- Christopher S McMahan
- School of Mathematics and Statistical Sciences, Clemson University, Clemson, SC, USA
| | - Stella Self
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC, USA
| | - Corey Kalbaugh
- Department of Public Health Sciences, Clemson University, Clemson, SC, USA
| | - David Kriebel
- Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts, Lowell, MA, USA
| | | | | | - Jessica A Deaver
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - Sudeep C Popat
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - Tanju Karanfil
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA
| | - David L Freedman
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, USA.
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Global internet search trends related to gastrointestinal symptoms predict regional COVID-19 outbreaks. J Infect 2021; 84:56-63. [PMID: 34767837 PMCID: PMC8625285 DOI: 10.1016/j.jinf.2021.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/26/2021] [Accepted: 11/07/2021] [Indexed: 01/08/2023]
Abstract
Background Real-time surveillance of search behavior on the internet has achieved accessibility in measuring disease activity. In this study, we systematically assessed the associations between internet search trends of gastrointestinal (GI) symptom terms and daily newly confirmed COVID-19 cases at both global and regional levels. Methods Relative search volumes (RSVs) of GI symptom terms were derived from internet search engines. Time-series analyses with autoregressive integrated moving average models were conducted to fit and forecast the RSV trends of each GI symptom term before and after the COVID-19 outbreak. Generalized additive models were used to quantify the effects of RSVs of GI symptom terms on the incidence of COVID-19. In addition, dose-response analyses were applied to estimate the shape of the associations. Results The RSVs of GI symptom terms could be characterized by seasonal variation and a high correlation with symptoms of “fever” and “cough” at both global and regional levels; in particular, “diarrhea” and “loss of taste” were abnormally increased during the outbreak period of COVID-19, with elevated point changes of 1.31 and 8 times, respectively. In addition, these symptom terms could effectively predict a COVID-19 outbreak in advance, underlying the lag correlation at 12 and 5 days, respectively, and with mutual independence. The dose-response curves showed a consistent increase in daily COVID-19 risk with increasing search volumes of “diarrhea” and “loss of taste”. Conclusion This is the first and largest epidemiologic study that comprehensively revealed the advanced prediction of COVID-19 outbreaks at both global and regional levels via GI symptom indicators.
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Silva FAFD, de Brito BB, Santos MLC, Marques HS, da Silva Júnior RT, de Carvalho LS, de Sousa Cruz S, Rocha GR, Correa Santos GL, de Souza KC, Maciel RGA, Lopes DS, Silva NOE, Oliveira MV, de Melo FF. Transmission of severe acute respiratory syndrome coronavirus 2 via fecal-oral: Current knowledge. World J Clin Cases 2021; 9:8280-8294. [PMID: 34754839 PMCID: PMC8554441 DOI: 10.12998/wjcc.v9.i28.8280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 93 million cases and 2 million deaths in the world. SARS-CoV-2 respiratory tract infection and its main clinical manifestations such as cough and shortness of breath are well known to the scientific community. However, a growing number of studies have reported SARS-CoV-2-related gastrointestinal involvement based on clinical manifestations, such as diarrhea, nausea, vomiting, and abdominal pain as well as on the pathophysiological mechanisms associated with coronavirus disease 2019. Furthermore, current evidence suggests SARS-CoV-2 transmission via the fecal-oral route and aerosol dissemination. Moreover, studies have shown a high risk of contamination through hospital surfaces and personal fomites. Indeed, viable SARS-CoV-2 specimens can be obtained from aerosols, which raises the possibility of transmission through aerosolized viral particles from feces. Therefore, the infection by SARS-CoV-2 via fecal-oral route or aerosolized particles should be considered. In addition, a possible viral spread to sources of drinking water, sewage, and rivers as well as the possible risk of viral transmission in shared toilets become a major public health concern, especially in the least developed countries. Since authors have emphasized the presence of viral RNA and even viable SARS-CoV-2 in human feces, studies on the possible fecal-oral coronavirus disease 2019 transmission become essential to understand better the dynamics of its transmission and, then, to reinforce preventive measures against this infection, leading to a more satisfactory control of the incidence of the infection.
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Affiliation(s)
| | - Breno Bittencourt de Brito
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Maria Luísa Cordeiro Santos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Hanna Santos Marques
- Departamento de Ciências Naturais, Universidade Estadual do Sudoeste da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | | | - Lorena Sousa de Carvalho
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Samuel de Sousa Cruz
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Gabriel Reis Rocha
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Gabriel Lima Correa Santos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Kathlen Coutinho de Souza
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | | | - Daiana Silva Lopes
- Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador 40.110-100, Bahia, Brazil
| | - Natália Oliveira e Silva
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Márcio Vasconcelos Oliveira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Fabrício Freire de Melo
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
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Ahmadinejad M, Ahmadinejad I, Soltanian A, Mardasi KG, Taherzade N. Using new technicque in sigmoid volvulus surgery in patients affected by COVID19. Ann Med Surg (Lond) 2021; 70:102789. [PMID: 34512969 PMCID: PMC8416359 DOI: 10.1016/j.amsu.2021.102789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Coronavirus pandemic-initiated Wuhan city, Hubei Province, China. It mainly involves respiratory system and cause fever, cough. However, it has other manifestations such as GI system, CNS and skin involvement. It is transmitted mostly through respiratory system, but some researchers claim that in can potentially spread by oral, fecal or intestinal gas. During colorectal surgeries such as volvulus sigmoid, surgeons are at risk of exposure to intestinal gas. CASE PRESENTATION A 57-year-old mentally retarded man came to our emergency department with complain of abdominal pain, constipation, obstipation, nausea, vomiting and abdominal distention. His vital sign was stable and his laboratory data revealed no abnormality. His abdominal x-ray showed intestinal obstruction with suspicious of sigmoid volvulus. His PCR for COVID 19 was positive and his chest CT scan has manifestations of lung involvement. He was proceeded for surgery. CONCLUSION Owing to odds of spread of coronavirus through intestinal gas, in this case, sigmoid colon was removed without evacuation of intestinal gas.
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Affiliation(s)
- Mojtaba Ahmadinejad
- Department of Surgery, School of Medicine, Shahid Madani Hostpital, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Ali Soltanian
- Department of Surgery, School of Medicine, Shahid Madani Hostpital, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Noshin Taherzade
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
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50
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Natarajan A, Han A, Zlitni S, Brooks EF, Vance SE, Wolfe M, Singh U, Jagannathan P, Pinsky BA, Boehm A, Bhatt AS. Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nat Commun 2021; 12:5753. [PMID: 34599164 PMCID: PMC8486790 DOI: 10.1038/s41467-021-25576-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Marlene Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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