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1
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Holmes EC. The Emergence and Evolution of SARS-CoV-2. Annu Rev Virol 2024; 11:21-42. [PMID: 38631919 DOI: 10.1146/annurev-virology-093022-013037] [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] [Indexed: 04/19/2024]
Abstract
The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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2
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Fappani C, Gori M, Bianchi S, Terraneo M, Bilardi E, Colzani D, Tanzi E, Canuti M, Amendola A. Differential diagnosis of fever and rash cases negative for measles and rubella to complement surveillance activities. J Med Virol 2023; 95:e29141. [PMID: 37796084 DOI: 10.1002/jmv.29141] [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: 05/08/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
In the quest to eliminate measles virus (MV) and rubella virus (Ruv), every suspected case must be properly identified and diagnosed. Since 2017, in Milan (Italy), a total of 978 measles and rubella suspected cases (fever and rash) were investigated and 310 were not laboratory confirmed (discarded cases). To improve surveillance activities, we investigated the presence in discarded cases of 8 other viral pathogens commonly associated with rash: human herpesvirus 6 (HHV-6) and 7 (HHV-7), parvovirus B19 (B19V), enterovirus (EV), Epstein-Barr virus (EBV), human adenovirus (HAdV), cytomegalovirus (HCMV), and SARS-CoV-2. Differential diagnosis was carried out on 289 discarded cases by multiplex real-time PCR assays. At least one pathogen was detected in 188 cases (65.1%) with HHV-7 being the most frequently detected virus. No difference in the number of detected infections overtime was observed and infections were identified in all age groups. As expected, most HHV-6, EV, HAdV, and HCMV-positive cases were found in children aged 0-4 years and HHV-7 was most frequent in the 15-39 age group. In light of the World Health Organization measles elimination goal, the introduction of laboratory methods for differential diagnosis is required for the final classification of clinically compatible cases. The used screening panel allowed us to increase the percentage of virus-positive cases to 87.5%, allowing us to clarify viral involvement and epidemiology, improve diagnosis, and strengthen surveillance activities. As all investigated pathogens were detected, this diagnostic panel was a suitable tool to complement MV and RuV surveillance activities.
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Affiliation(s)
- Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Silvia Bianchi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Mara Terraneo
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Erica Bilardi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Marta Canuti
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
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3
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Sciannameo V, Azzolina D, Lanera C, Acar AŞ, Corciulo MA, Comoretto RI, Berchialla P, Gregori D. Fitting Early Phases of the COVID-19 Outbreak: A Comparison of the Performances of Used Models. Healthcare (Basel) 2023; 11:2363. [PMID: 37628560 PMCID: PMC10454512 DOI: 10.3390/healthcare11162363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/06/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 outbreak involved a spread of prediction efforts, especially in the early pandemic phase. A better understanding of the epidemiological implications of the different models seems crucial for tailoring prevention policies. This study aims to explore the concordance and discrepancies in outbreak prediction produced by models implemented and used in the first wave of the epidemic. To evaluate the performance of the model, an analysis was carried out on Italian pandemic data from February 24, 2020. The epidemic models were fitted to data collected at 20, 30, 40, 50, 60, 70, 80, 90, and 98 days (the entire time series). At each time step, we made predictions until May 31, 2020. The Mean Absolute Error (MAE) and the Mean Absolute Percentage Error (MAPE) were calculated. The GAM model is the most suitable parameterization for predicting the number of new cases; exponential or Poisson models help predict the cumulative number of cases. When the goal is to predict the epidemic peak, GAM, ARIMA, or Bayesian models are preferable. However, the prediction of the pandemic peak could be made carefully during the early stages of the epidemic because the forecast is affected by high uncertainty and may very likely produce the wrong results.
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Affiliation(s)
- Veronica Sciannameo
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
- Center of Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Torino, 10124 Turin, Italy;
| | - Danila Azzolina
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
- Department of Environmental and Preventive Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Corrado Lanera
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
| | | | - Maria Assunta Corciulo
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
| | - Rosanna Irene Comoretto
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
- Department of Public Health and Pediatrics, University of Torino, 10124 Turin, Italy
| | - Paola Berchialla
- Center of Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Torino, 10124 Turin, Italy;
| | - Dario Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, 35131 Padova, Italy; (V.S.); (D.A.); (C.L.); (M.A.C.); (R.I.C.)
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4
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Cao Y, Chen L, Chen H, Cun Y, Dai X, Du H, Gao F, Guo F, Guo Y, Hao P, He S, He S, He X, Hu Z, Hoh BP, Jin X, Jiang Q, Jiang Q, Khan A, Kong HZ, Li J, Li SC, Li Y, Lin Q, Liu J, Liu Q, Lu J, Lu X, Luo S, Nie Q, Qiu Z, Shi T, Song X, Su J, Tao SC, Wang C, Wang CC, Wang GD, Wang J, Wu Q, Wu S, Xu S, Xue Y, Yang W, Yang Z, Ye K, Ye YN, Yu L, Zhao F, Zhao Y, Zhai W, Zhang D, Zhang L, Zheng H, Zhou Q, Zhu T, Zhang YP. Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. Natl Sci Rev 2023; 10:nwac287. [PMID: 37089192 PMCID: PMC10116607 DOI: 10.1093/nsr/nwac287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yanan Cao
- Ruijin Hospital, Shanghai Jiao Tong University, China
| | - Lingling Chen
- College of Life Science and Technology, Guangxi University, China
| | - Hua Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Yupeng Cun
- Children's Hospital of Chongqing Medical University, China
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, China
| | - Fengbiao Guo
- School of Pharmaceutical Sciences, Wuhan University, China
| | - Yalong Guo
- Institute of Botany, Chinese Academy of Sciences, China
| | - Pei Hao
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - Shunmin He
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Shunping He
- Institute of Hydrobiology, Chinese Academy of Sciences, China
| | - XiongLei He
- School of Life Sciences, Sun Yat-sen University, China
| | - Zheng Hu
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, University College Sedaya International, Malaysia
| | - Xin Jin
- School of Medicine, South China University of Technology, China
| | - Qian Jiang
- Department of Medical Genetics, Capital Institute of Pediatrics, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, China
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Pakistan
| | - Hong-Zhi Kong
- Institute of Botany, Chinese Academy of Sciences, China
| | - Jinchen Li
- Xiangya Hospital, Central South University, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, China
| | - Ying Li
- College of Life Science and Technology, Foshan University, China
| | - Qiang Lin
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | | | - Qi Liu
- School of Life Sciences and Technology, Tongji University, China
| | - Jian Lu
- School of Life Sciences, Peking University, China
| | - Xuemei Lu
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Shujin Luo
- School of Life Sciences, Peking University, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, China
| | - Zilong Qiu
- Institute of Neuroscience, Chinese Academy of Sciences, China
| | - Tieliu Shi
- School of Life Sciences, East China Normal University, China
| | - Xiaofeng Song
- Nanjing University of Aeronautics and Astronautics, China
| | - Jianzhong Su
- Wenzhou Institute, University of Chinese Academy of Sciences, China
| | - Sheng-ce Tao
- Institute of Systems Biomedicine, Shanghai Jiao Tong University, China
| | - Chaolong Wang
- Tongji Medical College, Huazhong University of Science and Technology, China
| | | | - Guo-Dong Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Jiguang Wang
- Division of Life Science and Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, China
| | - Qi Wu
- Institute of Microbiology, Chinese Academy of Sciences, China
| | - Shaoyuan Wu
- School of Life Sciences, Jiangsu Normal University, China
| | - Shuhua Xu
- School of Life Sciences, Fudan University, China
| | - Yu Xue
- College of Life Science and Technology, Huazhong University of Science and Technology, China
| | - Wenjun Yang
- International Center for Aging and Cancer, Hainan Medical University, China
| | - Zhaohui Yang
- Academy of Medical Science, Zhengzhou University, China
| | - Kai Ye
- Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, China
| | - Yuan-Nong Ye
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, China
| | - Li Yu
- School of Life Sciences, Yunnan University, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, China
| | - Yiqiang Zhao
- College of Biological Sciences, China Agricultural University, China
| | - Weiwei Zhai
- Institute of Zoology, Chinese Academy of Sciences, China
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, China
| | | | - Qi Zhou
- Life Sciences Institute, Zhejiang University, China
| | - Tianqi Zhu
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
| | - Ya-ping Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
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5
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Ruan Y, Wen H, Hou M, Zhai W, Xu S, Lu X. On the epicenter of COVID-19 and the origin of the pandemic strain. Natl Sci Rev 2023; 10:nwac286. [PMID: 37089190 PMCID: PMC10115162 DOI: 10.1093/nsr/nwac286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Weiwei Zhai
- Institute of Zoology, Chinese Academy of Sciences, China
| | - Shuhua Xu
- School of Life Sciences, Fudan University, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution; Yunnan Key Laboratory of Biodiversity Information Kunming Institute of Zoology, Chinese Academy of Sciences, China
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6
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Jankovics I, Müller C, Gönczöl É, Visontai I, Varga I, Lőrincz M, Kuti D, Hasitz Á, Malik P, Ursu K, Bányász B, Sarkadi J, Dénes B. Asymptomatic and Mild SARS-CoV-2 Infections in a Hungarian Outpatient Cohort in the First Year of the COVID-19 Pandemic. Trop Med Infect Dis 2023; 8:tropicalmed8040204. [PMID: 37104330 PMCID: PMC10146718 DOI: 10.3390/tropicalmed8040204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/14/2023] [Accepted: 03/25/2023] [Indexed: 04/28/2023] Open
Abstract
We aimed to estimate the proportion of the population infected with SARS-CoV-2 in the first year of the pandemic. The study population consisted of outpatient adults with mild or no COVID-19 symptoms and was divided into subpopulations with different levels of exposure. Among the subpopulation without known previous COVID-19 contacts, 4143 patients were investigated. Of the subpopulation with known COVID-19 contacts, 594 patients were investigated. IgG- and IgA-seroprevalence and RT-PCR positivity were determined in context with COVID-19 symptoms. Our results suggested no significant age-related differences between participants for IgG positivity but indicated that COVID-19 symptoms occurred most frequently in people aged between 20 and 29 years. Depending on the study population, 23.4-74.0% PCR-positive people (who were symptomless SARS-CoV-2 carriers at the time of the investigation) were identified. It was also observed that 72.7% of the patients remained seronegative for 30 days or more after their first PCR-positive results. This study hoped to contribute to the scientific understanding of the significance of asymptomatic and mild infections in the long persistence of the pandemic.
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Affiliation(s)
- István Jankovics
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary
| | - Cecília Müller
- Department of Chief Medical Officer, National Public Health Centre, 1097 Budapest, Hungary
| | - Éva Gönczöl
- Division of Project Coordination, National Public Health Centre, 1097 Budapest, Hungary
| | - Ildikó Visontai
- Division of Project Coordination, National Public Health Centre, 1097 Budapest, Hungary
| | - István Varga
- Division of Project Coordination, National Public Health Centre, 1097 Budapest, Hungary
| | - Márta Lőrincz
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary
| | - Dávid Kuti
- Division of Virology, Department of Reference Laboratory for Microbiology, National Public Health Center, 1097 Budapest, Hungary
| | - Ágnes Hasitz
- Family Doctor's Office, 2000 Szentendre, Hungary
| | - Péter Malik
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary
| | - Krisztina Ursu
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary
| | - Borbála Bányász
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary
| | - Júlia Sarkadi
- Division of Virology, Department of Reference Laboratory for Microbiology, National Public Health Center, 1097 Budapest, Hungary
| | - Béla Dénes
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary
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7
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Amendola A, Canuti M, Bianchi S, Kumar S, Fappani C, Gori M, Colzani D, Kosakovsky Pond SL, Miura S, Baggieri M, Marchi A, Borghi E, Zuccotti G, Raviglione MC, Magurano F, Tanzi E. Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. ENVIRONMENTAL RESEARCH 2022; 215:113979. [PMID: 36029839 PMCID: PMC9404229 DOI: 10.1016/j.envres.2022.113979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 05/12/2023]
Abstract
As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.
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Affiliation(s)
- Antonella Amendola
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Marta Canuti
- Department of Health Sciences, University of Milan, 20142, Milan, Italy.
| | - Silvia Bianchi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA; Center for Excellence in Genome Medicine and Research, King Abdulaziz University, 22252, Jeddah, Saudi Arabia.
| | - Clara Fappani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Maria Gori
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Daniela Colzani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisa Borghi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Gianvincenzo Zuccotti
- Department of Paediatrics, Children Hospital V. Buzzi, University of Milan, 20154, Milan, Italy; Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, 20154, Milan, Italy.
| | - Mario C Raviglione
- Centre for Multidisciplinary Research in Health Science, University of Milan, 20122, Milan, Italy.
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisabetta Tanzi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
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8
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Trombetta CM, Marchi S, Viviani S, Manenti A, Casa E, Dapporto F, Remarque EJ, Bollati V, Manini I, Lazzeri G, Montomoli E. A serological investigation in Southern Italy: was SARS-CoV-2 circulating in late 2019? Hum Vaccin Immunother 2022; 18:2047582. [PMID: 35289714 PMCID: PMC8935457 DOI: 10.1080/21645515.2022.2047582] [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] [Indexed: 12/18/2022] Open
Abstract
In March 2020, the first pandemic caused by a coronavirus was declared by the World Health Organization. Italy was one of the first and most severely affected countries, particularly the northern part of the country. The latest evidence suggests that the virus could have been circulating, at least in Italy, before the first autochthonous SARS-COV-2 case was detected in February 2020. The present study aimed to investigate the presence of antibodies against SARS-CoV-2 in human serum samples collected in the last months of 2019 (September–December) in the Apulia region, Southern Italy. Eight of 455 samples tested proved positive on in-house receptor-binding-domain-based ELISA. Given the month of collection of the positive samples, these findings may indicate early circulation of SARS-CoV-2 in Apulia region in the autumn of 2019. However, it cannot be completely ruled out that the observed sero-reactivity could be an unknown antigen specificity in another virus to which subjects were exposed containing an epitope adventitiously cross-reactive with an epitope of SARS-CoV-2.
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Affiliation(s)
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Simonetta Viviani
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | | | | | | | - Edmond J Remarque
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Ilaria Manini
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Giacomo Lazzeri
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy.,VisMederi srl, Siena, Italy.,VisMederi Research srl, Siena, Italy
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9
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Predicting health crises from early warning signs in patient medical records. Sci Rep 2022; 12:19267. [PMID: 36357666 PMCID: PMC9649019 DOI: 10.1038/s41598-022-23900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
The COVID-19 global pandemic has caused unprecedented worldwide changes in healthcare delivery. While containment and mitigation approaches have been intensified, the progressive increase in the number of cases has overwhelmed health systems globally, highlighting the need for anticipation and prediction to be the basis of an efficient response system. This study demonstrates the role of population health metrics as early warning signs of future health crises. We retrospectively collected data from the emergency department of a large academic hospital in the northeastern United States from 01/01/2019 to 08/07/2021. A total of 377,694 patient records and 303 features were included for analysis. Departing from a multivariate artificial intelligence (AI) model initially developed to predict the risk of high-flow oxygen therapy or mechanical ventilation requirement during the COVID-19 pandemic, a total of 19 original variables and eight engineered features showing to be most predictive of the outcome were selected for further analysis. The temporal trends of the selected variables before and during the pandemic were characterized to determine their potential roles as early warning signs of future health crises. Temporal analysis of the individual variables included in the high-flow oxygen model showed that at a population level, the respiratory rate, temperature, low oxygen saturation, number of diagnoses during the first encounter, heart rate, BMI, age, sex, and neutrophil percentage demonstrated observable and traceable changes eight weeks before the first COVID-19 public health emergency declaration. Additionally, the engineered rule-based features built from the original variables also exhibited a pre-pandemic surge that preceded the first pandemic wave in spring 2020. Our findings suggest that the changes in routine population health metrics may serve as early warnings of future crises. This justifies the development of patient health surveillance systems, that can continuously monitor population health features, and alarm of new approaching public health crises before they become devastating.
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10
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Hao Y, Wang Y, Wang M, Zhou L, Shi J, Cao J, Wang D. The origins of COVID-19 pandemic: A brief overview. Transbound Emerg Dis 2022; 69:3181-3197. [PMID: 36218169 PMCID: PMC9874793 DOI: 10.1111/tbed.14732] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.
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Affiliation(s)
- Ying‐Jian Hao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Yu‐Lan Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Mei‐Yue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Lan Zhou
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Jian‐Yun Shi
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Ji‐Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - De‐Ping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
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11
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Sachs JD, Karim SSA, Aknin L, Allen J, Brosbøl K, Colombo F, Barron GC, Espinosa MF, Gaspar V, Gaviria A, Haines A, Hotez PJ, Koundouri P, Bascuñán FL, Lee JK, Pate MA, Ramos G, Reddy KS, Serageldin I, Thwaites J, Vike-Freiberga V, Wang C, Were MK, Xue L, Bahadur C, Bottazzi ME, Bullen C, Laryea-Adjei G, Ben Amor Y, Karadag O, Lafortune G, Torres E, Barredo L, Bartels JGE, Joshi N, Hellard M, Huynh UK, Khandelwal S, Lazarus JV, Michie S. The Lancet Commission on lessons for the future from the COVID-19 pandemic. Lancet 2022; 400:1224-1280. [PMID: 36115368 PMCID: PMC9539542 DOI: 10.1016/s0140-6736(22)01585-9] [Citation(s) in RCA: 327] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023]
Affiliation(s)
- Jeffrey D Sachs
- Center for Sustainable Development, Columbia University, New York, NY, United States.
| | - Salim S Abdool Karim
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lara Aknin
- Department of Psychology, Simon Fraser University, Burnaby, BC, Canada
| | - Joseph Allen
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | - Francesca Colombo
- Health Division, Organisation for Economic Co-operation and Development, Paris, France
| | | | | | - Vitor Gaspar
- Fiscal Affairs Department, International Monetary Fund, Washington, DC, United States
| | | | - Andy Haines
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, UK; Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter J Hotez
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Phoebe Koundouri
- Department of International and European Economic Studies, Athens University of Economics and Business, Athens, Greece; Department of Technology, Management and Economics, Technical University of Denmark, Kongens Lyngby, Denmark; European Association of Environmental and Resource Economists, Athens, Greece
| | - Felipe Larraín Bascuñán
- Department of Economics and Administration, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jong-Koo Lee
- National Academy of Medicine of Korea, Seoul, Republic of Korea
| | - Muhammad Ali Pate
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | | | | | - John Thwaites
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | | | - Chen Wang
- National Clinical Research Center for Respiratory Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China; National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | | | - Lan Xue
- Schwarzman College, Tsinghua University, Beijing, China
| | - Chandrika Bahadur
- The Lancet COVID-19 Commission Regional Task Force: India, New Delhi, India
| | - Maria Elena Bottazzi
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Chris Bullen
- National Institute for Health Innovation, University of Auckland, Auckland, New Zealand
| | | | - Yanis Ben Amor
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Ozge Karadag
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | | | - Emma Torres
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Lauren Barredo
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Juliana G E Bartels
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Neena Joshi
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | | | | | | | - Jeffrey V Lazarus
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Susan Michie
- Centre for Behaviour Change, University College London, London, UK
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12
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Covid-19: Early Cases and Disease Spread. Ann Glob Health 2022; 88:83. [PMID: 36247198 PMCID: PMC9524236 DOI: 10.5334/aogh.3776] [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: 03/11/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022] Open
Abstract
The emergence and global spread of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is critical to understanding how to prevent or control a future viral pandemic. We review the tools used for this retrospective search, their limits, and results obtained from China, France, Italy and the USA. We examine possible scenarios for the emergence of SARS-CoV-2 in the human population. We consider the Chinese city of Wuhan where the first cases of atypical pneumonia were attributed to SARS-CoV-2 and from where the disease spread worldwide. Possible superspreading events include the Wuhan-based 7th Military World Games on October 18–27, 2019 and the Chinese New Year holidays from January 25 to February 2, 2020. Several clues point to an early regional circulation of SARS-CoV-2 in northern Italy (Lombardi) as soon as September/October 2019 and in France in November/December 2019, if not before. With the goal of preventing future pandemics, we call for additional retrospective studies designed to trace the origin of SARS-CoV-2.
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13
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Abstract
The Covid-19 pandemic appeared in China in December 2019 as a cluster of transmissible pneumonia caused by a new betacoronavirus. On March 11, 2020, the World Health Organization (WHO) declared it a pandemic. Covid-19 is a mild infection in 80% of cases, serious in 15% and critical in 5%. Symptomatic forms include a first phase of flu-like viral invasion, and at times a second phase, dysimmune and inflammatory, with acute respiratory distress syndrome, multiorgan failure and thromboembolic complications. Degree of severity is related to age and comorbidities. SARS-CoV-2 is the third highly pathogenic Betacoronavirus to cross the species barrier. Its genome, an RNA of 29,903 nucleotides, shows strong homogeneity with bat coronaviruses from southern China, but the conditions for its passage in humans have yet to be elucidated. Mutations can give rise to variants of concern (VOC) that are more transmissible and able to evade the host's immune response. Several VOCs have succeeded and replaced one another: Alpha in October 2020, Beta and Gamma in December 2020, Delta in spring 2021 and Omicron in November 2021. The Covid-19 pandemic has evolved in five waves of unequal amplitude and severity, with geographical disparities. Worldwide, it has caused 395,000,000 confirmed cases including 5,700,000 deaths. Epidemiological surveillance applies several indicators (incidence rate, test positivity rate, effective R and occupancy rate of intensive care beds) supplemented by genomic monitoring to detect variants by sequencing. Non-pharmacological measures, particularly face mask wearing, have been effective in preventing the transmission of SARS-CoV-2. Few currently available drugs have proven useful, with the exception of dexamethazone for patients requiring oxygen therapy. Development of SARS-CoV-2 vaccines began early on many platforms. Innovation was brought about by the Pfizer-BioNTech and Moderna messenger RNA vaccines, which claim protective efficacy of 95% and 94.1% respectively, far higher than the 70% minimum set by the WHO. Governments have hesitated between two strategies, mitigation and suppression. The second has been favored in critical periods such as April 2020, when 2.5 billion people throughout the world were confined. Vaccination campaigns got underway at the end of December 2020 and progressed without reaching sufficient herd immunity, leading some nations to consider compulsory vaccination or to require a vaccine or health pass, in order for persons to access different activities. Will the pandemic stop with Omicron and become endemic? This part of the Covid-19 story remains to be told.
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Affiliation(s)
- Yves Buisson
- Académie nationale de médecine, 4ème division, 16, rue Bonaparte, 75272 Paris Cedex06, France.
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14
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Krittanawong C, Maitra N, Kumar A, Hahn J, Wang Z, Carrasco D, Zhang HJ, Sun T, Jneid H, Virani SS. COVID-19 and preventive strategy. AMERICAN JOURNAL OF CARDIOVASCULAR DISEASE 2022; 12:153-169. [PMID: 36147788 PMCID: PMC9490164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
In December 2019, an unprecedented outbreak of the novel coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread internationally, now impacting more than 293,750,692 patients with 5,454,131 deaths globally as of January 5, 2022. COVID-19 is highly pathogenic and contagious which has caused a large-scale epidemic impacting more deaths than the severe acute respiratory syndrome (SARS) epidemic in 2002-2003 or the Middle East respiratory syndrome (MERS) epidemic in 2012-2013. Although COVID-19 symptoms are mild in most people, in those with pre-existing comorbidities there is an increased risk of progression to severe disease and death. In an attempt to mitigate this pandemic, urgent public health measures including quarantining exposed individuals and social distancing have been implemented in most states, while some states have even started the process of re-opening after considering both the economic and public health consequences of social distancing measures. While prevention is crucial, both novel agents and medications already in use with other indications are being investigated in clinical trials for patients with COVID-19. The collaboration between healthcare providers, health systems, patients, private sectors, and local and national governments is needed to protect both healthcare providers and patients to ultimately overcome this pandemic. The purpose of this review is to summarize the peer-reviewed and preprint literature on the epidemiology, transmission, clinical presentation, and available therapies as well as to propose a preventive strategy to overcome the present global pandemic.
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Affiliation(s)
- Chayakrit Krittanawong
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, Mount Sinai HeartNew York, NY, USA
| | - Neil Maitra
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
| | - Anirudh Kumar
- Heart and Vascular Institute, Cleveland ClinicCleveland, OH, USA
| | - Joshua Hahn
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
| | - Zhen Wang
- Robert D. and Patricia E. Kern Center for The Science of Health Care Delivery, Mayo ClinicRochester, MN, USA
- Division of Health Care Policy and Research, Department of Health Sciences Research, Mayo ClinicRochester, MN, USA
| | - Daniela Carrasco
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
| | - Hong Ju Zhang
- Division of Cardiology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthBeijing, China
| | - Tao Sun
- Division of Cardiology, Anzhen Hospital Capital Medical UniversityBeijing, China
| | - Hani Jneid
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
| | - Salim S Virani
- Section of Cardiology, Baylor College of MedicineHouston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical CenterHouston, TX, USA
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15
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Lai A, Tambuzzi S, Bergna A, Battistini A, Della Ventura C, Galli M, Zoja R, Zehender G, Cattaneo C. Evidence of SARS-CoV-2 Antibodies and RNA on Autopsy Cases in the Pre-Pandemic Period in Milan (Italy). Front Microbiol 2022; 13:886317. [PMID: 35783409 PMCID: PMC9240701 DOI: 10.3389/fmicb.2022.886317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, we analyzed blood samples obtained from 169 cadavers subjected to an autopsy from 1 October 2019 to 27 March 2020. The presence of anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) antibodies was searched by lateral flow immunochromatographic assay (LFIA) and ELISA tests and the SARS-CoV-2 RNA was tested in blood and available lung tissues by real-time PCR (RT-PCR) and droplet digital PCR (ddPCR). Five cases resulted in positives at the serological screening for anti-SARS-CoV-2. Three results were weakly positive for IgM while only one showed strong reactivity for IgG antibodies. The fifth subject (who died in December 2019) resulted positive for the ELISA test. The detection of SARS-CoV-2 RNA resulted in positive only in the blood and lung tissues of such cases. These data suggest that cadaveric blood may be a suitable substrate for the assessment of SARS-CoV-2 infection; moreover, they extend the observations of sporadic cases of SARS-CoV-2 infection in North Italy prior to the first confirmed cases.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- *Correspondence: Alessia Lai
| | - Stefano Tambuzzi
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Alessio Battistini
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Riccardo Zoja
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | | | - Cristina Cattaneo
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
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16
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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Affiliation(s)
- Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 Haping Road, Harbin 150069, China.
| | - Jiumeng Sun
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Dongyan Li
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Ningning Wang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Lifang Wang
- College of Veterinary Medicine, China Agricultural University, No. 17 Qinghua Donglu, Beijing 100083, China
| | - Chang Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Xiaorong Meng
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St., Charles Avenue, New Orleans, LA 70118, USA
| | - Marc A Suchard
- Departments of Biomathematics, Human Genetics and Biostatistics, David Geffen School of Medicine and Fielding School of Public Health, University of California, Los Angeles, Geffen Hall 885 Tiverton Drive, Los Angeles, CA 90095, USA
| | - Xu Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, 400 East Main St., Frankfort, KY 40601, USA
| | - Shuo Su
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany.
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17
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Li J, Jia H, Tian M, Wu N, Yang X, Qi J, Ren W, Li F, Bian H. SARS-CoV-2 and Emerging Variants: Unmasking Structure, Function, Infection, and Immune Escape Mechanisms. Front Cell Infect Microbiol 2022; 12:869832. [PMID: 35646741 PMCID: PMC9134119 DOI: 10.3389/fcimb.2022.869832] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/06/2022] [Indexed: 12/24/2022] Open
Abstract
As of April 1, 2022, over 468 million COVID-19 cases and over 6 million deaths have been confirmed globally. Unlike the common coronavirus, SARS-CoV-2 has highly contagious and attracted a high level of concern worldwide. Through the analysis of SARS-CoV-2 structural, non-structural, and accessory proteins, we can gain a deeper understanding of structure-function relationships, viral infection mechanisms, and viable strategies for antiviral therapy. Angiotensin-converting enzyme 2 (ACE2) is the first widely acknowledged SARS-CoV-2 receptor, but researches have shown that there are additional co-receptors that can facilitate the entry of SARS-CoV-2 to infect humans. We have performed an in-depth review of published papers, searching for co-receptors or other auxiliary membrane proteins that enhance viral infection, and analyzing pertinent pathogenic mechanisms. The genome, and especially the spike gene, undergoes mutations at an abnormally high frequency during virus replication and/or when it is transmitted from one individual to another. We summarized the main mutant strains currently circulating global, and elaborated the structural feature for increased infectivity and immune evasion of variants. Meanwhile, the principal purpose of the review is to update information on the COVID-19 outbreak. Many countries have novel findings on the early stage of the epidemic, and accruing evidence has rewritten the timeline of the outbreak, triggering new thinking about the origin and spread of COVID-19. It is anticipated that this can provide further insights for future research and global epidemic prevention and control.
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Affiliation(s)
| | | | | | | | | | | | | | - Feifei Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hongjun Bian
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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18
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Araujo da Silva AR, de Carvalho BRR, Esteves MDM, Teixeira CH, Souza CV. The Role of COVID-19 Vaccinal Status in Admitted Children during OMICRON Variant Circulation in Rio de Janeiro, City-Preliminary Report. Vaccines (Basel) 2022; 10:vaccines10040619. [PMID: 35455368 PMCID: PMC9025062 DOI: 10.3390/vaccines10040619] [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: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/16/2022] Open
Abstract
Objective: To evaluate COVID-19 vaccination status in admitted children in 2020−2021 and during the OMICRON variant circulation (2022), a period when children older than 12 years of age had received two doses of COVID-19 vaccines. Design: An observational retrospective study. Patients with confirmed COVID-19 were compared in two different periods: 2020−2021 when adolescents aged 12−18 years had not received the complete COVID-19 vaccine, and 2022 when children older than 12 years had received the complete Pfizer-BioNTech vaccine scheme. Setting: Two pediatric hospitals in Rio de Janeiro city. Patients: Children aged < 18 years with confirmed COVID-19. Intervention: None. Main outcome: Vaccination status for COVID-19 on admission. Results: In total, 300 patients were admitted with confirmed COVID-19 (240 in 2020−2021 and 60 in 2022). The distribution of patients according to the age-groups was: 0−2 years (33.3% in 2020−2021 and 53.4% in 2022), 2−5 years (21.7% in 2020−2021 and 10% in 2022), 5−11 years (29.2% in 2020−2021 and 28.3% in 2022), and 12−18 years (15.8% in 2020−2021 and 8.3% in 2022) (p = 0.076). The median length of stay was six days in 2020−2021 and six days in 2022 (p = 0.423). We verified six deaths in the first analysis period and one death in the second one (p = 0.894). Of the 60 children admitted in 2022, 58 (96.7%) did not receive the complete COVID-19 vaccine scheme available. Conclusions: We verified in a “real-world condition” the ability of the Pfizer-BioNTech vaccine to prevent hospitalization in children over 12 years of age.
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Affiliation(s)
- André Ricardo Araujo da Silva
- Materno-Infantil Department, Faculty of Medicine, Fluminense Federal University, Niterói 24033-900, Brazil; (B.R.R.d.C.); (M.d.M.E.)
- Correspondence:
| | | | - Monica del Monaco Esteves
- Materno-Infantil Department, Faculty of Medicine, Fluminense Federal University, Niterói 24033-900, Brazil; (B.R.R.d.C.); (M.d.M.E.)
| | | | - Cristina Vieira Souza
- Infection Control Committee, Prontobaby Group, Rio de Janeiro 20540-100, Brazil; (C.H.T.); (C.V.S.)
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19
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Ruan Y, Wen H, Hou M, He Z, Lu X, Xue Y, He X, Zhang YP, Wu CI. The twin-beginnings of COVID-19 in Asia and Europe-one prevails quickly. Natl Sci Rev 2022; 9:nwab223. [PMID: 35497643 PMCID: PMC9046579 DOI: 10.1093/nsr/nwab223] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
In the spread of SARS-CoV-2, there have been multiple waves of replacement between strains, each of which having a distinct set of mutations. The first wave is a group of four mutations (C241T, C3037T, C14408T and A23403G [this being the amino acid change D614G]; all designated 0 to 1 below). This DG (D614G) group, fixed at the start of the pandemic, is the foundation of all subsequent waves of strains. Curiously, the DG group is absent in early Asian samples but present (and likely common) in Europe from the beginning. European data show that the high fitness of DG1111 requires the synergistic effect of all four mutations. However, the European strains would have had no time to evolve the four DG mutations (0 to 1), had they come directly from the early Asian DG0000 strain. Very likely, the European DG1111 strain had acquired the highly adaptive DG mutations in pre-pandemic Europe and had been spreading in parallel with the Asian strains. Two recent reports further support this twin-beginning interpretation. There was a period of two-way spread between Asia and Europe but, by May 2020, the European strains had supplanted the Asian strains globally. This large-scale replacement of one set of mutations for another has since been replayed many times as COVID-19 progresses.
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Yongbiao Xue
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing100101, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing100101, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL60637, USA
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20
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On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses 2022; 14:v14030580. [PMID: 35336987 PMCID: PMC8951735 DOI: 10.3390/v14030580] [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: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.
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21
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Canuti M, Bianchi S, Kolbl O, Pond SLK, Kumar S, Gori M, Fappani C, Colzani D, Borghi E, Zuccotti G, Raviglione MC, Tanzi E, Amendola A. Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ Glob Health 2022; 7:e008386. [PMID: 35296465 PMCID: PMC8927931 DOI: 10.1136/bmjgh-2021-008386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/19/2022] [Indexed: 01/22/2023] Open
Abstract
Two years after the start of the COVID-19 pandemic, key questions about the emergence of its aetiological agent (SARS-CoV-2) remain a matter of considerable debate. Identifying when SARS-CoV-2 began spreading among people is one of those questions. Although the current canonically accepted timeline hypothesises viral emergence in Wuhan, China, in November or December 2019, a growing body of diverse studies provides evidence that the virus may have been spreading worldwide weeks, or even months, prior to that time. However, the hypothesis of earlier SARS-CoV-2 circulation is often dismissed with prejudicial scepticism and experimental studies pointing to early origins are frequently and speculatively attributed to false-positive tests. In this paper, we critically review current evidence that SARS-CoV-2 had been circulating prior to December of 2019, and emphasise how, despite some scientific limitations, this hypothesis should no longer be ignored and considered sufficient to warrant further larger-scale studies to determine its veracity.
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Affiliation(s)
- Marta Canuti
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Bianchi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Otto Kolbl
- Faculty of Arts, University of Lausanne, Lausanne, Switzerland
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Sudhir Kumar
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Elisa Borghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, Ospedale dei Bambini, Università degli Studi di Milano, Milan, Italy
- Romeo and Enrica Invernizzi Pediatric Research Center, Università degli Studi di Milano, Milan, Italy
| | - Mario C Raviglione
- Centre for Multidisciplinary Research in Health Science, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
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22
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Lukowsky LR, Der-Martirosian C, Steers WN, Kamble KS, Dobalian A. Using an Administrative and Clinical Database to Determine the Early Spread of COVID-19 at the US Department of Veterans Affairs during the Beginning of the 2019-2020 Flu Season: A Retrospective Longitudinal Study. Viruses 2022; 14:200. [PMID: 35215795 PMCID: PMC8879908 DOI: 10.3390/v14020200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Previous studies examining the early spread of COVID-19 have used influenza-like illnesses (ILIs) to determine the early spread of COVID-19. We used COVID-19 case definition to identify COVID-like symptoms (CLS) independently of other influenza-like illnesses (ILIs). METHODS Using data from Emergency Department (ED) visits at VA Medical Centers in CA, TX, and FL, we compared weekly rates of CLS, ILIs, and non-influenza ILIs encounters during five consecutive flu seasons (2015-2020) and estimated the risk of developing each illness during the first 23 weeks of the 2019-2020 season compared to previous seasons. RESULTS Patients with CLS were significantly more likely to visit the ED during the first 23 weeks of the 2019-2020 compared to prior seasons, while ED visits for influenza and non-influenza ILIs did not differ substantially. Adjusted CLS risk was significantly lower for all seasons relative to the 2019-2020 season: RR15-16 = 0.72, 0.75, 0.72; RR16-17 = 0.81, 0.77, 0.79; RR17-18 = 0.80, 0.89, 0.83; RR18-19 = 0.82, 0.96, 0.81, in CA, TX, and FL, respectively. CONCLUSIONS The observed increase in ED visits for CLS indicates the likely spread of COVID-19 in the US earlier than previously reported. VA data could potentially help identify emerging infectious diseases and supplement existing syndromic surveillance systems.
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Affiliation(s)
- Lilia R. Lukowsky
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
| | - Claudia Der-Martirosian
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
| | - William Neil Steers
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Kiran S. Kamble
- School of Public Health, University of Memphis, Memphis, TN 38152, USA;
| | - Aram Dobalian
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
- School of Public Health, University of Memphis, Memphis, TN 38152, USA;
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23
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Liu W, Liu P, Liu WJ, Wang Q, Tong Y, Gao GF. Origins of HIV, HCoV-HKU1, SFTSV, and MERS-CoV and Beyond. China CDC Wkly 2022; 4:823-827. [PMID: 36284537 PMCID: PMC9547735 DOI: 10.46234/ccdcw2022.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/15/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wenli Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Peipei Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Yigang Tong,
| | - George F. Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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24
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Montomoli E, Apolone G, Manenti A, Boeri M, Suatoni P, Sabia F, Marchianò A, Bollati V, Pastorino U, Sozzi G. Timeline of SARS-CoV-2 Spread in Italy: Results from an Independent Serological Retesting. Viruses 2021; 14:61. [PMID: 35062265 PMCID: PMC8778320 DOI: 10.3390/v14010061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022] Open
Abstract
The massive emergence of COVID-19 cases in the first phase of pandemic within an extremely short period of time suggest that an undetected earlier circulation of SARS-CoV-2 might have occurred. Given the importance of this evidence, an independent evaluation was recommended by the World Health Organization (WHO) to test a subset of samples selected on the level of positivity in ELISA assays (positive, low positive, negative) detected in our previous study of prepandemic samples collected in Italy. SARS-CoV-2 antibodies were blindly retested by two independent centers in 29 blood samples collected in the prepandemic period in Italy, 29 samples collected one year before and 11 COVID-19 control samples. The methodologies used included IgG-RBD/IgM-RBD ELISA assays, a qualitative micro-neutralization CPE-based assay, a multiplex IgG protein array, an ELISA IgM kit (Wantai), and a plaque-reduction neutralization test. The results suggest the presence of SARS-CoV-2 antibodies in some samples collected in the prepandemic period, with the oldest samples found to be positive for IgM by both laboratories collected on 10 October 2019 (Lombardy), 11 November 2019 (Lombardy) and 5 February 2020 (Lazio), the latter with neutralizing antibodies. The detection of IgM and/or IgG binding and neutralizing antibodies was strongly dependent on the different serological assays and thresholds employed, and they were not detected in control samples collected one year before. These findings, although gathered in a small and selected set of samples, highlight the importance of harmonizing serological assays for testing the spread of the SARS-CoV-2 virus and may contribute to a better understanding of future virus dynamics.
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Affiliation(s)
- Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy;
- VisMederi S.r.l., 53200 Siena, Italy;
| | - Giovanni Apolone
- Scientific Direction, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy;
| | - Alessandro Manenti
- VisMederi S.r.l., 53200 Siena, Italy;
- VisMederi Research S.r.l., 53100 Siena, Italy
| | - Mattia Boeri
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy;
| | - Paola Suatoni
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy; (P.S.); (F.S.)
| | - Federica Sabia
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy; (P.S.); (F.S.)
| | - Alfonso Marchianò
- Department of Radiology, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy;
| | - Valentina Bollati
- EPIGET-Epidemiology, Epigenetics and Toxicology Lab., University of Milan, 20100 Milan, Italy;
| | - Ugo Pastorino
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy; (P.S.); (F.S.)
| | - Gabriella Sozzi
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy;
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25
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Mainardi PH, Bidoia ED. Challenges and emerging perspectives of an international SARS-CoV-2 epidemiological surveillance in wastewater. AN ACAD BRAS CIENC 2021; 93:e20210163. [PMID: 34878048 DOI: 10.1590/0001-3765202120210163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/23/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 is a new type of coronavirus capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing huge impacts across the Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in feces and urine samples. Therefore, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a viral tracking tool in communities. This type of monitoring, in addition to serve as a non-invasive early warning of COVID-19 outbreaks, would provide better predictions about the SARS-CoV-2 spread and strongly contribute to maintenance the global health. Although current methods to detect viruses in wastewater, based on molecular RT-PCR and RT-qPCR techniques, were considered as reliable and provided accurate qualitative and quantitative results, they have been facing considerable challenges concerning the SARS-CoV-2 surveillance. In this review, the methods used to detect the SARS-CoV-2 in wastewater and the challenges to implement an international viral monitoring network were described. The article also addressed the emerging perspectives associated with the SARS-CoV-2 epidemiological surveillance in this environment and the importance of a worldwide collaboration to generate and disseminate the detection results.
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Affiliation(s)
- Pedro H Mainardi
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
| | - Ederio D Bidoia
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
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26
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Panatto D, Orsi A, Pennati BM, Lai PL, Mosca S, Bruzzone B, Caligiuri P, Napoli C, Bertamino E, Orsi GB, Manini I, Loconsole D, Centrone F, Pandolfi E, Ciofi Degli Atti ML, Concato C, Linardos G, Onetti Muda A, Raponi M, Piccioni L, Rizzo C, Chironna M, Icardi G. No evidence of SARS-CoV-2 in hospitalized patients with severe acute respiratory syndrome in five Italian hospitals from 1st November 2019 to 29th February 2020. PLoS One 2021; 16:e0260947. [PMID: 34874956 PMCID: PMC8653811 DOI: 10.1371/journal.pone.0260947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/19/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 - 29th February 2020). OBJECTIVES To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. MATERIALS AND METHODS Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. RESULTS In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0-17 years (40.3%) followed by those aged 18-64 years (24.4%) and ≥65 years (14.8%). CONCLUSIONS In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- COVID-19/diagnosis
- COVID-19/virology
- Female
- Hospitals
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/pathology
- Influenza, Human/virology
- Italy/epidemiology
- Male
- Middle Aged
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Retrospective Studies
- SARS-CoV-2/genetics
- SARS-CoV-2/isolation & purification
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/pathology
- Severe Acute Respiratory Syndrome/virology
- Young Adult
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Affiliation(s)
- Donatella Panatto
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
| | - Andrea Orsi
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
- Policlinico San Martino Hospital, Genoa, Italy
| | - Beatrice Marina Pennati
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
| | - Piero Luigi Lai
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
| | - Stefano Mosca
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
| | | | | | - Christian Napoli
- Department of Medical Surgical Sciences and Translational Medicine,
University La Sapienza, Rome, Italy
| | | | - Giovanni Battista Orsi
- Department of Public Health and Infectious Diseases, University La
Sapienza, Rome, Italy
| | - Ilaria Manini
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Molecular and Developmental Medicine, University of Siena,
Siena, Italy
| | - Daniela Loconsole
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | - Francesca Centrone
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | | | | | | | | | | | | | | | | | - Maria Chironna
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | - Giancarlo Icardi
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
- Policlinico San Martino Hospital, Genoa, Italy
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27
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Singh S, McNab C, Olson RM, Bristol N, Nolan C, Bergstrøm E, Bartos M, Mabuchi S, Panjabi R, Karan A, Abdalla SM, Bonk M, Jamieson M, Werner GK, Nordström A, Legido-Quigley H, Phelan A. How an outbreak became a pandemic: a chronological analysis of crucial junctures and international obligations in the early months of the COVID-19 pandemic. Lancet 2021; 398:2109-2124. [PMID: 34762857 PMCID: PMC8575464 DOI: 10.1016/s0140-6736(21)01897-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/01/2021] [Accepted: 08/17/2021] [Indexed: 12/11/2022]
Abstract
Understanding the spread of SARS-CoV-2, how and when evidence emerged, and the timing of local, national, regional, and global responses is essential to establish how an outbreak became a pandemic and to prepare for future health threats. With that aim, the Independent Panel for Pandemic Preparedness and Response has developed a chronology of events, actions, and recommendations, from December, 2019, when the first cases of COVID-19 were identified in China, to the end of March, 2020, by which time the outbreak had spread extensively worldwide and had been characterised as a pandemic. Datapoints are based on two literature reviews, WHO documents and correspondence, submissions to the Panel, and an expert verification process. The retrospective analysis of the chronology shows a dedicated initial response by WHO and some national governments, but also aspects of the response that could have been quicker, including outbreak notifications under the International Health Regulations (IHR), presumption and confirmation of human-to-human transmission of SARS-CoV-2, declaration of a Public Health Emergency of International Concern, and, most importantly, the public health response of many national governments. The chronology also shows that some countries, largely those with previous experience with similar outbreaks, reacted quickly, even ahead of WHO alerts, and were more successful in initially containing the virus. Mapping actions against IHR obligations, the chronology shows where efficiency and accountability could be improved at local, national, and international levels to more quickly alert and contain health threats in the future. In particular, these improvements include necessary reforms to international law and governance for pandemic preparedness and response, including the IHR and a potential framework convention on pandemic preparedness and response.
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Affiliation(s)
- Sudhvir Singh
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Christine McNab
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Rose McKeon Olson
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nellie Bristol
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Cody Nolan
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elin Bergstrøm
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Michael Bartos
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; School of Sociology, Australian National University, Canberra, ACT, Australia
| | - Shunsuke Mabuchi
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Raj Panjabi
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Abraar Karan
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Salma M Abdalla
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Boston University School of Public Health, Boston, MA, USA
| | - Mathias Bonk
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Margaret Jamieson
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - George K Werner
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Anders Nordström
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Helena Legido-Quigley
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; London School of Hygiene & Tropical Medicine, London, UK; Saw Swee Hock School of Public Health, Singapore
| | - Alexandra Phelan
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Center for Global Health Science & Security, Georgetown University, Washington, DC, USA
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Wu Z, Jin Q, Wu G, Lu J, Li M, Guo D, Lan K, Feng L, Qian Z, Ren L, Tan W, Xu W, Yang W, Wang J, Wang C. SARS-CoV-2's origin should be investigated worldwide for pandemic prevention. Lancet 2021; 398:1299-1303. [PMID: 34543611 PMCID: PMC8448491 DOI: 10.1016/s0140-6736(21)02020-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Affiliation(s)
- Zhiqiang Wu
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Qi Jin
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Guizhen Wu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PR China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, PR China
| | - Deyin Guo
- School of Medicine, Sun Yat-sen University, Shenzhen, PR China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Luzhao Feng
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Zhaohui Qian
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Weizhong Yang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Jianwei Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| | - Chen Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China; Chinese Academy of Engineering, Beijing, PR China
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29
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Mira-Iglesias A, Mengual-Chuliá B, Cano L, García-Rubio J, Tortajada-Girbés M, Carballido-Fernández M, Mollar-Maseres J, Schwarz-Chavarri G, García-Esteban S, Puig-Barberà J, Díez-Domingo J, López-Labrador FX. Retrospective screening for SARS-CoV-2 among influenza-like illness hospitalizations: 2018-2019 and 2019-2020 seasons, Valencia region, Spain. Influenza Other Respir Viruses 2021; 16:166-171. [PMID: 34528756 PMCID: PMC8652788 DOI: 10.1111/irv.12899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
On 9 March 2020, the World Health Organization (WHO) Global Influenza Programme (GIP) asked participant sites on the Global Influenza Hospital Surveillance Network (GIHSN) to contribute to data collection concerning severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). We re‐analysed 5833 viral RNA archived samples collected prospectively from hospital admissions for influenza‐like illness (ILI) in the Valencia Region of Spain by the Valencia Hospital Surveillance Network for the Study of Influenza and Other Respiratory Viruses (VAHNSI) network (four hospitals, catchment area population 1 118 732) during the pre‐pandemic 2018/2019 (n = 4010) and pandemic 2019/2020 (n = 1823) influenza seasons for the presence of SARS‐CoV‐2. We did not find evidence for community‐acquired SARS‐CoV‐2 infection in hospital admissions for ILI in our region before early March 2020.
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Affiliation(s)
- Ainara Mira-Iglesias
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Beatriz Mengual-Chuliá
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain.,Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Cano
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Javier García-Rubio
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | | | - Mario Carballido-Fernández
- Hospital General Universitario de Castellón, Castellón, Spain.,Universidad CEU Cardenal Herrera, Castellón, Spain
| | | | | | - Sandra García-Esteban
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Joan Puig-Barberà
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Javier Díez-Domingo
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - F Xavier López-Labrador
- Virology Laboratory, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain.,Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Microbiology and Ecology, University of Valencia, Spain
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30
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Russo T, Pizuorno A, Oskrochi G, Latella G, Massironi S, Schettino M, Aghemo A, Pugliese N, Brim H, Ashktorab H. Gastrointestinal Manifestations, Clinical Characteristics and Outcomes of COVID-19 in Adult and Pediatric Patients. SOJ MICROBIOLOGY & INFECTIOUS DISEASES 2021; 8:109. [PMID: 35611315 PMCID: PMC9126507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Italy was the first country in Europe to report a SARS-CoV-2 case. Since then, the country has suffered a large number of COVID-19 infections both in adults and children. This disease has been shown to lead to different outcomes in these two groups, which often present varying symptoms and comorbidities. AIM Therefore, we aimed to evaluate the symptoms, comorbidities and laboratory values in adults and children. METHODS We present the characteristics of 1,324 adults and 563 pediatric COVID-19 Italian patients. The data was retrieved from studies published in Italy and found via PubMed and Google Scholar. RESULTS The virus appeared to affect adults more than children and men more than women, and to result in more severe outcomes in patients with abnormal laboratory values and a higher number of comorbidities. Adults are at higher risk for complications and death, and they usually present with fever, respiratory symptoms, cough, fatigue, diarrhea, myalgia, and/or loss of taste, smell, or appetite. Children usually have a milder disease progression and usually present with fever, cough, rhinorrhea, pharyngitis, sore throat, pneumonia, GI symptoms (diarrhea, vomiting, abdominal pain), fatigue, and dyspnea. CONCLUSION Our findings support early reports that showed that SARS-CoV-2 is associated with more common asymptomatic cases and milder clinical outcome in children than in adults. Acute respiratory distress syndrome and Multisystem inflammatory syndrome in children (systemic vasculitis) are the most severe disease progressions for adults and children, respectively.
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Affiliation(s)
- Tiziano Russo
- Department of Medicine, Department of Pathology and Cancer Center, Department of Biochemistry & Molecular Biology, Howard University College of Medicine, Washington DC
| | - Antonio Pizuorno
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Gholamreza Oskrochi
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Giovanni Latella
- Gastroenterology Unit, Department of Life, Health and Environmental Sciences, University of L’Aquila, Italy
| | - Sara Massironi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, and European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Mario Schettino
- Gastroenterology Unit, ASST Rhodense, Garbagnate Milanese, Lombardia, Italy
| | - Alessio Aghemo
- Division of Internal Medicine and Hepatology, Department of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Rozzano, Milan, Italy
| | - Nicola Pugliese
- Division of Internal Medicine and Hepatology, Department of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Rozzano, Milan, Italy
| | - Hassan Brim
- Department of Medicine, Department of Pathology and Cancer Center, Department of Biochemistry & Molecular Biology, Howard University College of Medicine, Washington DC
| | - Hassan Ashktorab
- Department of Medicine, Department of Pathology and Cancer Center, Department of Biochemistry & Molecular Biology, Howard University College of Medicine, Washington DC
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31
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Petti S. Undetected and relatively sustained SARS-CoV-2 circulation worldwide during the year 2019. Clin Infect Dis 2021; 74:1313-1314. [PMID: 34420046 PMCID: PMC8499797 DOI: 10.1093/cid/ciab727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Stefano Petti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
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32
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Air Quality in the Italian Northwestern Alps during Year 2020: Assessment of the COVID-19 «Lockdown Effect» from Multi-Technique Observations and Models. ATMOSPHERE 2021. [DOI: 10.3390/atmos12081006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The effect of COVID-19 confinement regulations on air quality in the northwestern Alps is assessed here based on measurements at five valley sites in different environmental contexts. Surface concentrations of nitrogen oxides (NO and NO2), ozone (O3), particulate matter (PM2.5 and PM10), together with a thorough microphysical (size), chemical, and optical (light absorption) aerosol characterisation, complemented by observations along the vertical column are considered. Even in the relatively pristine environment of the Alps, the «lockdown effect» is well discernible, both in the early confinement phase and in late 2020. The variations observed during the first confinement period in the city of Aosta (−61% NO, −43% NO2, +5% O3, +9% PM2.5, −12% PM10, relative to average 2015–2019 conditions) are attributed to the competing effects of air pollution lockdown-induced changes (−74%, −52%, +18%, −13%, −27%, relative to the counterfactual scenario for 2020 provided by a predictive statistical model trained on past measurements) and meteorology (+52%, +18%, −11%, +25%, +20%, relative to average conditions). These changes agree well with the ones obtained from a chemical transport model with modified emissions according to the restrictions. With regard to column-integrated quantities and vertical profiles, the NO2 column density decreases by >20% due to the lockdown, whereas tropospheric aerosols are mainly influenced by large-scale dynamics (transport of secondary particles from the Po basin and mineral dust from the Sahara desert and the Caspian Sea), except a shallow layer about 500 m thick close to the surface, possibly sensitive to curtailed emissions (especially exhaust and non-exhaust particles from road traffic and fugitive emissions from the industry).
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33
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Pietroboni AM, Lanfranconi S, Novella A, Carandini T, Arighi A, Abati E, Brusa R, Costamagna G, Lazzeri G, Mauri E, Pozzato M, Sacchi L, Valcamonica G, Villa D, Bonato S, Comi GP, Bresolin N, Galimberti D, Scarpini E, Nobili A. Clinical features and disease course of patients with acute ischaemic stroke just before the Italian index case: Was COVID-19 already there? Intern Emerg Med 2021; 16:1247-1252. [PMID: 33565035 PMCID: PMC7872881 DOI: 10.1007/s11739-021-02634-x] [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] [Received: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 12/02/2022]
Abstract
Since the end of February 2020, Italy has suffered one of the most severe outbreaks of coronavirus disease 2019 (COVID-19). However, what happened just before the Italian index case has not yet been investigated. To answer this question, we evaluated the potential impact of COVID-19 on the clinical features of a cohort of neurological inpatients admitted right before the Italian index case, as compared to the same period of the previous year. Demographic, clinical, treatment and laboratory data were extracted from medical records. The data collected included all inpatients who had been admitted to the Neurology and Stroke Units of the Ospedale Maggiore Policlinico, Milan, Italy, from December 15, 2018 to February 20, 2019 and from December 15, 2019 to February 20, 2020. Of the 248 patients, 97 subjects (39.1%) were admitted for an acute cerebrovascular event: 46 in the 2018/2019 period (mean [SD] age, 72.3 [15.6] years; 22 men [47.8%]), and 51 in the 2019/2020 interval (mean [SD] age, 72.8 [12.4] years; 24 men [47.1%]). The number of cryptogenic strokes has increased during the 2019-2020 year, as compared to the previous year (30 [58.8%] vs. 18 [39.1%], p = 0.05). These patients had a longer hospitalization (mean [SD] day, 15.7 [10.5] days vs. mean [SD] day, 11.7 [7.2] days, p = 0.03) and more frequent cerebrovascular complications (9 [30.0%] vs. 2 [11.1%]), but presented a lower incidence of cardiocerebral risk factors (18 [60.0%] vs. 14 [77.8%]). Right before the Italian index case, an increase in cryptogenic strokes has occurred, possibly due to the concomitant COVID-19.
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Affiliation(s)
- Anna M Pietroboni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy.
- University of Milan, Dino Ferrari Center, Milan, Italy.
| | - Silvia Lanfranconi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Alessio Novella
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Tiziana Carandini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Andrea Arighi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Elena Abati
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Roberta Brusa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Gianluca Costamagna
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Giulia Lazzeri
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Eleonora Mauri
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Mattia Pozzato
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Luca Sacchi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Gloria Valcamonica
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Davide Villa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Sara Bonato
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Giacomo P Comi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Nereo Bresolin
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Daniela Galimberti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
| | - Elio Scarpini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122, Milan, Italy
- University of Milan, Dino Ferrari Center, Milan, Italy
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Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic. Mol Biol Evol 2021; 38:3046-3059. [PMID: 33942847 PMCID: PMC8135569 DOI: 10.1093/molbev/msab118] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).
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Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Marcos A Caraballo-Ortiz
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
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35
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Saeed NK, Al-Khawaja S, Alsalman J, Almusawi S, Albalooshi NA, Al-Biltagi M. Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain. World J Virol 2021. [PMID: 34367932 DOI: 10.5501/wjv.v10.i4.168.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19. AIM To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain. METHODS The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes. RESULTS The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections. CONCLUSION Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.
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Affiliation(s)
- Nermin Kamal Saeed
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
| | - Safaa Al-Khawaja
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 00000, Bahrain
| | - Jameela Alsalman
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 00000, Bahrain
| | - Safiya Almusawi
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
| | - Noor Ahmed Albalooshi
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
| | - Mohammed Al-Biltagi
- Department of Pediatrics, University Medical Center, King Abdulla Medical City, Arabian Gulf University, Manama 00000, Bahrain
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36
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Saeed NK, Al-Khawaja S, Alsalman J, Almusawi S, Albalooshi NA, Al-Biltagi M. Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain. World J Virol 2021; 10:168-181. [PMID: 34367932 PMCID: PMC8316874 DOI: 10.5501/wjv.v10.i4.168] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.
AIM To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.
METHODS The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.
RESULTS The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.
CONCLUSION Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.
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Affiliation(s)
- Nermin Kamal Saeed
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
- Microbiology Department, Royal College of Surgeons in Ireland - Bahrain, Manama 00000, Bahrain
| | - Safaa Al-Khawaja
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 00000, Bahrain
- Department of Infectious Disease, Arabian Gulf University, Manama 00000, Bahrain
| | - Jameela Alsalman
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 00000, Bahrain
- Department of Infectious Disease, Arabian Gulf University, Manama 00000, Bahrain
| | - Safiya Almusawi
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
- Microbiology Department, Royal College of Surgeons in Ireland - Bahrain, Manama 00000, Bahrain
| | - Noor Ahmed Albalooshi
- Medical Microbiology Section, Pathology Department, Salmaniya Medical Complex, Manama 00000, Bahrain
| | - Mohammed Al-Biltagi
- Department of Pediatrics, University Medical Center, King Abdulla Medical City, Arabian Gulf University, Manama 00000, Bahrain
- Department of Pediatrics, Faculty of Medicine, Tanta University, Tanta 000000, Al Gharbia, Egypt
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Huang YK, Li YJ, Li B, Wang P, Wang QH. Dysregulated liver function in SARS-CoV-2 infection: Current understanding and perspectives. World J Gastroenterol 2021; 27:4358-4370. [PMID: 34366609 PMCID: PMC8316914 DOI: 10.3748/wjg.v27.i27.4358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/15/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Since it was first reported in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has spread rapidly around the world to cause the ongoing pandemic. Although the clinical manifestations of SARS-CoV-2 infection are predominantly in the respiratory system, liver enzyme abnormalities exist in around half of the cases, which indicate liver injury, and raise clinical concern. At present, there is no consensus whether the liver injury is directly caused by viral replication in the liver tissue or indirectly by the systemic inflammatory response. This review aims to summarize the clinical manifestations and to explore the underlying mechanisms of liver dysfunction in patients with SARS-CoV-2 infection.
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Affiliation(s)
- Yi-Ke Huang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu 610052, Sichuan Province, China
| | - Yu-Jia Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu 610052, Sichuan Province, China
- Joint laboratory on Transfusion-transmitted Diseases between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Bin Li
- Joint laboratory on Transfusion-transmitted Diseases between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Pan Wang
- Department of Emergency, The Traditional Chinese Medicine Hospital of Wenjiang District, Chengdu 611130, Sichuan Province, China
| | - Qing-Hua Wang
- Department of Emergency, The Traditional Chinese Medicine Hospital of Wenjiang District, Chengdu 611130, Sichuan Province, China
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Vega C. From Hume to Wuhan: An Epistemological Journey on the Problem of Induction in COVID-19 Machine Learning Models and its Impact Upon Medical Research. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:97243-97250. [PMID: 34812399 PMCID: PMC8545192 DOI: 10.1109/access.2021.3095222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/03/2021] [Indexed: 05/08/2023]
Abstract
Advances in computer science have transformed the way artificial intelligence is employed in academia, with Machine Learning (ML) methods easily available to researchers from diverse areas thanks to intuitive frameworks that yield extraordinary results. Notwithstanding, current trends in the mainstream ML community tend to emphasise wins over knowledge, putting the scientific method aside, and focusing on maximising metrics of interest. Methodological flaws lead to poor justification of method choice, which in turn leads to disregard the limitations of the methods employed, ultimately putting at risk the translation of solutions into real-world clinical settings. This work exemplifies the impact of the problem of induction in medical research, studying the methodological issues of recent solutions for computer-aided diagnosis of COVID-19 from chest X-Ray images.
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Affiliation(s)
- Carlos Vega
- Luxembourg Centre for Systems Biomedicine, Bioinformatics Core GroupUniversité du Luxembourg4365Esch-sur-AlzetteLuxembourg
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Marchi S, Viviani S, Remarque EJ, Ruello A, Bombardieri E, Bollati V, Milani GP, Manenti A, Lapini G, Rebuffat A, Montomoli E, Trombetta CM. Characterization of antibody response in asymptomatic and symptomatic SARS-CoV-2 infection. PLoS One 2021; 16:e0253977. [PMID: 34214116 PMCID: PMC8253392 DOI: 10.1371/journal.pone.0253977] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/16/2021] [Indexed: 12/30/2022] Open
Abstract
SARS-CoV-2 pandemic is causing high morbidity and mortality burden worldwide with unprecedented strain on health care systems. To investigate the time course of the antibody response in relation to the outcome we performed a study in hospitalized COVID-19 patients. As comparison we also investigated the time course of the antibody response in SARS-CoV-2 asymptomatic subjects. Study results show that patients produce a strong antibody response to SARS-CoV-2 with high correlation between different viral antigens (spike protein and nucleoprotein) and among antibody classes (IgA, IgG, and IgM and neutralizing antibodies). The antibody peak is reached by 3 weeks from hospital admission followed by a sharp decrease. No difference was observed in any parameter of the antibody classes, including neutralizing antibodies, between subjects who recovered or with fatal outcome. Only few asymptomatic subjects developed antibodies at detectable levels.
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Affiliation(s)
- Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Simonetta Viviani
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Edmond J. Remarque
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Gregorio P. Milani
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Pediatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Annunziata Rebuffat
- Presidio Ospedaliero di Campostaggia, Località Campostaggia, Poggibonsi, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
- VisMederi srl, Siena, Italy
- VisMederi Research srl, Siena, Italy
| | - Claudia M. Trombetta
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
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Jamison DT, Wu KB. The East-West Divide in Response to COVID-19. ENGINEERING (BEIJING, CHINA) 2021; 7:936-947. [PMID: 34150351 PMCID: PMC8196471 DOI: 10.1016/j.eng.2021.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/25/2021] [Accepted: 05/16/2021] [Indexed: 05/03/2023]
Abstract
Coronavirus disease 2019 (COVID-19) deaths per million population in the countries of the West had often exceeded those in the countries of the East by factor of 100 by May 2021. In this paper, we refer to the West as represented by the United States plus the five most populous countries of Western Europe (France, Germany, Italy, Spain, and the United Kingdom), and the East as the 15 countries in East Asia and Oceania that are members of the Regional Comprehensive Economic Partnership, RCEP (Australia, Brunei, Cambodia, China, Indonesia, Japan, the Republic of Korea, Laos, Malaysia, Myanmar, New Zealand, Philippines, Singapore, Thailand, and Vietnam). This paper argues that currently available information points to the factors most responsible for the East-West divide. Warnings by early January 2020 about an atypical viral pneumonia in Wuhan, China, prompted rapid responses in many jurisdictions in East Asia. Publication of the virus's genome on 10 January 2020 provided essential information for making diagnostic tests and launching vaccine development. China's lockdown of Wuhan on 23 January 2020 provided a final, decisive signal of the danger of the new disease. By late March 2020, China had fully controlled its epidemic, and many other RCEP countries had taken early and decisive measures, including restrictions on travel, that aborted serious outcomes. Inaction during the critical month of February 2020 in the United States and most other Western countries allowed the disease to take hold and spread. In both the East and the West, stringent population-wide non-pharmaceutical interventions were widely implemented at great cost to societies, economies, and school systems. Without these measures, the outcomes could have been even worse. Most countries in the East also implemented tightly focused policies to isolate infectious individuals. Even today, most countries in the West allow infectious individuals to mingle with their families, coworkers, and communities. Much of the East-West divide plausibly results from failure in the West to implement the basic public health policies of early action and the isolation of infectious individuals. Widespread immunization in some RCEP and high-income countries will soon attenuate their outbreaks, while the slow rollout of vaccines in lower income countries is replacing the East-West divide in outcomes with a North-South one. The South is thus replacing the West as the breeding ground for more dangerous variants as exemplified by the highly contagious Delta variant, which may undermine hitherto successful control strategies in many countries.
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Affiliation(s)
- Dean T Jamison
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 98158, USA
| | - Kin Bing Wu
- Independent Consultant, Atherton, CA 94027, USA
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Milani GP, Casazza G, Corsello A, Marchisio P, Rocchi A, Colombo G, Agostoni C, Costantino G. Early evidence of SARS-CoV-2 in Milan, Jan-Feb 2020. Ital J Pediatr 2021; 47:145. [PMID: 34193222 PMCID: PMC8243623 DOI: 10.1186/s13052-021-01095-4] [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: 01/18/2021] [Accepted: 05/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A few studies have suggested that the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) was present in Northern Italy several weeks before its official detection on February 21, 2020. On the other hand, no clinical data have been provided so far to support such hypothesis. We investigated clinical-epidemiological evidence of SARS-CoV-2 infection among children and adults referring to emergency department (ED) in the main hospital of the center of Milan (Italy) before February 21, 2020. METHODS A retrospective analysis of medical records of ED visits at the Fondazione Ca' Granda Policlinico, Milan between January 11 and February 15 in 2017, 2018, 2019 and in 2020 was performed. The number of subjects referring with fever, cough or dyspnea was compared between the studied period of 2020 and the previous 3 years, by calculating a standardized referral ratio (SRR, number of observed cases in 2020 divided by the number of expected cases according to 2017-2019) and the corresponding 95% confidence interval (CI). RESULTS In the pediatric ED, 7709 (average 2570/year) and 2736 patients were visited during the period 2017-2019 and in the 2020, respectively. Among adults, 13,465 (average 4488/year) and 4787 were visited during the period 2017-2019 and in the 2020, respectively. The SRR was 1.16 (95% CI 1.10-1.23) in children and 1.25 (95% CI 1.16-1.35) in adults. The ratio for the two (children and adults) SRRs was 0.93 (0.84-1.02), suggesting a trend towards a higher frequency in adults compared to children. CONCLUSIONS This study suggests that SARS-CoV-2 might have spread in Milan before February 21, 2020 with a minor trend among children.
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Affiliation(s)
- Gregorio P Milani
- Pediatric Emergency Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Giovanni Casazza
- Dipartimento di Scienze Biomediche e Cliniche "L. Sacco", Università degli Studi di Milano, Milan, Italy
| | - Antonio Corsello
- Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Paola Marchisio
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Rocchi
- Pediatric Emergency Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giulia Colombo
- Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Carlo Agostoni
- Department of Clinical Science and Community Health, University of Milan, Milan, Italy. .,Pediatric Intermediate Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy.
| | - Giorgio Costantino
- Department of Clinical Science and Community Health, University of Milan, Milan, Italy.,Emergency Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, Armanfard N, Sagan SM, Jahanshahi-Anbuhi S. Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021; 34:e00228-20. [PMID: 33980687 PMCID: PMC8142517 DOI: 10.1128/cmr.00228-20] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.
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Affiliation(s)
- Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
- Department of Mechanical, Industrial, and Aerospace Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Jason J LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Oyejide Damilola Oyewunmi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Carolina Camargo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Bahareh Nikpour
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
| | - Narges Armanfard
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
- Mila-Quebec AI Institute, Montréal, Québec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
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Rotulo GA, Casalini E, Brisca G, Piccotti E, Castagnola E. Unexpected peak of bronchiolitis requiring oxygen therapy in February 2020: Could an undetected SARS-CoV2-RSV co-infection be the cause? Pediatr Pulmonol 2021; 56:1803-1805. [PMID: 33657272 PMCID: PMC8014649 DOI: 10.1002/ppul.25331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Gioacchino Andrea Rotulo
- Pediatric Emergency Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Emilio Casalini
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Giacomo Brisca
- Subintensive Care Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Emanuela Piccotti
- Pediatric Emergency Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Elio Castagnola
- Infectious Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Casale M, Di Maio N, Verde V, Scianguetta S, Di Girolamo MG, Tomeo R, Roberti D, Misso S, Perrotta S. Response to Measles, Mumps and Rubella (MMR) Vaccine in Transfusion-Dependent Patients. Vaccines (Basel) 2021; 9:vaccines9060561. [PMID: 34072263 PMCID: PMC8227230 DOI: 10.3390/vaccines9060561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Measles, mumps and rubella (MMR) still determine significant morbidity and mortality, although a highly effective vaccine is available. Postponing the MMR vaccination until 6 months after the last red blood cell (RBC) transfusion is recommended, but this delay is incompatible with chronic transfusions. The present study aimed at investigating the impact of blood transfusions on the immunogenicity of the MMR vaccine. In this observational study, a group of 45 transfusion- dependent (TD) patients was compared to 24 non-transfusion-dependent (NTD) patients. Immunity to measles was achieved in 35 (78%) TD and 21 (88%) NTD subjects (p = 0.7), to mumps in 36 (80%) TD and 21 (88%) NTD subjects (p = 0.99), and to rubella in 40 (89%) TD and 23 (96%) NTD subjects (p = 0.99). No significant difference was observed in the number of non-immune individuals or those with doubtful protection between the two groups (p > 0.05). The mean IgG value, assayed in 50 pre-storage leukoreduced RBC units, was 0.075 ± 0.064 mg/mL, ten times lower than the level assumed in blood units and considered detrimental to the immune response in TD patients. This work shows a favorable response to MMR vaccination in TD and NTDT patients and paves the way for further larger studies assessing the impact of chronic transfusions on vaccine response.
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Affiliation(s)
- Maddalena Casale
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
- Correspondence: ; Tel.: +39-08-1566-5698
| | - Nicoletta Di Maio
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
| | - Valentina Verde
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
| | - Saverio Scianguetta
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
| | | | - Rita Tomeo
- Immuno-Transfusion Service, ASL Caserta, 81031 Aversa, Italy; (M.G.D.G.); (R.T.); (S.M.)
| | - Domenico Roberti
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
| | - Saverio Misso
- Immuno-Transfusion Service, ASL Caserta, 81031 Aversa, Italy; (M.G.D.G.); (R.T.); (S.M.)
| | - Silverio Perrotta
- Department of Women, Child and General and Specialized Surgery, University “Luigi Vanvitelli”, 80138 Naples, Italy; (N.D.M.); (V.V.); (S.S.); (D.R.); (S.P.)
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Rizzo C, Loconsole D, Pandolfi E, Ciofi Degli Atti ML, van Summeren J, Paget J, Russo L, Campagna I, Croci I, Gesualdo F, Concato C, Linardos G, Bartolucci V, Ciampini S, Muda AO, Raponi M, Chironna M. Sars-Cov2 Not Detected in a Pediatric Population With Acute Respiratory Infection in Primary Care in Central and Southern Italy From November 2019 to Early March 2020. Front Pediatr 2021; 9:620598. [PMID: 34046372 PMCID: PMC8147864 DOI: 10.3389/fped.2021.620598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Background: In December 2019, a novel coronavirus named SARS-CoV-2 started circulating in China and this led to a major epidemic in Northern Italy between February and May 2020. Young children (aged <5 years) seem to be less affected by this coronavirus disease (COVID-19) compared to adults, although there is very little information on the circulation of this new virus among children in Italy. We retrospectively tested nasopharyngeal swabs for SARS-CoV-2 in samples collected in young children between November, 2019 and March, 2020 in the context of the RSV ComNet study. Methods: Two networks of primary care pediatricians in Lazio (Central Italy) and Puglia (Southern Italy) collected nasopharyngeal swabs from children, aged <5 years, presenting with symptoms for an acute respiratory infection (ARI). The RSV ComNet study is a multicenter study implemented to estimate the burden of RSV in young children (aged <5 years) in the community. Swabs were sent to a central reference laboratory and tested for 14 respiratory viruses through RT-PCR. All collected samples were retrospectively tested for SARS-CoV-2 using RT-PCR (Istituto Superiore di Sanità protocol). Results: A total of 293 children with ARI were identified in the two participating networks. The highest number of cases were recruited in weeks 51/2019 and 3/2020. The majority of patients (57%) came from the Lazio region. All of the 293 samples tested negative for SARS-Cov2. Rhinovirus was the most frequently detected virus (44%), followed by RSV (41%) and influenza viruses (14%). Conclusions: Our study shows that in Lazio (a region of intermediate SARS-COV-2 incidence) and Puglia (a region of low incidence), the SARS-Cov2 virus did not circulate in a sample of ARI pediatric cases consulting primary care pediatricians between November 2019 and March 2020.
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Affiliation(s)
- Caterina Rizzo
- Clinical Pathways and Epidemiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniela Loconsole
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - Elisabetta Pandolfi
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | | | | | - John Paget
- Nivel, Netherlands Institute for Health Services Research, Utrecht, Netherlands
| | - Luisa Russo
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Ilaria Campagna
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Ileana Croci
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Francesco Gesualdo
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Carlo Concato
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Giulia Linardos
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Veronica Bartolucci
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - Sara Ciampini
- Public Health Service, Local Health Authority Rome 1, Rome, Italy
| | - Andrea Onetti Muda
- Department of Laboratories, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Maria Chironna
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
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Neagu M, Calina D, Docea AO, Constantin C, Filippini T, Vinceti M, Drakoulis N, Poulas K, Nikolouzakis TK, Spandidos DA, Tsatsakis A. Back to basics in COVID-19: Antigens and antibodies-Completing the puzzle. J Cell Mol Med 2021; 25:4523-4533. [PMID: 33734600 PMCID: PMC8107083 DOI: 10.1111/jcmm.16462] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
The outbreak of the coronavirus disease 2019 (COVID-19) has gathered 1 year of scientific/clinical information. This informational asset should be thoroughly and wisely used in the coming year colliding in a global task force to control this infection. Epidemiology of this infection shows that the available estimates of SARS-CoV-2 infection prevalence largely depended on the availability of molecular testing and the extent of tested population. Within molecular diagnosis, the viability and infectiousness of the virus in the tested samples should be further investigated. Moreover, SARS-CoV-2 has a genetic normal evolution that is a dynamic process. The immune system participates to the counterattack of the viral infection by pathogen elimination, cellular homoeostasis, tissue repair and generation of memory cells that would be reactivated upon a second encounter with the same virus. In all these stages, we still have knowledge to be gathered regarding antibody persistence, protective effects and immunological memory. Moreover, information regarding the intense pro-inflammatory action in severe cases still lacks and this is important in stratifying patients for difficult to treat cases. Without being exhaustive, the review will cover these important issues to be acknowledged to further advance in the battle against the current pandemia.
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Affiliation(s)
- Monica Neagu
- Department of ImmunologyVictor Babes National Institute of PathologyBucharestRomania
- Department of PathologyColentina Clinical HospitalBucharestRomania
- Doctoral SchoolUniversity of BucharestBucharestRomania
| | - Daniela Calina
- Department of Clinical PharmacyUniversity of Medicine and Pharmacy of CraiovaCraiovaRomania
| | - Anca Oana Docea
- Department of ToxicologyUniversity of Medicine and Pharmacy of CraiovaCraiovaRomania
| | - Carolina Constantin
- Department of ImmunologyVictor Babes National Institute of PathologyBucharestRomania
- Department of PathologyColentina Clinical HospitalBucharestRomania
| | - Tommaso Filippini
- Section of Public HealthDepartment of Biomedical, Metabolic and Neural SciencesEnvironmental, Genetic and Nutritional Epidemiology Research Center (CREAGEN)University of Modena and Reggio EmiliaModenaItaly
| | - Marco Vinceti
- Section of Public HealthDepartment of Biomedical, Metabolic and Neural SciencesEnvironmental, Genetic and Nutritional Epidemiology Research Center (CREAGEN)University of Modena and Reggio EmiliaModenaItaly
- Department of EpidemiologyBoston University School of Public HealthBostonMAUSA
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and PharmacogenomicsFaculty of PhrarmacySchool of Health SciencesNational and Kapodistrian University of AthensAthensGreece
| | - Konstantinos Poulas
- Department of PharmacyLaboratory of Molecular Biology and ImmunologyUniversity of PatrasPatrasGreece
| | | | | | - Aristidis Tsatsakis
- Department of Forensic Sciences and ToxicologyFaculty of MedicineUniversity of CreteHeraklionGreece
- Department of Analytical and Forensic Medical ToxicologySechenov UniversityMoscowRussia
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Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. Timing the SARS-CoV-2 index case in Hubei province. Science 2021; 372:412-417. [PMID: 33737402 PMCID: PMC8139421 DOI: 10.1126/science.abf8003] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated before the time of the most recent common ancestor of all sequenced SARS-CoV-2 genomes. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province, China. By characterizing the likely dynamics of the virus before it was discovered, we show that more than two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.
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Affiliation(s)
- Jonathan Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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He S, Han J. Biorepositories (biobanks) of human body fluids and materials as archives for tracing early infections of COVID-19. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 274:116525. [PMID: 33516955 PMCID: PMC7813484 DOI: 10.1016/j.envpol.2021.116525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/26/2020] [Accepted: 01/15/2021] [Indexed: 05/22/2023]
Abstract
Identifying the individuals and geographical regions witnessing early infections or outbreaks of SARS-CoV-2 and its variants is helpful for studying the early epidemiology or even the origin of the novel coronavirus. Here, we put forward a strategy that can potentially contribute to this goal. Human body fluids and biological materials collected before the COVID-19 pandemic may serve as archives for retrospective testing of early human infections before the recent outbreaks. These have been routinely donated, collected, and archived, creating biorepositories or "biobanks" for clinical or research purposes. SARS-CoV-2 genetic materials and its antibodies have been confirmed in various types of biological samples from COVID-19 patients, including blood, sperm, umbilical cord blood, lung, heart, kidney and so on, making these biological archives as candidates for detecting early COVID-19 infections. Unlike sewage-based epidemiology which only provides information on the geographical aspect, viruses identified in archived human biological samples provide direct links to individuals, from whom a wealth of personal information including their profession, hobbies and activities, travel history, and previous exposure to wildlife can all be retrieved. By analyzing the patterns and links in the behavior of those early infected individuals, it is possible to trace the origin of the virus, for instance, in certain wild animals or local environments.
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Affiliation(s)
- Shanshan He
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Jie Han
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China.
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Sarker T, Sarkar A, Rabbany MG, Barmon M, Roy R, Rahman MA, Hossain KZ, Hoque F, Asaduzzaman M. Evaluation of preventive, supportive and awareness building measures among international students in China in response to COVID-19: a structural equation modeling approach. Glob Health Res Policy 2021; 6:10. [PMID: 33712081 PMCID: PMC7954668 DOI: 10.1186/s41256-021-00192-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 02/18/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Education institutions promptly implemented a set of steps to prevent the spread of COVID-19 among international Chinese students, such as restrictive physical exercise, mask wear, daily health reporting, etc. Success of such behavioral change campaigns largely depends on awareness building, satisfaction and trust on the authorities. The purpose of this current study is to assess the preventive, supportive and awareness-building steps taken during the COVID-19 pandemic for international students in China, that will be useful for planning such a behavioral change campaign in the potential pandemic situation in other parts of the world. METHODS We conducted an online-based e-questionnaire survey among 467 international students in China through WeChat. The data collection duration was from February 20, 2020 to March 10, 2020 and we focused on their level of awareness, satisfaction, and trust in authorities regarding pandemic measures. Simple bivariate statistics was used to describe the background characteristics of the respondents along with adoption of the partial least squares-structural equation modeling (PLS-SEM) as the final model to demonstrate the relationship between the variables. RESULTS In our study, the leading group of the respondents were within 31 to 35 years' age group (39.82%), male (61.88%), living single (58.24%) and doctoral level students (39.8%). The preventive and supportive measures taken by students and/or provided by the respective institution or authorities were positively related to students' satisfaction and had an acceptable strength (β = 0.611, t = 9.679, p < 0.001). The trust gained in authorities also showed an acceptable strength (β = 0.381, t = 5.653, p < 0.001) with a positive direction. Again, the personnel awareness building related to both students' satisfaction (β = 0.295, t = 2.719, p < 0.001) and trust gain (β = 0.131, t = 1.986, p < 0.05) in authorities had a positive and acceptable intensity. Therefore, our study clearly demonstrates the great impact of preventive and supportive measures in the development of students' satisfaction (R2 = 0.507 indicating moderate relationship). The satisfied students possessed a strong influence which eventually helped in building sufficient trust on their institutions (R2 = 0.797 indicating above substantial relationship). CONCLUSIONS The worldwide student group is one of the most affected and vulnerable communities in this situation. So, there is a profound ground of research on how different states or authorities handle such situation. In this study, we have depicted the types and magnitude of care taken by Chinese government and educational institutions towards international students to relieve the panic of pandemic situation. Further research and such initiatives should be taken in to consideration for future emerging conditions.
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Affiliation(s)
- Tanwne Sarker
- School of Economics and Finance, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 People’s Republic of China
| | - Apurbo Sarkar
- College of economics and management, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Md. Ghulam Rabbany
- College of economics and management, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
- Department of agribusiness and marketing, Sher-e-Bangla Agricultural University, Dhaka, 1207 Bangladesh
| | - Milon Barmon
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Rana Roy
- College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
- Department of Agroforestry & Environmental Science, Sylhet Agricultural University, Sylhet, 3100 Bangladesh
| | - Md. Ashfikur Rahman
- College of economics and management, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Kh. Zulfikar Hossain
- College of economics and management, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
- Department of agribusiness and marketing, Sher-e-Bangla Agricultural University, Dhaka, 1207 Bangladesh
| | - Fazlul Hoque
- Department of agribusiness and marketing, Sher-e-Bangla Agricultural University, Dhaka, 1207 Bangladesh
| | - Muhammad Asaduzzaman
- Centre for Global Health, University of Oslo, Kirkeveien 166, Frederik Holsts hus, 0450 Oslo, Norway
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