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Zhang J, Liu X, Li Z, Li X, Li Q, Li W, Li J. Whole-Cell Molecularly Imprinted Fluorescent Photonic Microsphere Microarray for High-Throughput Detection of Foodborne Pathogens. Anal Chem 2025; 97:9779-9788. [PMID: 40305329 DOI: 10.1021/acs.analchem.4c06821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
Abstract
Rapid, sensitive, high-throughput, and cost-effective detection of multiplex foodborne pathogens is still challenging in public health. We designed a whole-cell imprinted microarray platform based on the surface of three-dimensional photonic microspheres for multiplex foodborne pathogenic bacteria using 3-formylphenylboric acid-functionalized silane as the functional monomer and fluorescein isothiocyanate-functionalized silane as the fluorescent monomer. After incubation with the multiplex pathogens, the fluorescent molecularly imprinted photonic microspheres can specifically capture the target pathogenic bacteria, and their fluorescence intensities can report the concentrations of the pathogens in samples. The new microsphere microarray showed wide linear detection ranges (10 to 109 CFU/mL for Salmonella, 102 to 106 CFU/mL for Shigella, and 10 to 107 CFU/mL for Escherichia coli O157:H7) and low limits of detection (LODs) (3 CFU/mL for Salmonella, 20 CFU/mL for Shigella, and 1 CFU/mL for E. coli O157:H7) for multiplex pathogens. The new system does not require molecular probes such as antibody, aptamer, or DNA sequence and without enrichment culture and DNA amplification processes. The newly developed method has great potential applications in rapid, cost-effective, and high-throughput simultaneous detection of multiplex foodborne pathogens.
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Affiliation(s)
- Jingshuang Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiaomeng Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ziqiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Qianjin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Weiwei Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jianlin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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Ibañez JM, Zambrana R, Carreras P, Obregón V, Irazoqui JM, Vera PA, Lattar TE, Blanco Fernández MD, Puebla AF, Amadio AF, Torres C, López Lambertini PM. Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina. Viruses 2025; 17:533. [PMID: 40284976 PMCID: PMC12031183 DOI: 10.3390/v17040533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 03/20/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025] Open
Abstract
Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV's global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.
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Affiliation(s)
- Julia M. Ibañez
- Estación Experimental Agropecuaria Bella Vista, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 27-Km 38,3, Bella Vista, Corrientes 3432, Argentina; (J.M.I.); (V.O.); (T.E.L.)
| | - Romina Zambrana
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 956, 4th floor, Ciudad Autónoma de Buenos Aires 1113, Argentina; (R.Z.); (M.D.B.F.); (C.T.)
| | - Pamela Carreras
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Av. 11 de Septiembre, X5014MGO, Córdoba 4755, Argentina;
- Unidad de Fitopatología y Modelización Agrícola (UFYMA) INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 11 de Septiembre, X5014MGO, Córdoba 4755, Argentina
| | - Verónica Obregón
- Estación Experimental Agropecuaria Bella Vista, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 27-Km 38,3, Bella Vista, Corrientes 3432, Argentina; (J.M.I.); (V.O.); (T.E.L.)
| | - José M. Irazoqui
- Instituto de Investigaciones de la Cadena Láctea (IDICAL) INTA-CONICET, Ruta 34 km 227, Rafaela, Santa Fe 2300, Argentina; (J.M.I.); (A.F.A.)
| | - Pablo A. Vera
- Unidad de Genómica y Bioinformática (UGB), Instituto de Agrobiotecnología y Biología Molecular (IABiMo), INTA-CONICET, De los Reseros y N. Repetto, Hurlingham, Ciudad Autónoma de Buenos Aires 1686, Argentina; (P.A.V.); (A.F.P.)
| | - Tatiana E. Lattar
- Estación Experimental Agropecuaria Bella Vista, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 27-Km 38,3, Bella Vista, Corrientes 3432, Argentina; (J.M.I.); (V.O.); (T.E.L.)
| | - María D. Blanco Fernández
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 956, 4th floor, Ciudad Autónoma de Buenos Aires 1113, Argentina; (R.Z.); (M.D.B.F.); (C.T.)
| | - Andrea F. Puebla
- Unidad de Genómica y Bioinformática (UGB), Instituto de Agrobiotecnología y Biología Molecular (IABiMo), INTA-CONICET, De los Reseros y N. Repetto, Hurlingham, Ciudad Autónoma de Buenos Aires 1686, Argentina; (P.A.V.); (A.F.P.)
| | - Ariel F. Amadio
- Instituto de Investigaciones de la Cadena Láctea (IDICAL) INTA-CONICET, Ruta 34 km 227, Rafaela, Santa Fe 2300, Argentina; (J.M.I.); (A.F.A.)
| | - Carolina Torres
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 956, 4th floor, Ciudad Autónoma de Buenos Aires 1113, Argentina; (R.Z.); (M.D.B.F.); (C.T.)
| | - Paola M. López Lambertini
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Av. 11 de Septiembre, X5014MGO, Córdoba 4755, Argentina;
- Unidad de Fitopatología y Modelización Agrícola (UFYMA) INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 11 de Septiembre, X5014MGO, Córdoba 4755, Argentina
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Singh A, Yasheshwar, Kaushik NK, Kala D, Nagraik R, Gupta S, Kaushal A, Walia Y, Dhir S, Noorani MS. Conventional and cutting-edge advances in plant virus detection: emerging trends and techniques. 3 Biotech 2025; 15:100. [PMID: 40151342 PMCID: PMC11937476 DOI: 10.1007/s13205-025-04253-1] [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: 08/07/2024] [Accepted: 02/20/2025] [Indexed: 03/29/2025] Open
Abstract
Plant viruses pose a significant threat to global agriculture. For a long time, conventional methods including detection based on visual symptoms, host range investigations, electron microscopy, serological assays (e.g., ELISA, Western blotting), and nucleic acid-based techniques (PCR, RT-PCR) have been used for virus identification. With increased sensitivity, speed, and specificity, new technologies like loop-mediated isothermal amplification (LAMP), high-throughput sequencing (HTS), nanotechnology-based biosensors, and CRISPR diagnostics have completely changed the way plant viruses are detected. Recent advances in detection techniques integrate artificial intelligence (AI), machine learning (ML), and the Internet of Things (IoT) for real-time monitoring. Innovations like hyperspectral imaging, deep learning, and cloud-based IoT platforms further support disease identification and surveillance. Nanotechnology-based lateral flow assays and CRISPR-Cas systems provide rapid, field-deployable solutions. Despite these advancements, challenges such as sequence limitations, multiplexing constraints, and environmental concerns remain. Future research should focus on refining portable on-site diagnostic kits, optimizing nanotechnology applications, and enhancing global surveillance systems. Interdisciplinary collaboration across molecular biology, bioinformatics, and engineering is essential to developing scalable, cost-effective solutions for plant virus detection, ensuring agricultural sustainability and ecosystem protection.
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Affiliation(s)
- Anjana Singh
- Plant Molecular Virology Lab, Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062 India
- Deshbandhu College, University of Delhi, New Delhi, 110019 India
| | - Yasheshwar
- Department of Botany, Acharya Narendra Dev College, University of Delhi, New Delhi, 110019 India
| | - Naveen K. Kaushik
- Department of Industrial Biotechnology, College of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Deepak Kala
- NL-11 Centera Tetrahertz Laboratory, Institute of High-Pressure Physics, Polish Academy of Sciences, 29/37 Sokolowska Street, 01142 Warsaw, Poland
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh 173229 India
| | - Shagun Gupta
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Ankur Kaushal
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Yashika Walia
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Sunny Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
| | - Md Salik Noorani
- Plant Molecular Virology Lab, Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062 India
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Bhatt P, Li Y, Xagoraraki I. Genomic mapping of wastewater bacteriophage may predict potential bacterial pathogens infecting the community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176834. [PMID: 39396796 DOI: 10.1016/j.scitotenv.2024.176834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 09/14/2024] [Accepted: 10/07/2024] [Indexed: 10/15/2024]
Abstract
Most existing wastewater surveillance studies that focus on viruses have identified a large fraction of bacteriophages. Identifying bacteria by considering bacteriophage-host interactions is a novel method for detecting bacterial pathogens circulating in a community, using wastewater surveillance. This study aims to identify human-related bacterial pathogens in municipal wastewater collected in metro Detroit, using high-throughput sequencing and bioinformatics. Untreated municipal wastewater samples were collected on August 11, 2020, and bacteriophages were concentrated using the VIRus ADsorption-ELution (VIRADEL) method. Bacteriophage-related contigs in samples ranged from 15.53 % to 18.91 %, with 2477 classified and 8853 unclassified contigs. Most identified bacteriophages were from Caudoviricetes and Malgrandaviricetes classes belonging to 19 families. Hosts of bacteriophages were predicted with the PhaBOX (CHERRY) tool. The results indicated that out of the 2477 classified phages, 2373 were associated with known bacterial hosts. Also, out of 8853 unclassified bacteriophages, 8421 were associated with known bacterial hosts, and the remaining 432 were with unknown bacterial hosts. Among all bacteriophage-associated hosts, 399 were identified as pathogenic bacteria at the species level. Approximately, 85 % of the identified pathogenic bacteria are reported to be associated with human diseases. Genome quality assessments showed that 15 bacteriophages had nearly complete genomes, which were further analyzed to understand bacteriophage-bacteria interactions in wastewater. Identified hosts of these complete-genome phages included human pathogens such as Salmonella enterica, Bacillus cereus, Achromobacter xylosoxidans, and Escherichia coli. The S. enterica bacteriophage (k141_1005294) genomic map was annotated, and responsible open reading frames (ORFs) were characterized to illustrate bacteriophage behavior during infection of pathogenic bacteria in untreated wastewater. To the best of our knowledge, this is the first attempt to characterize human bacterial pathogens in wastewater through bacteriophage-pathogen interactions. Novel bioinformatic approaches enhance pathogen detection and improve the understanding of community wastewater microbiomes.
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Affiliation(s)
- Pankaj Bhatt
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
| | - Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
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Wambugu EN, Kimita G, Kituyi SN, Washington MA, Masakhwe C, Mutunga LM, Jaswant G, Thumbi SM, Schaefer BC, Waitumbi JN. Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya. Emerg Infect Dis 2024; 30:1642-1650. [PMID: 39043404 PMCID: PMC11286075 DOI: 10.3201/eid3008.230876] [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: 07/25/2024] Open
Abstract
Rabies, a viral disease that causes lethal encephalitis, kills ≈59,000 persons worldwide annually, despite availability of effective countermeasures. Rabies is endemic in Kenya and is mainly transmitted to humans through bites from rabid domestic dogs. We analyzed 164 brain stems collected from rabid animals in western and eastern Kenya and evaluated the phylogenetic relationships of rabies virus (RABV) from the 2 regions. We also analyzed RABV genomes for potential amino acid changes in the vaccine antigenic sites of nucleoprotein and glycoprotein compared with RABV vaccine strains commonly used in Kenya. We found that RABV genomes from eastern Kenya overwhelmingly clustered with the Africa-1b subclade and RABV from western Kenya clustered with Africa-1a. We noted minimal amino acid variances between the wild and vaccine virus strains. These data confirm minimal viral migration between the 2 regions and that rabies endemicity is the result of limited vaccine coverage rather than limited efficacy.
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Bleotu C, Matei L, Dragu LD, Necula LG, Pitica IM, Chivu-Economescu M, Diaconu CC. Viruses in Wastewater-A Concern for Public Health and the Environment. Microorganisms 2024; 12:1430. [PMID: 39065197 PMCID: PMC11278728 DOI: 10.3390/microorganisms12071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/26/2024] Open
Abstract
Wastewater monitoring provides essential information about water quality and the degree of contamination. Monitoring these waters helps identify and manage risks to public health, prevent the spread of disease, and protect the environment. Standardizing the appropriate and most accurate methods for the isolation and identification of viruses in wastewater is necessary. This review aims to present the major classes of viruses in wastewater, as well as the methods of concentration, isolation, and identification of viruses in wastewater to assess public health risks and implement corrective measures to prevent and control viral infections. Last but not least, we propose to evaluate the current strategies in wastewater treatment as well as new alternative methods of water disinfection.
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Affiliation(s)
- Coralia Bleotu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
- Research Institute of the University of Bucharest (ICUB), University of Bucharest, 060023 Bucharest, Romania
- The Academy of Romanian Scientist, 050711 Bucharest, Romania
| | - Lilia Matei
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Laura Denisa Dragu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Laura Georgiana Necula
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Ioana Madalina Pitica
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Mihaela Chivu-Economescu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Carmen Cristina Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
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Kourout M, Espich S, Fisher C, Tiper I, Purkayastha A, Smith S, Santana-Quintero L, Duncan R. Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform. Front Mol Biosci 2024; 11:1419213. [PMID: 38966129 PMCID: PMC11222771 DOI: 10.3389/fmolb.2024.1419213] [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: 04/17/2024] [Accepted: 05/23/2024] [Indexed: 07/06/2024] Open
Abstract
Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.
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Affiliation(s)
- Moussa Kourout
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Scott Espich
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Carolyn Fisher
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Irina Tiper
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | | | - Sean Smith
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Luis Santana-Quintero
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Robert Duncan
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
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Miyani B, Li Y, Guzman HP, Briceno RK, Vieyra S, Hinojosa R, Xagoraraki I. Bioinformatics-based screening tool identifies a wide variety of human and zoonotic viruses in Trujillo-Peru wastewater. One Health 2024; 18:100756. [PMID: 38798735 PMCID: PMC11127556 DOI: 10.1016/j.onehlt.2024.100756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Peru was one of the most affected countries during the COVID-19 pandemic. Moreover, multiple other viral diseases (enteric, respiratory, bloodborne, and vector-borne) are endemic and rising. According to Peru's Ministry of Health, various health facilities in the country were reallocated for the COVID-19 pandemic, thereby leading to reduced action to curb other diseases. Many viral diseases in the area are under-reported and not recognized. The One Health approach, in addition to clinical testing, incorporates environmental surveillance for detection of infectious disease outbreaks. The purpose of this work is to use a screening tool that is based on molecular methods, high throughput sequencing and bioinformatics analysis of wastewater samples to identify virus-related diseases circulating in Trujillo-Peru. To demonstrate the effectiveness of the tool, we collected nine untreated wastewater samples from the Covicorti wastewater utility in Trujillo-Peru on October 22, 2022. High throughput metagenomic sequencing followed by bioinformatic analysis was used to assess the viral diversity of the samples. Our results revealed the presence of sequences associated with multiple human and zoonotic viruses including Orthopoxvirus, Hepatovirus, Rhadinovirus, Parechovirus, Mamastrovirus, Enterovirus, Varicellovirus, Norovirus, Kobuvirus, Bocaparvovirus, Simplexvirus, Spumavirus, Orthohepevirus, Cardiovirus, Molliscipoxvirus, Salivirus, Parapoxvirus, Gammaretrovirus, Alphavirus, Lymphocryptovirus, Erythroparvovirus, Sapovirus, Cosavirus, Deltaretrovirus, Roseolovirus, Flavivirus, Betacoronavirus, Rubivirus, Lentivirus, Betapolyomavirus, Rotavirus, Hepacivirus, Alphacoronavirus, Mastadenovirus, Cytomegalovirus and Alphapapillomavirus. For confirmation purposes, we tested the samples for the presence of selective viruses belonging to the genera detected above. PCR based molecular methods confirmed the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), monkeypox virus (MPXV), noroviruses GI and GII (NoVGI and NoVGII), and rotavirus A (RoA) in our samples. Furthermore, publicly available clinical data for selected viruses confirm our findings. Wastewater or other environmental media surveillance, combined with bioinformatics methods, has the potential to serve as a systematic screening tool for the identification of human or zoonotic viruses that may cause disease. The results of this method can guide further clinical surveillance efforts and allocation of resources. Incorporation of this bioinformatic-based screening tool by public health officials in Peru and other Latin American countries will help manage endemic and emerging diseases that could save human lives and resources.
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Affiliation(s)
- Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Heidy Peidro Guzman
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Ruben Kenny Briceno
- Institute for Global Health, Michigan State University, East Lansing, MI, United States of America
| | - Sabrina Vieyra
- Institute for Global Health, Michigan State University, East Lansing, MI, United States of America
| | - Rene Hinojosa
- Institute for Global Health, Michigan State University, East Lansing, MI, United States of America
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America
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9
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Gao H, Liu Q, Wang X, Li T, Li H, Li G, Tan L, Chen Y. Deciphering the role of female reproductive tract microbiome in reproductive health: a review. Front Cell Infect Microbiol 2024; 14:1351540. [PMID: 38562966 PMCID: PMC10982509 DOI: 10.3389/fcimb.2024.1351540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Relevant studies increasingly indicate that female reproductive health is confronted with substantial challenges. Emerging research has revealed that the microbiome interacts with the anatomy, histology, and immunity of the female reproductive tract, which are the cornerstone of maintaining female reproductive health and preventing adverse pregnancy outcomes. Currently, the precise mechanisms underlying their interaction and impact on physiological functions of the reproductive tract remain elusive, constituting a prominent area of investigation within the field of female reproductive tract microecology. From this new perspective, we explore the mechanisms of interactions between the microbiome and the anatomy, histology, and immunity of the female reproductive tract, factors that affect the composition of the microbiome in the female reproductive tract, as well as personalized medicine approaches in managing female reproductive tract health based on the microbiome. This study highlights the pivotal role of the female reproductive tract microbiome in maintaining reproductive health and influencing the occurrence of reproductive tract diseases. These findings support the exploration of innovative approaches for the prevention, monitoring and treatment of female reproductive tract diseases based on the microbiome.
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Affiliation(s)
- Hong Gao
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada
| | - Qiao Liu
- School of Nursing, University of South China, Hengyang, China
| | - Xiaolan Wang
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Li
- Department of Obstetrics, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Huanhuan Li
- Department of Gynaecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Genlin Li
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Lingling Tan
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yahui Chen
- School of Nursing, University of South China, Hengyang, China
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Zuo K, Gao W, Wu Z, Zhang L, Wang J, Yuan X, Li C, Xiang Q, Lu L, Liu H. Evolution of Virology: Science History through Milestones and Technological Advancements. Viruses 2024; 16:374. [PMID: 38543740 PMCID: PMC10975421 DOI: 10.3390/v16030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 05/23/2024] Open
Abstract
The history of virology, which is marked by transformative breakthroughs, spans microbiology, biochemistry, genetics, and molecular biology. From the development of Jenner's smallpox vaccine in 1796 to 20th-century innovations such as ultrafiltration and electron microscopy, the field of virology has undergone significant development. In 1898, Beijerinck laid the conceptual foundation for virology, marking a pivotal moment in the evolution of the discipline. Advancements in influenza A virus research in 1933 by Richard Shope furthered our understanding of respiratory pathogens. Additionally, in 1935, Stanley's determination of viruses as solid particles provided substantial progress in the field of virology. Key milestones include elucidation of reverse transcriptase by Baltimore and Temin in 1970, late 20th-century revelations linking viruses and cancer, and the discovery of HIV by Sinoussi, Montagnier, and Gallo in 1983, which has since shaped AIDS research. In the 21st century, breakthroughs such as gene technology, mRNA vaccines, and phage display tools were achieved in virology, demonstrating its potential for integration with molecular biology. The achievements of COVID-19 vaccines highlight the adaptability of virology to global health.
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Affiliation(s)
- Kunlan Zuo
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Wanying Gao
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Zongzhen Wu
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Lei Zhang
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Jiafeng Wang
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Xuefan Yuan
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Chun Li
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Qiangyu Xiang
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China;
| | - Huan Liu
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei 230026, China; (K.Z.); (W.G.); (Z.W.); (L.Z.); (J.W.); (X.Y.); (C.L.); (Q.X.)
- State Key Laboratory of Virology, Wuhan 430072, China
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11
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Li Y, Miyani B, Faust RA, David RE, Xagoraraki I. A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan. Hum Genomics 2024; 18:14. [PMID: 38321488 PMCID: PMC10845806 DOI: 10.1186/s40246-024-00581-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing. RESULTS During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated. Clinical cases of the diseases caused by human viruses were tabulated and compared with data from viral wastewater monitoring. In addition to Betacoronavirus, comparison using assembled contigs against a custom Swiss-Prot human virus database indicated the potential prevalence of other pathogenic virus genera, including: Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Bocaparvovirus, Molluscipoxvirus, Parechovirus, Roseolovirus, Lymphocryptovirus, Alphavirus, Spumavirus, Lentivirus, Deltaretrovirus, Enterovirus, Kobuvirus, Gammaretrovirus, Cardiovirus, Erythroparvovirus, Salivirus, Rubivirus, Orthohepevirus, Cytomegalovirus, Norovirus, and Mamastrovirus. Four nearly complete genomes were recovered from the Astrovirus, Enterovirus, Norovirus and Betapolyomavirus genera and viral species were identified. CONCLUSIONS The presented findings in wastewater samples are primarily at the genus level and can serve as a preliminary "screening" tool that may serve as indication to initiate further testing for the confirmation of the presence of species that may be associated with human disease. Integrating innovative environmental microbiology technologies like metagenomic sequencing with viral epidemiology offers a significant opportunity to improve the monitoring of, and predictive intelligence for, pathogenic viruses, using wastewater.
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Affiliation(s)
- Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Russell A Faust
- Oakland County Health Division, 1200 Telegraph Rd, Pontiac, MI, 48341, USA
| | - Randy E David
- School of Medicine, Wayne State University, Detroit, MI, 48282, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA.
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12
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Li Y, Miyani B, Childs KL, Shiu SH, Xagoraraki I. Effect of wastewater collection and concentration methods on assessment of viral diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168128. [PMID: 37918732 DOI: 10.1016/j.scitotenv.2023.168128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
Monitoring of potentially pathogenic human viruses in wastewater is of crucial importance to understand disease trends in communities, predict potential outbreaks, and boost preparedness and response by public health departments. High throughput metagenomic sequencing opens an opportunity to expand the capabilities of wastewater surveillance. However, there are major bottlenecks in the metagenomic enabled wastewater surveillance, including the complexities in selecting appropriate sampling and concentration/virus enrichment methods as well as in bioinformatic analysis of complex samples with low human virus concentrations. To evaluate the abilities of two commonly used sampling and concentration methods in virus identification, virus communities concentrated with Virus Adsorption-Elution (VIRADEL) and PolyEthylene Glycol (PEG) precipitation were compared for three interceptor sites. Results indicated that more viral reads were obtained by the VIRADEL concentration method, with 2.84 ± 0.57 % viral reads in the sample. For samples concentrated with PEG, the average proportion of viral reads in the sample was 0.63 ± 0.19 %. In all wastewater samples, bacteriophage affiliated with the families Siphoviridae, Myoviridae and Podoviridae were found to be the abundant populations. Comparison against a custom Swiss-Prot human virus database indicated that the relatively abundant human viruses (average proportions in human virus community greater than 1.00 %) in samples concentrated with the VIRADEL method were Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Molluscipoxvirus, Parechovirus, Lymphocryptovirus, and Spumavirus. In samples concentrated with the PEG method, fewer human viruses were found to be relatively abundant. These were Orthopoxvirus, Rhadinovirus, Varicellovirus, Simplexvirus, Molluscipoxvirus, Lymphocryptovirus, and Betacoronavirus. Contigs of Betacoronavirus, which contains severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were identified in VIRADEL and PEG samples. Our study demonstrates the feasibility of using metagenomics in wastewater surveillance as a first screening tool and the need for selecting the appropriate virus concentration methods and optimizing bioinformatic approaches in analyzing metagenomic data of wastewater samples.
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Affiliation(s)
- Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, United States
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, United States
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States; Department of Energy (DOE) Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, United States.
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13
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Vigil K, Aw TG. Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals. Front Microbiol 2023; 14:1248323. [PMID: 37808316 PMCID: PMC10556685 DOI: 10.3389/fmicb.2023.1248323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals. Methods In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals. Results Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species. Discussion Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.
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Affiliation(s)
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
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14
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Makela M, Lin Z, Lin PT. Rapid Detection of SARS-CoV-2 Genetic Targets Using Nanoporous Waveguide Based Competitive Displacement Assay. GIANT (OXFORD, ENGLAND) 2023:100173. [PMID: 37360824 PMCID: PMC10279466 DOI: 10.1016/j.giant.2023.100173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Rapid detection of unlabeled SARS-CoV-2 genetic target was demonstrated using a competitive displacement hybridization assay made by a nanostructured anodized alumina oxide (AAO) membrane. The assay applied the toehold-mediated strand displacement reaction. The nanoporous surface of the membrane was functionalized with a complementary pair consisting of Cy3-labeled probe and quencher-labeled nucleic acids through a chemical immobilization process. In the presence of the unlabeled SARS-CoV-2 target, the quencher-tagged strand of the immobilized probe-quencher duplex was separated from the Cy3-modifed strand. A stable probe-target duplex formed and regained a strong fluorescence signal, thus enabling real-time and label-free SARS-CoV-2 detection. Assay designs with different numbers of base pair (bp) matches were synthesized to compare their affinities. Because of the large surface of a free-standing nanoporous membrane, two orders enhancement of the fluorescence was observed, where the detection limit of the unlabeled concentration can be improved to 1 nM. The assay was miniaturized by integrating a nanoporous AAO layer onto an optical waveguide device. The detection mechanism and the sensitivity improvement of the AAO-waveguide device were illustrated from the finite difference method (FDM) simulation and the experimental results. Light-analyte interaction was further improved due to the presence of the AAO layer, which created an intermediate refractive index and enhanced the waveguide's evanescent field. Our competitive hybridization sensor is an accurate and label-free testing platform applicable to the deployment of compact and sensitive virus detection strategies.
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Affiliation(s)
- Megan Makela
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843
| | - Zhihai Lin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843
| | - Pao Tai Lin
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, Texas 77843
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15
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Xiao X, Liu S, Deng H, Song Y, Zhang L, Song Z. Advances in the oral microbiota and rapid detection of oral infectious diseases. Front Microbiol 2023; 14:1121737. [PMID: 36814562 PMCID: PMC9939651 DOI: 10.3389/fmicb.2023.1121737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Several studies have shown that the dysregulation of the oral microbiota plays a crucial role in human health conditions, such as dental caries, periodontal disease, oral cancer, other oral infectious diseases, cardiovascular diseases, diabetes, bacteremia, and low birth weight. The use of traditional detection methods in conjunction with rapidly advancing molecular techniques in the diagnosis of harmful oral microorganisms has expanded our understanding of the diversity, location, and function of the microbiota associated with health and disease. This review aimed to highlight the latest knowledge in this field, including microbial colonization; the most modern detection methods; and interactions in disease progression. The next decade may achieve the rapid diagnosis and precise treatment of harmful oral microorganisms.
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Affiliation(s)
- Xuan Xiao
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Shangfeng Liu
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yuhan Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China,Liang Zhang,
| | - Zhifeng Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,*Correspondence: Zhifeng Song,
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16
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Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM, Ng C, Chen H, Chandra F, Gin KY. A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant. IMETA 2022; 1:e39. [PMID: 38868719 PMCID: PMC10989988 DOI: 10.1002/imt2.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/30/2022] [Accepted: 06/19/2022] [Indexed: 06/14/2024]
Abstract
Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method. We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment. In all, bulk and FACS-coupled metagenomics are complementary approaches that enable a more thorough understanding of the community structure of DNA and RNA viruses in complex environmental samples, of which the latter is critical for increasing the sensitivity of detection of viral signatures that would otherwise be lost through bulk viral metagenomics.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Yi Yang
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
| | - Feijian Mao
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Fang You
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - David M. Needham
- Monterey Bay Aquarium Research InstituteMoss LandingCaliforniaUSA
- GEOMAR Helmholtz Centre for Ocean ResearchOcean EcoSystems Biology UnitKielGermany
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Charmaine Ng
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Hongjie Chen
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Franciscus Chandra
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Karina Yew‐Hoong Gin
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
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17
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Ao Y, Xu J, Duan Z. A novel cardiovirus species identified in feces of wild Himalayan marmots. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105347. [PMID: 35932998 DOI: 10.1016/j.meegid.2022.105347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/17/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Recently a growing number of novel cardioviruses have been frequently discovered, which boosts interest in the search for the genetic diversity of cardioviruses. However, wild-marmot cardioviruses have been rarely reported. Here, a novel cardiovirus (tentatively named HHMCDV) was identified in fecal samples from wild Himalayan marmots in Qinghai Tibetan Plateau, China, by viral metagenomics analysis. 3 out of 99 fecal samples from Himalayan marmots were positive for HHMCDV, with the viral loads ranging from 2.7 × 105 to 1.3 × 107 gene copies/g. The complete genomic sequence of HHMCDV was 8108 nucleotides in length, with the typical cardiovirus genome organization and motifs. Coincidentally, while the data was analyzing, one marmot cardiovirus HT7 partial sequence was available in the Genbank, showing 95.1%, 95.6% and 96.0% amino acid (aa) identity in P1, P2 and P3, respectively. However, sequence analysis revealed that HHMCDV and HT7 are more closely related to species Cardiovirus F strain with 65.7%, 61.9-65.6%, 58.9-59.7%, 71.1-71.7%, 69.1-69.4% and 71.4-72.2% aa identity in polyprotein, P1, P2, P3, 2C and 3CD proteins, respectively. Phylogenetic analysis of P1, P2, P3 and 3CD aa sequences indicated that HHMCDV and HT7 clustered tightly and formed a distinct cluster in the Cardiovirus genus. Based on these data, we propose that HHMCDV and HT7 should be two different members of a potential novel species within the genus Cardiovirus. Further studies are needed to investigate the epidemiology and potential pathogenicity of the virus in Himalayan marmots.
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Affiliation(s)
- Yuanyun Ao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 201102, China.
| | - Zhaojun Duan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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18
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Pan J, Li Y, Wang T, Chang J, Hao L, Chen J, Peng W, Deng J, Huang B, Tian K. A poly(dimethylsiloxane)-based solid-phase microchip platform for dual detection of Pseudorabies virus gD and gE antibodies. Front Cell Infect Microbiol 2022; 12:912108. [PMID: 35959367 PMCID: PMC9360482 DOI: 10.3389/fcimb.2022.912108] [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: 04/21/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudorabies caused by pseudorabies virus (PRV) infection is still a major disease affecting the pig industry; its eradication depends on effective vaccination and antibody (Ab) detection. For a more rapid and accurate PRV detection method that is suitable for clinical application, here, we established a poly(dimethylsiloxane)-based (efficient removal of non-specific binding) solid-phase protein chip platform (blocking ELISA) for dual detection of PRV gD and gE Abs. The purified gD and gE proteins expressed in baculovirus were coated into the highly hydrophobic nanomembrane by an automatic spotter, and the gray values measured by a scanner were used for the S/N (sample/negative) value calculation (gD and gE Abs standard, positive: S/N value ≤0.6; negative: S/N value >0.7; suspicious: 0.6 < S/N ≤ 0.7). The method showed an equal sensitivity in the gD Ab test of immunized pig serum samples compared to the neutralization test and higher sensitivity in the gE Ab test compared to the commercial gE Ab detection kit. In the clinical evaluation, we found an agreement of 100% (122/122) in the gD Ab detection compared to the neutralization test and an agreement of 97.5% (119/122) in the gE Ab detection compared to the commercial PRV gE Ab detection kit. In summary, the protein chip platform for dual detection of PRV gD and gE Abs showed high sensitivity and specificity, which is suitable for PRV immune efficacy evaluation and epidemic monitoring.
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Affiliation(s)
| | - Yufang Li
- Luoyang Zhongke Biochip Technology Co., Ltd., Luoyang, China
| | - Tongyan Wang
- National Research Center for Veterinary Medicine, Luoyang, China
| | | | - Liying Hao
- Luoyang Putai Biotech Co., Ltd., Luoyang, China
| | - Junjie Chen
- Department of Statistical Science, University College London, London, United Kingdom
| | - Wuping Peng
- Luoyang Putai Biotech Co., Ltd., Luoyang, China
| | - Junhua Deng
- Luoyang Putai Biotech Co., Ltd., Luoyang, China
| | - Baicheng Huang
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Kegong Tian
- National Research Center for Veterinary Medicine, Luoyang, China
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19
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Liu J, Wang H, Zhang L, Lu Y, Wang X, Shen M, Li N, Feng L, Jing J, Cao B, Zou X, Cheng J, Xu Y. Sensitive and Rapid Diagnosis of Respiratory Virus Coinfection Using a Microfluidic Chip-Powered CRISPR/Cas12a System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200854. [PMID: 35599436 DOI: 10.1002/smll.202200854] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/19/2022] [Indexed: 06/15/2023]
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 is profoundly influencing the global healthcare system and people's daily lives. The high resource consumption of coronavirus disease 2019 (COVID-19) is resulting in insufficient surveillance of coinfection or resurgence of other critical respiratory epidemics, which is of public concern. To facilitate evaluation of the current coinfection situation, a microfluidic system (MAPnavi) is developed for the rapid (<40 min) and sensitive diagnosis of multiple respiratory viruses from swab samples in a fully sealed and automated manner, in which a nested-recombinase polymerase amplification and the CRISPR-based amplification system is first proposed to ensure the sensitivity and specificity. This novel system has a remarkably low limit of detection (50-200 copies mL-1 ) and is successfully applied to detect 171 clinical samples (98.5% positive predictive agreement; 100% negative predictive agreement), and the results identify 45.6% coinfection among clinical samples from patients with COVID-19. This approach has the potential to shift diagnostic and surveillance efforts from targeted testing for a high-priority virus to comprehensive testing of multiple virus sets and to greatly benefit the implementation of decentralized testing.
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Affiliation(s)
- Jiajia Liu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Huili Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Ying Lu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xu Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Minjie Shen
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Nan Li
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing, 101111, China
| | - Juhui Jing
- CapitalBiotech Technology, Beijing, 101111, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Cheng
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
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20
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Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
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21
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Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
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Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
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22
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High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach. Microbiol Spectr 2022; 10:e0185321. [PMID: 35196791 PMCID: PMC8865552 DOI: 10.1128/spectrum.01853-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life. IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.
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23
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Shim J, Williams L, Kim D, Ko K, Kim MS. Application of Engineered Zinc Finger Proteins Immobilized on Paramagnetic Beads for Multiplexed Detection of Pathogenic DNA. J Microbiol Biotechnol 2021; 31:1323-1329. [PMID: 34261849 PMCID: PMC9705829 DOI: 10.4014/jmb.2106.06057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
Micro-scale magnetic beads are widely used for isolation of proteins, DNA, and cells, leading to the development of in vitro diagnostics. Efficient isolation of target biomolecules is one of the keys to developing a simple and rapid point-of-care diagnostic. A zinc finger protein (ZFP) is a double-stranded (ds) DNA-binding domain, providing a useful scaffold for direct reading of the sequence information. Here, we utilized two engineered ZFPs (Stx2-268 and SEB-435) to detect the Shiga toxin (stx2) gene and the staphylococcal enterotoxin B (seb) gene present in foodborne pathogens, Escherichia coli O157 and Staphylococcus aureus, respectively. Engineered ZFPs are immobilized on a paramagnetic bead as a detection platform to efficiently isolate the target dsDNA-ZFP bound complex. The small paramagnetic beads provide a high surface area to volume ratio, allowing more ZFPs to be immobilized on the beads, which leads to increased target DNA detection. The fluorescence signal was measured upon ZFP binding to fluorophore-labeled target dsDNA. In this study, our system provided a detection limit of ≤ 60 fmol and demonstrated high specificity with multiplexing capability, suggesting a potential for development into a simple and reliable diagnostic for detecting multiple pathogens without target amplification.
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Affiliation(s)
- Jiyoung Shim
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101, USA
| | - Langley Williams
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101, USA
| | - Dohyun Kim
- Department of Mechanical Engineering, Myongji University, Yongin 17058, Republic of Korea
| | - Kisung Ko
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101, USA,Corresponding author Phone: +1-270-745-4362 Fax: +1-270-745-5361 E-mail:
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24
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Afshar D, Moghadam SO, Heidarzadeh S, Fardsanei F, Arshadi M, Ranjbar R. Current and Emerging Technologies for the Diagnosis of SARS-CoV-2. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Currently, there are numerous under development or developed assays with various sensitivities and specificities for diagnosis of the Coronavirus Disease 2019 (COVID-19) caused by the SARS-CoV-2 virus. The World Health Organization (WHO) has approved several detection protocols based on real-time reverse transcription PCR (RT-qPCR) and the reliability of tests to detect the N, S, or RdRp/Hel genes of the SARS-Cov-2 virus has also investigated. Among these targets, COVID-19-RdRp/Hel targets represented the highest sensitivity. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has also been developed to rapidly and efficiently amplify RNA under isothermal conditions. Other isothermal amplification approaches such as nucleic acid sequence-based amplification (NASBA), recombinase polymerase amplification (RPA), and rolling circle amplification (RCA) have also been reported for detecting coronaviruses but like LAMP assay. Different serological tests, including neutralization tests, immunofluorescent (IFA), enzyme-linked immunosorbent (ELISA), and western blotting assays, are available. Point-of-care tests (POCT) are emerging to detect the virus genome, IgG, or IgM antibodies against SARS-CoV-2. The advent of more sensitive, cheaper, and easier-to-perform diagnostic tests seems to be a fundamental prerequisite to improve the diagnosis of COVID-19 infection. Herein, we reviewed several commercially available diagnostic methods used in many clinical laboratories to detect COVID-19.
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Alfano N, Dayaram A, Axtner J, Tsangaras K, Kampmann M, Mohamed A, Wong ST, Gilbert MTP, Wilting A, Greenwood AD. Non‐invasive surveys of mammalian viruses using environmental DNA. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Niccolò Alfano
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Biology and Biotechnology University of Pavia Pavia Italy
| | - Anisha Dayaram
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Charité‐Universitätsmedizin Berlin Corporate Member of Freie Universitäts Berlin and Humboldt‐Universität of BerlinInstitut für Neurophysiologie Berlin Germany
| | - Jan Axtner
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences University of Nicosia Nicosia Cyprus
| | - Marie‐Louise Kampmann
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Azlan Mohamed
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- WWF‐MalaysiaPJCC Petaling Jaya Malaysia
| | - Seth T. Wong
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - M. Thomas P. Gilbert
- The GLOBE Institute University of Copenhagen Copenhagen Denmark
- University MuseumNTNU Trondheim Norway
| | - Andreas Wilting
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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26
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Gars A, Ronczkowski NM, Chassaing B, Castillo-Ruiz A, Forger NG. First Encounters: Effects of the Microbiota on Neonatal Brain Development. Front Cell Neurosci 2021; 15:682505. [PMID: 34168540 PMCID: PMC8217657 DOI: 10.3389/fncel.2021.682505] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/11/2021] [Indexed: 12/20/2022] Open
Abstract
The microbiota plays important roles in host metabolism and immunity, and its disruption affects adult brain physiology and behavior. Although such findings have been attributed to altered neurodevelopment, few studies have actually examined microbiota effects on the developing brain. This review focuses on developmental effects of the earliest exposure to microbes. At birth, the mammalian fetus enters a world teeming with microbes which colonize all body sites in contact with the environment. Bacteria reach the gut within a few hours of birth and cause a measurable response in the intestinal epithelium. In adults, the gut microbiota signals to the brain via the vagus nerve, bacterial metabolites, hormones, and immune signaling, and work in perinatal rodents is beginning to elucidate which of these signaling pathways herald the very first encounter with gut microbes in the neonate. Neural effects of the microbiota during the first few days of life include changes in neuronal cell death, microglia, and brain cytokine levels. In addition to these effects of direct exposure of the newborn to microbes, accumulating evidence points to a role for the maternal microbiota in affecting brain development via bacterial molecules and metabolites while the offspring is still in utero. Hence, perturbations to microbial exposure perinatally, such as through C-section delivery or antibiotic treatment, alter microbiota colonization and may have long-term neural consequences. The perinatal period is critical for brain development and a close look at microbiota effects during this time promises to reveal the earliest, most primary effects of the microbiota on neurodevelopment.
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Affiliation(s)
- Aviva Gars
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | | | - Benoit Chassaing
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR 8104, Université de Paris, Paris, France
| | | | - Nancy G Forger
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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27
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Folgueiras-González A, van den Braak R, Deijs M, van der Hoek L, de Groof A. A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA. Diagnostics (Basel) 2021; 11:diagnostics11050791. [PMID: 33925752 PMCID: PMC8145099 DOI: 10.3390/diagnostics11050791] [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: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
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Affiliation(s)
- Alba Folgueiras-González
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Robin van den Braak
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Correspondence:
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28
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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29
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Lipkin WI, Mishra N, Briese T. Screening for Viral Infections. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7836304 DOI: 10.1016/b978-0-12-814515-9.00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.
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30
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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31
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Tang Z, Kong N, Zhang X, Liu Y, Hu P, Mou S, Liljeström P, Shi J, Tan W, Kim JS, Cao Y, Langer R, Leong KW, Farokhzad OC, Tao W. A materials-science perspective on tackling COVID-19. NATURE REVIEWS. MATERIALS 2020; 5:847-860. [PMID: 33078077 PMCID: PMC7556605 DOI: 10.1038/s41578-020-00247-y] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 05/08/2023]
Abstract
The ongoing SARS-CoV-2 pandemic highlights the importance of materials science in providing tools and technologies for antiviral research and treatment development. In this Review, we discuss previous efforts in materials science in developing imaging systems and microfluidic devices for the in-depth and real-time investigation of viral structures and transmission, as well as material platforms for the detection of viruses and the delivery of antiviral drugs and vaccines. We highlight the contribution of materials science to the manufacturing of personal protective equipment and to the design of simple, accurate and low-cost virus-detection devices. We then investigate future possibilities of materials science in antiviral research and treatment development, examining the role of materials in antiviral-drug design, including the importance of synthetic material platforms for organoids and organs-on-a-chip, in drug delivery and vaccination, and for the production of medical equipment. Materials-science-based technologies not only contribute to the ongoing SARS-CoV-2 research efforts but can also provide platforms and tools for the understanding, protection, detection and treatment of future viral diseases.
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Affiliation(s)
- Zhongmin Tang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Xingcai Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Yuan Liu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ping Hu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China
| | - Shan Mou
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peter Liljeström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jianlin Shi
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | | | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY USA
| | - Omid C. Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
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Aguado-García Y, Taboada B, Morán P, Rivera-Gutiérrez X, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, Arias CF. Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life. Sci Rep 2020; 10:13595. [PMID: 32788688 PMCID: PMC7423923 DOI: 10.1038/s41598-020-70684-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant's immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.
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Affiliation(s)
- Yarenci Aguado-García
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Xaira Rivera-Gutiérrez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06726, Cuauhtémoc, Ciudad de México, Mexico.
| | - Cecilia Ximénez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico.
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico.
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Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TSF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC. Massively multiplexed nucleic acid detection with Cas13. Nature 2020; 582:277-282. [PMID: 32349121 PMCID: PMC7332423 DOI: 10.1038/s41586-020-2279-8] [Citation(s) in RCA: 463] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022]
Abstract
The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.
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Affiliation(s)
- Cheri M Ackerman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Sri Gowtham Thakku
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Hayden C Metsky
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon H Ye
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Jared Kehe
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Tien G Nguyen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Amber Carter
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Anthony Kulesa
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivien G Dugan
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Deborah T Hung
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Goodchild SA, Gao R, Shenton DP, McIntosh AJS, Brown T, Bartlett PN. Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes. Front Chem 2020; 8:381. [PMID: 32478035 PMCID: PMC7235368 DOI: 10.3389/fchem.2020.00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023] Open
Abstract
A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.
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Affiliation(s)
- Sarah A Goodchild
- Defence Science and Technology Laboratory, Salisbury, United Kingdom.,University of Southampton, Southampton, United Kingdom
| | - Rachel Gao
- University of Southampton, Southampton, United Kingdom
| | - Daniel P Shenton
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Philip N Bartlett
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
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36
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Malfatti MA, Kuhn EA, Murugesh DK, Mendez ME, Hum N, Thissen JB, Jaing CJ, Loots GG. Manipulation of the Gut Microbiome Alters Acetaminophen Biodisposition in Mice. Sci Rep 2020; 10:4571. [PMID: 32165665 PMCID: PMC7067795 DOI: 10.1038/s41598-020-60982-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 02/19/2020] [Indexed: 12/30/2022] Open
Abstract
The gut microbiota is a vast and diverse microbial community that has co-evolved with its host to perform a variety of essential functions involved in the utilization of nutrients and the processing of xenobiotics. Shifts in the composition of gut microbiota can disturb the balance of organisms which can influence the biodisposition of orally administered drugs. To determine how changes in the gut microbiome can alter drug disposition, the pharmacokinetics (PK), and biodistribution of acetaminophen were assessed in C57Bl/6 mice after treatment with the antibiotics ciprofloxacin, amoxicillin, or a cocktail of ampicillin/neomycin. Altered PK, and excretion profiles of acetaminophen were observed in antibiotic exposed animals. Plasma Cmax was significantly decreased in antibiotic treated animals suggesting decreased bioavailability. Urinary metabolite profiles revealed decreases in acetaminophen-sulfate metabolite levels in both the amoxicillin and ampicillin/neomycin treated animals. The ratio between urinary and fecal excretion was also altered in antibiotic treated animals. Analysis of gut microbe composition revealed that changes in microbe content in antibiotic treated animals was associated with changes in acetaminophen biodisposition. These results suggest that exposure to amoxicillin or ampicillin/neomycin can alter the biodisposition of acetaminophen and that these alterations could be due to changes in gut microbiome composition.
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Affiliation(s)
- Michael A Malfatti
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
| | - Edward A Kuhn
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Deepa K Murugesh
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Melanie E Mendez
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Nicholas Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - James B Thissen
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Crystal J Jaing
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Gabriela G Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
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37
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A Survey of Analytical Techniques for Noroviruses. Foods 2020; 9:foods9030318. [PMID: 32164213 PMCID: PMC7142446 DOI: 10.3390/foods9030318] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 12/17/2022] Open
Abstract
As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses.
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38
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Abstract
Once the genome of a microbial organism has been sequenced, it becomes possible to utilize portions of the genome, known as “signatures” to identify when that organism is present in a complex clinical or environmental sample. Genomic signatures can be at multiple levels of resolution depending on the questions being asked. (“Is this white powder anthrax?”; “Does this white powder match any of the anthrax samples taken from every laboratory in the United States that possesses anthrax?”) Multiple technologies exist to turn abstract genomic signatures into assays that can interrogate complex samples with varying degrees of speed, sensitivity, specificity, and cost. The recent flood of microbial genomic data has complicated the task of designing genomic signatures.
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39
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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40
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Liu L, Gong T, Tao W, Lin B, Li C, Zheng X, Zhu S, Jiang W, Zhou R. Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling. Nat Immunol 2019; 20:1681-1691. [PMID: 31636462 DOI: 10.1038/s41590-019-0513-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 09/06/2019] [Indexed: 01/05/2023]
Abstract
Much attention has focused on commensal bacteria in health and disease, but the role of commensal viruses is understudied. Although metagenomic analysis shows that the intestine of healthy humans and animals harbors various commensal viruses and the dysbiosis of these viruses can be associated with inflammatory diseases, there is still a lack of causal data and underlying mechanisms to understand the physiological role of commensal viruses in intestinal homeostasis. In the present study, we show that commensal viruses are essential for the homeostasis of intestinal intraepithelial lymphocytes (IELs). Mechanistically, the cytosolic viral RNA-sensing receptor RIG-I in antigen-presenting cells can recognize commensal viruses and maintain IELs via a type I interferon-independent, but MAVS-IRF1-IL-15 axis-dependent, manner. The recovery of IELs by interleukin-15 administration reverses the susceptibility of commensal virus-depleted mice to dextran sulfate sodium-induced colitis. Collectively, our results indicate that commensal viruses maintain the IELs and consequently sustain intestinal homeostasis via noncanonical RIG-I signaling.
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Affiliation(s)
- Lei Liu
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Tao Gong
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Wanyin Tao
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Bolong Lin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Xuesen Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Shu Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
| | - Wei Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
| | - Rongbin Zhou
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China. .,CAS Centre for Excellence in Cell and Molecular Biology, University of Science and Technology of China, Hefei, China.
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41
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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42
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Development of an oligonucleotide-based microarray for the detection of foodborne viruses. J Verbrauch Lebensm 2019. [DOI: 10.1007/s00003-019-01234-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Narayanan M. New technologies in microbiology and their potential impact on paediatric practice. Arch Dis Child 2019; 104:513-517. [PMID: 30154181 DOI: 10.1136/archdischild-2017-314189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 11/04/2022]
Affiliation(s)
- Manjusha Narayanan
- Department of Microbiology, Infection Prevention and Control, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
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44
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Kwit E, Rzeżutka A. Molecular methods in detection and epidemiologic studies of rabbit and hare viruses: a review. J Vet Diagn Invest 2019; 31:497-508. [PMID: 31131728 DOI: 10.1177/1040638719852374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Various PCR-based assays for rabbit viruses have gradually replaced traditional virologic assays, such as virus isolation, because they offer high-throughput analysis, better test sensitivity and specificity, and allow vaccine and wild-type virus strains to be fully typed and differentiated. In addition, PCR is irreplaceable in the detection of uncultivable or fastidious rabbit pathogens or those occurring in low quantity in a tested sample. We provide herein an overview of the current state of the art in the molecular detection of lagomorph viral pathogens along with details of their targeted gene or nucleic acid sequence and recommendations for their application. Apart from the nucleic acids-based methods used for identification and comprehensive typing of rabbit viruses, novel methods such as microarray, next-generation sequencing, and mass spectrometry (MALDI-TOF MS) could also be employed given that they offer greater throughput in sample screening for viral pathogens. Molecular methods should be provided with an appropriate set of controls, including an internal amplification control, to confirm the validity of the results obtained.
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Affiliation(s)
- Ewa Kwit
- Department of Food and Environmental Virology, National Veterinary Research Institute, Puławy, Poland
| | - Artur Rzeżutka
- Department of Food and Environmental Virology, National Veterinary Research Institute, Puławy, Poland
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45
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De Giorgi V, Zhou H, Alter HJ, Allison RD. A microarray-based pathogen chip for simultaneous molecular detection of transfusion-transmitted infectious agents. J Transl Med 2019; 17:156. [PMID: 31088488 PMCID: PMC6518760 DOI: 10.1186/s12967-019-1905-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND New and emerging transfusion-transmitted infections remain a threat to the blood supply. Blood donors are currently screened for less than half of known agents, primarily by individual tests. A screening platform that could simultaneously detect all known transfusion-transmitted pathogens and allow rapid addition of new targets would significantly increase blood safety and could improve the response to new agents. We describe the early stage development and validation of a microarray-based platform (pathogen chip) for simultaneous molecular detection of transfusion-transmitted RNA viruses. METHODS Sixteen RNA viruses that pose a significant risk for transfusion-transmission were selected for inclusion on the pathogen chip. Viruses were targeted for detection by 1769 oligonucleotide probes selected by Agilent eArray software. Differentially concentrated positive plasma samples were used to evaluate performance and limits of detection in the context of individual pathogens or combinations to simulate coinfection. RNA-viruses detection and concentration were validated by RT-qPCR. RESULTS Hepatitis A, B and C, Chikungunya, dengue 1-4, HIV 1-2, HTLV I-II, West Nile and Zika viruses were all correctly identified by the pathogen chip within the range of 105 to 102 copies/mL; hepatitis E virus from 105 to 104. In mixtures of 3-8 different viruses, all were correctly identified between 105 and 103 copies/mL. CONCLUSIONS This microarray-based multi-pathogen screening platform accurately and reproducibly detected individual and mixed RNA viruses in one test from single samples with limits of detection as low as 102 copies mL.
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Affiliation(s)
- Valeria De Giorgi
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Building 10, Room 1C711, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Huizhi Zhou
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Building 10, Room 1C711, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Harvey J Alter
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Building 10, Room 1C711, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Robert D Allison
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Building 10, Room 1C711, 10 Center Drive, Bethesda, MD, 20892, USA
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46
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Ellwanger JH, Kaminski VDL, Chies JAB. Emerging infectious disease prevention: Where should we invest our resources and efforts? J Infect Public Health 2019; 12:313-316. [PMID: 30928239 DOI: 10.1016/j.jiph.2019.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Strategies focused on the prevention of emerging infectious disease outbreaks are currently in the spotlight of discussions among researchers committed to infectious disease control. In this mini-review, we provided a brief update on this discussion and characterized the three main targets for investments in emerging infectious disease prevention: animals, human sentinels for spillover events, and the general human population. Furthermore, the pros and cons of each target are highlighted. Despite the particularities of the proposed targets, each of them can fill different gaps in the surveillance of infectious diseases. When all three targets are focused on together, they create a powerful strategy of emerging infectious disease prevention.
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Affiliation(s)
- Joel H Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José A B Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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47
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Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. Eur J Clin Microbiol Infect Dis 2019; 38:1059-1070. [PMID: 30834996 PMCID: PMC6520317 DOI: 10.1007/s10096-019-03520-3] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of (‘difficult-to-culture’) microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform (‘MYcrobiota’) is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.
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48
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Pontremoli C, Forni D, Sironi M. Arenavirus genomics: novel insights into viral diversity, origin, and evolution. Curr Opin Virol 2019; 34:18-28. [DOI: 10.1016/j.coviro.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022]
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49
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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50
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Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 2019; 37:160-168. [PMID: 30718881 PMCID: PMC6587591 DOI: 10.1038/s41587-018-0006-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
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Affiliation(s)
- Hayden C. Metsky
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Katherine J. Siddle
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | | | - James Qu
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - David K. Yang
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Patrick Brehio
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andrew Goldfarb
- 000000041936754Xgrid.38142.3cFaculty of Arts and Sciences, Harvard University, Cambridge, MA USA
| | - Anne Piantadosi
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Shirlee Wohl
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Amber Carter
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Aaron E. Lin
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kayla G. Barnes
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA
| | - Damien C. Tully
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Bjӧrn Corleis
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Scott Hennigan
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Giselle Barbosa-Lima
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R. Vieira
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M. Paul
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Amanda L. Tan
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Kimberly F. Garcia
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A. Parham
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Philomena Eromon
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria
| | - Onikepe A. Folarin
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Etienne Simon-Lorière
- 0000 0001 2353 6535grid.428999.7Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Lisa Hensley
- 0000 0001 2164 9667grid.419681.3Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD USA
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- 0000 0001 2181 7878grid.47840.3fDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Douglas S. Kwon
- 0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Todd M. Allen
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Jonathan A. Runstadler
- 0000 0004 1936 7531grid.429997.8Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA USA
| | - Sandra Smole
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Fernando A. Bozza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago M. L. Souza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sharon Isern
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Scott F. Michael
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Ivette Lorenzana
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Lee Gehrke
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA USA
| | - Irene Bosch
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Gregory Ebel
- 0000 0004 1936 8083grid.47894.36Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Donald S. Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone ,0000 0001 2290 9707grid.442296.fCollege of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Christian T. Happi
- 000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Daniel J. Park
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andreas Gnirke
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Pardis C. Sabeti
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Chevy Chase, MD USA
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