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Carmo dos Santos M, Cerqueira Silva AC, dos Reis Teixeira C, Pinheiro Macedo Prazeres F, Fernandes dos Santos R, de Araújo Rolo C, de Souza Santos E, Santos da Fonseca M, Oliveira Valente C, Saraiva Hodel KV, Moraes dos Santos Fonseca L, Sampaio Dotto Fiuza B, de Freitas Bueno R, Bittencourt de Andrade J, Aparecida Souza Machado B. Wastewater surveillance for viral pathogens: A tool for public health. Heliyon 2024; 10:e33873. [PMID: 39071684 PMCID: PMC11279281 DOI: 10.1016/j.heliyon.2024.e33873] [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: 01/03/2024] [Revised: 06/03/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
A focus on water quality has intensified globally, considering its critical role in sustaining life and ecosystems. Wastewater, reflecting societal development, profoundly impacts public health. Wastewater-based epidemiology (WBE) has emerged as a surveillance tool for detecting outbreaks early, monitoring infectious disease trends, and providing real-time insights, particularly in vulnerable communities. WBE aids in tracking pathogens, including viruses, in sewage, offering a comprehensive understanding of community health and lifestyle habits. With the rise in global COVID-19 cases, WBE has gained prominence, aiding in monitoring SARS-CoV-2 levels worldwide. Despite advancements in water treatment, poorly treated wastewater discharge remains a threat, amplifying the spread of water-, sanitation-, and hygiene (WaSH)-related diseases. WBE, serving as complementary surveillance, is pivotal for monitoring community-level viral infections. However, there is untapped potential for WBE to expand its role in public health surveillance. This review emphasizes the importance of WBE in understanding the link between viral surveillance in wastewater and public health, highlighting the need for its further integration into public health management.
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Affiliation(s)
- Matheus Carmo dos Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Ana Clara Cerqueira Silva
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Carine dos Reis Teixeira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Filipe Pinheiro Macedo Prazeres
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Rosângela Fernandes dos Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Carolina de Araújo Rolo
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Emanuelle de Souza Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Maísa Santos da Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Camila Oliveira Valente
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Larissa Moraes dos Santos Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Bianca Sampaio Dotto Fiuza
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Rodrigo de Freitas Bueno
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | - Jailson Bittencourt de Andrade
- University Center SENAI CIMATEC, SENAI CIMATEC, Salvador, 41650-010, Bahia, Brazil
- Centro Interdisciplinar de Energia e Ambiente – CIEnAm, Federal University of Bahia, Salvador, 40170-115, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
- University Center SENAI CIMATEC, SENAI CIMATEC, Salvador, 41650-010, Bahia, Brazil
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Kuba Y, Nidaira M, Maeshiro N, Komase K, Kamiya H, Kyan H. Analysis of Suspected Measles Cases with Discrepant Measles-Specific IgM and rRT-PCR Test Results, Japan. Emerg Infect Dis 2024; 30:926-933. [PMID: 38579738 PMCID: PMC11060445 DOI: 10.3201/eid3005.231757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
We investigated clinically suspected measles cases that had discrepant real-time reverse transcription PCR (rRT-PCR) and measles-specific IgM test results to determine diagnoses. We performed rRT-PCR and measles-specific IgM testing on samples from 541 suspected measles cases. Of the 24 IgM-positive and rRT-PCR--negative cases, 20 were among children who received a measles-containing vaccine within the previous 6 months; most had low IgG relative avidity indexes (RAIs). The other 4 cases were among adults who had an unknown previous measles history, unknown vaccination status, and high RAIs. We detected viral nucleic acid for viruses other than measles in 15 (62.5%) of the 24 cases with discrepant rRT-PCR and IgM test results. Measles vaccination, measles history, and contact history should be considered in suspected measles cases with discrepant rRT-PCR and IgM test results. If in doubt, measles IgG avidity and PCR testing for other febrile exanthematous viruses can help confirm or refute the diagnosis.
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Affiliation(s)
| | - Minoru Nidaira
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan (Y. Kuba, M. Nidaira, N. Maeshiro, H. Kyan)
- National Institute of Infectious Diseases, Tokyo, Japan (K. Komase, H. Kamiya)
| | - Noriyuki Maeshiro
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan (Y. Kuba, M. Nidaira, N. Maeshiro, H. Kyan)
- National Institute of Infectious Diseases, Tokyo, Japan (K. Komase, H. Kamiya)
| | - Katsuhiro Komase
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan (Y. Kuba, M. Nidaira, N. Maeshiro, H. Kyan)
- National Institute of Infectious Diseases, Tokyo, Japan (K. Komase, H. Kamiya)
| | - Hajime Kamiya
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan (Y. Kuba, M. Nidaira, N. Maeshiro, H. Kyan)
- National Institute of Infectious Diseases, Tokyo, Japan (K. Komase, H. Kamiya)
| | - Hisako Kyan
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan (Y. Kuba, M. Nidaira, N. Maeshiro, H. Kyan)
- National Institute of Infectious Diseases, Tokyo, Japan (K. Komase, H. Kamiya)
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Tulloch RL, Kim K, Sikazwe C, Michie A, Burrell R, Holmes EC, Dwyer DE, Britton PN, Kok J, Eden JS. RAPID prep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 2023; 15:v15041006. [PMID: 37112986 PMCID: PMC10146689 DOI: 10.3390/v15041006] [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: 12/21/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
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Affiliation(s)
- Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karan Kim
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Alice Michie
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Philip N Britton
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jen Kok
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods 2023; 314:114677. [PMID: 36657602 PMCID: PMC10009504 DOI: 10.1016/j.jviromet.2023.114677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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Santiago-Rodriguez TM, Hollister EB. Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach. Viruses 2023; 15:236. [PMID: 36680277 PMCID: PMC9863393 DOI: 10.3390/v15010236] [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: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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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: 1.5] [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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Zhang D, Zheng M, Zhang Y, Feng G, Peng C, Li C, Li Y, Zhang H, Li N, Xiao P. Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome. Front Cell Infect Microbiol 2022; 12:874003. [PMID: 35846764 PMCID: PMC9277073 DOI: 10.3389/fcimb.2022.874003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/04/2022] [Indexed: 01/01/2023] Open
Abstract
Swab samples were collected from 34 pangolins in Guangxi Province, China. Metavirome sequencing and bioinformatics approaches were undertaken to determine the abundant viral sequences in the viromes. The results showed that the viral sequences belong to 24 virus taxonomic families. To verify the results, PCR combined with phylogenetic analysis was conducted. Some viral sequences including Japanese encephalitis virus (JEV), Getah virus (GETV), and chikungunya virus (CHIKV) were detected. On the basis of the metavirome analysis, seven segments belonging to JEV were further identified through PCR amplification. Sequence comparison showed that, among seven sequences, JEV-China/P2020E-1 displayed the highest nucleotide (80.6%), with the JEV isolated in South Korea, 1988, and all of which belonging to genotype III. Seven CHIKV sequences were detected, with the highest homology (80.6%) to the Aedes africanus in Côte d’Ivoire, 1993. Moreover, passage from BHK-21 to Vero cells makes the newly isolated CHIKV-China/P2020-1 more contagious. In addition, the newly verified GETV sequences shared 86.4% identity with the 1955 GETV isolated from Malaysia. Some sudden and recurrent viruses have also been observed from the virome of pangolin in Guangxi Province, China; hence, dissemination tests will be implemented in the future.
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Affiliation(s)
- Duo Zhang
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Min Zheng
- Guangxi Centre for Animal Disease Control and Prevention, Nanning, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Guanrong Feng
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chengcheng Peng
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chenghui Li
- College of Agriculture, Yanbian University, Yanji, China
| | - Yiquan Li
- Academician Workstation of Jilin Province, Changchun University of Chinese Medicine, Changchun, China
| | - He Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Nan Li
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Pengpeng Xiao
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
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Ramalingam VV, Fletcher GJ, Kasirajan A, Demosthenes JP, Rupali P, Varghese GM, Pulimood SA, Rebekah G, Kannangai R. Can In-house HIV-2 Viral Load Assay be a Reliable Alternative to Commercial Assays for Clinical and Therapeutic Monitoring? Curr HIV Res 2022; 20:274-286. [PMID: 35692165 DOI: 10.2174/1570162x20666220609155237] [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: 11/16/2021] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Currently, there is a global contemplation to end the AIDS epidemic by 2030. HIV-2 poses unique challenges to this end. The burden of HIV-2 is higher in resource-limited countries, and it is intrinsically resistant to NNRTI drugs. In addition, there is no FDA-approved plasma viral load assay to monitor disease progression and therapeutic efficacy. To overcome these challenges, we have developed and evaluated an in-house quantitative HIV-2 viral load assay. METHODS Blood samples were collected from 28 HIV-2 treatment-naïve monoinfected individuals and tested using an in-house qPCR HIV-2 viral load assay. The extracted RNA was amplified using Quantifast pathogen + IC kit. RESULTS The in-house qPCR has a limit of detection of 695 copies/ml. The intra- and inter-assay variation (% CV) of the assay was 0.61 and 0.95, respectively. The in-house assay quantified HIV-2 NIBSC accurately (1000 IU) with a mean of 1952 copies/mL. Among the 28 samples tested by in-house qPCR assay, 11 (39.2%) samples were quantified, whereas 17 (60.7%) samples were not detected. In comparison with Altona RealStar HIV-2 RT PCR and Exavir Load RT assay, the results were 96.4% and 69.6% concordant, respectively. No significant (p = 0.99 and p = 0.13) difference in quantifying viral load between the three assays. Based on clinical and immunological (CD4) staging, the performance characteristics were comparable. CONCLUSION To the best of our knowledge, this is the first in-house qPCR developed in India. The performance characteristics of the in-house assay are comparable to the commercial assays, and they can be used assertively to monitor HIV-2 patients.
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Affiliation(s)
| | | | - Anand Kasirajan
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - John Paul Demosthenes
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Priscilla Rupali
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - George Mannil Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | | | - Grace Rebekah
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
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Effect of mismatch between types of viral nucleic acid and intended targets of extraction kits on polymerase chain reaction-based testing. Biotechniques 2022; 73:75-79. [PMID: 35762215 DOI: 10.2144/btn-2022-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lab personnel generally select an extraction kit based on the nucleic acid (NA) type of the target. This study investigated the effect of mismatch between the NA type of the target and the intended target NA of the extraction kit on the polymerase chain reaction outcome. DNA, RNA and total NA extraction kits manufactured by the same company were used to isolate NA from serial dilutions of four viruses representing different genome types. All extracts were tested for the viruses by either conventional or real-time polymerase chain reactions with and without reverse transcription. While the DNA kit specifically isolated DNA from samples, the RNA kit extracted both DNA and RNA as efficiently as the total NA kit, suggesting that RNA kits can be an economical alternative.
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11
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Feng G, Zhang J, Zhang Y, Li C, Zhang D, Li Y, Zhou H, Li N, Xiao P. Metagenomic Analysis of Togaviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes from Chikungunya and Ross River Viruses. Front Cell Infect Microbiol 2022; 12:849662. [PMID: 35223559 PMCID: PMC8878809 DOI: 10.3389/fcimb.2022.849662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
We collected 5,500 mosquitoes belonging to six species in three locations in China. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The affluent viral sequences that were detected and annotated belong to 22 viral taxonomic families. Then, PCR was performed to confirm the results, followed by phylogenetic analysis. Herein, part of mosquito virome was identified, including chikungunya virus (CHIKV), Getah virus (GETV), and Ross river virus (RRV). After metagenomic analysis, seven CHIKV sequences were verified by PCR amplification, among which CHIKV-China/YN2018-1 had the highest homology with the CHIKV isolated in Senegal, 1983, with a nucleotide (nt) identity of at least 81%, belonging to genotype West Africa viral genes. Five GETV sequences were identified, which had a high homology with the GETV sequences isolated from Equus caballus in Japan, 1978, with a (nt) identity of at least 97%. The newly isolated virus CHIKV-China/YN2018-1 became more infectious after passage of the BHK-21 cell line to the Vero cell line. The newly identified RRV gene had the highest homology with the 2006 RRV isolate from Australia, with a (nt) identity of at least 94%. In addition, numerous known and unknown viruses have also been detected in mosquitoes from Yunnan province, China, and propagation tests will be carried out.
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Affiliation(s)
- Guanrong Feng
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Jinyong Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Chenghui Li
- College of Agriculture, Yanbian University, Yanji, China
| | - Duo Zhang
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Yiquan Li
- Academician Workstation of Jilin Province, Changchun University of Chinese Medicine, Changchun, China
| | | | - Nan Li
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
- *Correspondence: Nan Li, ; Pengpeng Xiao,
| | - Pengpeng Xiao
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
- *Correspondence: Nan Li, ; Pengpeng Xiao,
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12
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 34818780 DOI: 10.20944/preprints202104.0481.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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13
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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14
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Liao Q, Ouyang G, Zhu J, Cai X, Yu G, Zhou Z, Liu X, Wang J, Xiao W. Zebrafish sirt7 Negatively Regulates Antiviral Responses by Attenuating Phosphorylation of irf3 and irf7 Independent of Its Enzymatic Activity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:3050-3059. [PMID: 34799424 DOI: 10.4049/jimmunol.2100318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
Sirt7 is one member of the sirtuin family proteins with NAD (NAD+)-dependent histone deacetylase activity. In this study, we report that zebrafish sirt7 is induced upon viral infection, and overexpression of sirt7 suppresses cellular antiviral responses. Disruption of sirt7 in zebrafish increases the survival rate upon spring viremia of carp virus infection. Further assays indicate that sirt7 interacts with irf3 and irf7 and attenuates phosphorylation of irf3 and irf7 by preventing tbk1 binding to irf3 and irf7. In addition, the enzymatic activity of sirt7 is not required for sirt7 to repress IFN-1 activation. To our knowledge, this study provides novel insights into sirt7 function and sheds new light on the regulation of irf3 and irf7 by attenuating phosphorylation.
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Affiliation(s)
- Qian Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Gang Ouyang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Junji Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Xiaolian Cai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Guangqing Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Ziwen Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Xing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China; .,Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China; and.,Hubei Hongshan Laboratory, Wuhan, People's Republic of China
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15
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Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples. Viruses 2021; 13:v13102006. [PMID: 34696436 PMCID: PMC8541124 DOI: 10.3390/v13102006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/27/2022] Open
Abstract
According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.
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16
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Clinical performance and potential of a SARS-CoV-2 detection kit without RNA purification steps. J LAB MED 2021. [DOI: 10.1515/labmed-2021-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Objectives
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is rapidly spreading globally. Early diagnosis plays an essential role in controlling the infection. Therefore, early and accurate SARS-CoV-2 detection assays along with easy operation are required. The aim of this study was to compare the clinical performance of the Ampdirect™ 2019-nCoV Detection Kit (SHIMADZU assay), which does not require RNA purification steps, with that of the preexisting SARS-CoV-2 detection assays, which use a purified RNA template.
Methods
A total of 71 samples (65 nasopharyngeal specimens and 6 sputum specimens) were collected from 32 individuals, including patients infected with SARS-CoV-2 and those with suspected infection. The sensitivity and kappa (κ) coefficient were assessed between the SARS-CoV-2 detection assays using the reference standard, which was defined as a true positive result by any one of the four SARS-CoV-2 detection assays.
Results
The overall sensitivity and κ coefficient of the SHIMADZU assay were 86.0% (95% confidence interval [CI]: 77.9–94.2) and 0.83 (95% CI: 0.69–0.96), respectively. In particular, among the 18 samples collected within 10 days from symptom onset, the sensitivity and κ coefficient of the SHIMADZU assay were 100% and 1.0, respectively.
Conclusions
Although a relatively small number of samples was evaluated, the SHIMADZU assay showed good analytical performance and as such would be highly useful for the detection of SARS-CoV-2. The test can be performed easily and quickly and has the potential for future applications in situations where a highly sensitive diagnosis is required.
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17
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Yoo HM, Kim IH, Kim S. Nucleic Acid Testing of SARS-CoV-2. Int J Mol Sci 2021; 22:6150. [PMID: 34200331 PMCID: PMC8201071 DOI: 10.3390/ijms22116150] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.
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Affiliation(s)
- Hee Min Yoo
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Il-Hwan Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
| | - Seil Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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18
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Chan SK, Du P, Ignacio C, Mehta S, Newton IG, Steinmetz NF. Biomimetic Virus-Like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools. ACS NANO 2021; 15:1259-1272. [PMID: 33237727 PMCID: PMC7724985 DOI: 10.1021/acsnano.0c08430] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible disease that has affected more than 90% of the countries worldwide. At least 17 million individuals have been infected, and some countries are still battling first or second waves of the pandemic. Nucleic acid tests, especially reverse transcription polymerase chain reaction (RT-PCR), have become the workhorse for early detection of COVID-19 infection. Positive controls for the molecular assays have been developed to validate each test and to provide high accuracy. However, most available positive controls require cold-chain distribution and cannot serve as full-process control. To overcome these shortcomings, we report the production of biomimetic virus-like particles (VLPs) as SARS-CoV-2 positive controls. A SARS-CoV-2 detection module for RT-PCR was encapsidated into VLPs from a bacteriophage and a plant virus. The chimeric VLPs were obtained either by in vivo reconstitution and coexpression of the target detection module and coat proteins or by in vitro assembly of purified detection module RNA sequences and coat proteins. These VLP-based positive controls mimic SARS-CoV-2 packaged ribonucleic acid (RNA) while being noninfectious. Most importantly, we demonstrated that the positive controls are scalable, stable, and can serve broadly as controls, from RNA extraction to PCR in clinical settings.
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Affiliation(s)
- Soo Khim Chan
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Pinyi Du
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Caroline Ignacio
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Sanjay Mehta
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Isabel G. Newton
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Nicole F. Steinmetz
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
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19
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Tahmasebi R, Luchs A, Tardy K, Hefford PM, Tinker RJ, Eilami O, de Padua Milagres FA, Brustulin R, Teles MDAR, Dos Santos Morais V, Moreira CHV, Buccheri R, Araújo ELL, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Charlys da Costa A. Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics. J Gen Virol 2020; 101:1280-1288. [PMID: 33044150 DOI: 10.1099/jgv.0.001500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8 % (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9 % (55/251) of samples and mixed infections in 37.4 % (94/251), with RVA/HAdV-F being the most frequent association (21.5 %; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.
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Affiliation(s)
- Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Kaelan Tardy
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Rory J Tinker
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Owrang Eilami
- School of Medicine Social, Determinants of Health Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil
| | | | | | | | - Renata Buccheri
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, DF, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
| | - Xutao Deng
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
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20
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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21
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Assessment of Metagenomic Sequencing and qPCR for Detection of Influenza D Virus in Bovine Respiratory Tract Samples. Viruses 2020; 12:v12080814. [PMID: 32731471 PMCID: PMC7472010 DOI: 10.3390/v12080814] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
High throughput sequencing is currently revolutionizing the genomics field and providing new approaches to the detection and characterization of microorganisms. The objective of this study was to assess the detection of influenza D virus (IDV) in bovine respiratory tract samples using two sequencing platforms (MiSeq and Nanopore (GridION)), and species-specific qPCR. An IDV-specific qPCR was performed on 232 samples (116 nasal swabs and 116 tracheal washes) that had been previously subject to virome sequencing using MiSeq. Nanopore sequencing was performed on 19 samples positive for IDV by either MiSeq or qPCR. Nanopore sequence data was analyzed by two bioinformatics methods: What’s In My Pot (WIMP, on the EPI2ME platform), and an in-house developed analysis pipeline. The agreement of IDV detection between qPCR and MiSeq was 82.3%, between qPCR and Nanopore was 57.9% (in-house) and 84.2% (WIMP), and between MiSeq and Nanopore was 89.5% (in-house) and 73.7% (WIMP). IDV was detected by MiSeq in 14 of 17 IDV qPCR-positive samples with Cq (cycle quantification) values below 31, despite multiplexing 50 samples for sequencing. When qPCR was regarded as the gold standard, the sensitivity and specificity of MiSeq sequence detection were 28.3% and 98.9%, respectively. We conclude that both MiSeq and Nanopore sequencing are capable of detecting IDV in clinical specimens with a range of Cq values. Sensitivity may be further improved by optimizing sequence data analysis, improving virus enrichment, or reducing the degree of multiplexing.
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22
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Lu G, Peng X, Li R, Liu Y, Wu Z, Wang X, Zhang D, Zhao J, Sun Y, Zhang L, Yang P, Wang Q. An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55. BMC Infect Dis 2020; 20:537. [PMID: 32703176 PMCID: PMC7376533 DOI: 10.1186/s12879-020-05258-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. METHODS In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. RESULTS We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). CONCLUSIONS We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55.
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Affiliation(s)
- Guilan Lu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Xiaomin Peng
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Renqing Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Yimeng Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Zhanguo Wu
- Daxing District Center for Disease Prevention and Control, Beijing, 102600, China
| | - Xifeng Wang
- Daxing District Center for Disease Prevention and Control, Beijing, 102600, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Jiachen Zhao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Ying Sun
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Li Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Peng Yang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, 16# He Ping Li Middle Street, Dongcheng District, Beijing, 100013, China.
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23
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Akello JO, Leib SL, Engler O, Beuret C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses 2020; 12:v12050562. [PMID: 32438629 PMCID: PMC7290855 DOI: 10.3390/v12050562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
Identification and characterization of viral genomes in vectors including ticks and mosquitoes positive for pathogens of great public health concern using metagenomic next generation sequencing (mNGS) has challenges. One such challenge is the ability to efficiently recover viral RNA which is typically dependent on sample processing. We evaluated the quantitative effect of six different extraction methods in recovering viral RNA in vectors using negative tick homogenates spiked with serial dilutions of tick-borne encephalitis virus (TBEV) and surrogate Langat virus (LGTV). Evaluation was performed using qPCR and mNGS. Sensitivity and proof of concept of optimal method was tested using naturally positive TBEV tick homogenates and positive dengue, chikungunya, and Zika virus mosquito homogenates. The amount of observed viral genome copies, percentage of mapped reads, and genome coverage varied among different extractions methods. The developed Method 5 gave a 120.8-, 46-, 2.5-, 22.4-, and 9.9-fold increase in the number of viral reads mapping to the expected pathogen in comparison to Method 1, 2, 3, 4, and 6, respectively. Our developed Method 5 termed ROVIV (Recovery of Viruses in Vectors) greatly improved viral RNA recovery and identification in vectors using mNGS. Therefore, it may be a more sensitive method for use in arbovirus surveillance.
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Affiliation(s)
- Joyce Odeke Akello
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 4, 3012 Bern, Switzerland
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
| | - Olivier Engler
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
| | - Christian Beuret
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
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24
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Jeong S, Park MJ, Song W, Kim HS. Advances in laboratory assays for detecting human metapneumovirus. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:608. [PMID: 32566634 PMCID: PMC7290561 DOI: 10.21037/atm.2019.12.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human metapneumovirus (HMPV) is one of the major causes of acute respiratory tract infection (ARI) and shows high morbidity and mortality, particularly in children and immunocompromised patients. Various methods for detecting HMPV have been developed and applied in clinical laboratories. When reviewing the literature, we found that polymerase chain reaction (PCR)-based assays have been most frequently and consistently used to detect HMPV. The most commonly used method was multiplex reverse transcriptase-PCR (RT-PCR; 57.4%), followed by real-time RT-PCR (38.3%). Multiplex RT-PCR became the more popular method in 2011-2019 (69.7%), in contrast to 2001-2009 (28.6%). The advent of multiplex PCR in detecting broader viral pathogens in one run and coinfected viruses influenced the change in user preference. Further, newly developed microarray technologies and ionization mass spectrometry were introduced in 2011-2019. Viral culture (including shell vial assays) and fluorescent immunoassays (with or without culture) were once the mainstays. However, the percentage of studies employing culture and fluorescent immunoassays decreased from 21.4% in 2001-2010 to 15.2% in 2011-2019. Meanwhile, the use of PCR-based methods of HMPV detection increased from 78.6% in 2001-2010 to 84.8% in 2011-2019. The increase in PCR-based methods might have occurred because PCR methods demonstrated better diagnostic performance, shorter hands-on and run times, less hazards to laboratory personnel, and more reliable results than traditional methods. When using these assays, it is important to acquire a comprehensive understanding of the principles, advantages, disadvantages, and precautions for data interpretation. In the future, the combination of nanotechnology and advanced genetic platforms such as next-generation sequencing will benefit patients with HMPV infection by facilitating efficient therapeutic intervention. Analytical and clinical validation are required before using new techniques in clinical laboratories.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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25
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Metagenomic Detection of Two Vientoviruses in a Human Sputum Sample. Viruses 2020; 12:v12030327. [PMID: 32197299 PMCID: PMC7150755 DOI: 10.3390/v12030327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
We used metagenomics to analyze one sputum sample from a patient with symptoms of a respiratory infection that yielded negative results for all pathogens tested. We detected two viral genomes that could be assembled and showed sequence similarity to redondoviruses, a recently described group within the CRESS-DNA viruses. One hundred sputum samples were screened for the presence of these viruses using specific primers. One sample was positive for the same two viruses, and another was positive for one of them. These findings raise questions about a possible role of redondoviruses in respiratory infections in humans.
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26
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Rodríguez A, Duyvejonck H, Van Belleghem JD, Gryp T, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS One 2020; 15:e0229423. [PMID: 32084228 PMCID: PMC7034890 DOI: 10.1371/journal.pone.0229423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
RNA quality and quantity are important factors for ensuring the accuracy of gene expression analysis and other RNA-based downstream applications. Thus far, only a limited number of methodological studies have compared sample storage and RNA extraction procedures for human cells. We compared three commercially available RNA extraction kits, i.e., (NucliSENS) easyMAG, RNeasy (Mini Kit) and RiboPure (RNA Purification Kit–blood). In addition, additional conditions, such as storage medium and storage temperature of human peripheral blood mononuclear cells were evaluated, i.e., 4 °C for RNAlater or -80 °C for QIAzol and for the respective cognate lysis buffers; easyMAG, RNeasy or RiboPure. RNA was extracted from aliquots that had been stored for one day (Run 1) or 83 days (Run 2). After DNase treatment, quantity and quality of RNA were assessed by means of a NanoDrop spectrophotometer, 2100 Bioanalyzer and RT-qPCR for the ACTB reference gene. We observed that high-quality RNA can be obtained using RNeasy and RiboPure, regardless of the storage medium, whereas samples stored in RNAlater resulted in the least amount of RNA extracted. In addition, RiboPure combined with storage of samples in its cognate lysis buffer yielded twice as much RNA as all other procedures. These results were supported by RT-qPCR and by the reproducibility observed for two independent extraction runs.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Jonas D. Van Belleghem
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tessa Gryp
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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27
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Chen HL, Cheng JY, Yang YF, Li Y, Jiang XH, Yang L, Wu L, Shi M, Liu B, Duan J, Li X, Li QW. Phospholipase C inhibits apoptosis of porcine oocytes cultured in vitro. J Cell Biochem 2020; 121:3547-3559. [DOI: 10.1002/jcb.29636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Hua Li Chen
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Jian Yong Cheng
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - You Fu Yang
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Yuan Li
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Xiao Han Jiang
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Li Yang
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Lin Wu
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Meihong Shi
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Boyang Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Jiaxin Duan
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Xiaoya Li
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
| | - Qing Wang Li
- College of Animal Science and TechnologyNorthwest A&F UniversityYangling Shaanxi China
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28
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Jacob JJ, Veeraraghavan B, Vasudevan K. Metagenomic next-generation sequencing in clinical microbiology. Indian J Med Microbiol 2019; 37:133-140. [PMID: 31745012 DOI: 10.4103/ijmm.ijmm_19_401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
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29
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Chen L, Gu W, Liu C, Wang W, Li N, Chen Y, Lu C, Sun X, Han Y, Kuang D, Tong P, Dai J. Characteristics of the tree shrew gut virome. PLoS One 2019; 14:e0212774. [PMID: 30807598 PMCID: PMC6391014 DOI: 10.1371/journal.pone.0212774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
The tree shrew (Tupaia belangeri) has been proposed as an alternative laboratory animal to primates in biomedical research in recent years. However, characteristics of the tree shrew gut virome remain unclear. In this study, the metagenomic analysis method was used to identify the features of gut virome from fecal samples of this animal. Results showed that 5.80% of sequence reads in the libraries exhibited significant similarity to sequences deposited in the viral reference database (NCBI non-redundant nucleotide databases, viral protein databases and ACLAME database), and these reads were further classified into three major orders: Caudovirales (58.0%), Picornavirales (16.0%), and Herpesvirales (6.0%). Siphoviridae (46.0%), Myoviridae (45.0%), and Podoviridae (8.0%) comprised most Caudovirales. Picornaviridae (99.9%) and Herpesviridae (99.0%) were the primary families of Picornavirales and Herpesvirales, respectively. According to the host types and nucleic acid classifications, all of the related viruses in this study were divided into bacterial phage (61.83%), animal-specific virus (34.50%), plant-specific virus (0.09%), insect-specific virus (0.08%) and other viruses (3.50%). The dsDNA virus accounted for 51.13% of the total, followed by ssRNA (33.51%) and ssDNA virus (15.36%). This study provides an initial understanding of the community structure of the gut virome of tree shrew and a baseline for future tree shrew virus investigation.
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Affiliation(s)
- Linxia Chen
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- Department of Pathogenic Biology, School of Basic Medical Science, Gannan Medical University, Ganzhou, China
| | - Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Chenxiu Liu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Dexuan Kuang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- * E-mail:
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