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Tao L, Zhang X, Wang X, Ding J. Using molecular methods to delineate norovirus outbreaks: a systematic review. Arch Virol 2024; 169:16. [PMID: 38172375 DOI: 10.1007/s00705-023-05953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Noroviruses are among the major causative agents of human acute gastroenteritis, and the nature of norovirus outbreaks can differ considerably. The number of single-nucleotide polymorphisms (SNPs) between strains is used to assess their relationships. There is currently no universally accepted cutoff value for clustering strains that define an outbreak or linking the individuals involved. This study was conducted to estimate the threshold value of genomic variations among related strains within norovirus outbreaks. We carried out a literature search in the PubMed and Web of Science databases. SNP rates were defined as the number of SNPs/sequence length (bp) × 100%. The Mann-Whitney U-test was used in comparisons of the distribution of SNP rates for different sequence regions, genogroups (GI and GII), transmission routes, and sequencing methods. A total of 25 articles reporting on 108 norovirus outbreaks were included. In 99.1% of the outbreaks, the SNP rates were below 0.50%, and in 89.8%, the SNP rates were under 0.20%. Outbreak strains showed higher SNP rates when the P2 domain was used for sequence analysis (Z = -2.652, p = 0.008) and when an NGS method was used (Z = -3.686, p < 0.001). Outbreaks caused by different norovirus genotypes showed no significant difference in SNP rates. Compared with person-to-person outbreaks, SNP rates were lower in common-source outbreaks, but no significant difference was found when differences in sequencing methods were taken into consideraton. SNP rates under 0.20% and 0.50% could be considered as the rigorous and relaxed threshold, respectively, of strain similarity within a norovirus outbreak. More data are needed to evaluate differences within and between various norovirus outbreaks.
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Affiliation(s)
- Luqiu Tao
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xinyang Zhang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xuan Wang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China.
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China.
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2
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Chaimongkol N, Dábilla N, Tohma K, Matsushima Y, Yardley AB, Levenson EA, Johnson JA, Ahorrio C, Oler AJ, Kim DY, Souza M, Sosnovtsev SV, Parra GI, Green KY. Norovirus evolves as one or more distinct clonal populations in immunocompromised hosts. mBio 2023; 14:e0217723. [PMID: 37905910 PMCID: PMC10746188 DOI: 10.1128/mbio.02177-23] [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: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 11/02/2023] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis worldwide and can establish chronic infection in immunocompromised individuals. To investigate the mechanisms of norovirus evolution during chronic infection, we selected seven representative patients from a National Institutes of Health study cohort who sustained norovirus infection for periods ranging from 73 to 1,492 days. Six patients shed viruses belonging to a single genotype (GII.2[PNA], GII.4 New Orleans[P4], GII.4 Den Haag[P4], GII.3[P21], GII.6[P7], or GII.14[P7]) over the period examined, while one patient sequentially shed two genotypes (GII.6[P7] followed by GII.4 Sydney[P31]). Norovirus genomes from consecutive stool samples were sequenced at high resolution (>3,300 reads/nucleotide position) using the Illumina platform and subjected to bioinformatics analysis. Norovirus sequences could be resolved into one or more discrete clonal RNA genomes that persisted within these patients over time. Phylogenetic analyses inferred that clonal populations originated from a single founder virus and not by reinfection with community strains. Estimated evolutionary rates of clonal populations during persistent infection were similar to those of noroviruses from acute infection in the global database, suggesting that inherently higher RNA-dependent polymerase error rates were not associated with the ability to persist. The high-resolution analysis of norovirus diversity and evolution at the population level described here should allow a better understanding of adaptive mutations sustained during chronic infection. IMPORTANCE Noroviruses are an important cause of chronic diarrhea in patients with compromised immune systems. Presently, there are no effective therapies to clear the virus, which can persist for years in the intestinal tract. The goal of our study was to develop a better understanding of the norovirus strains that are associated with these long-term infections. With the remarkable diversity of norovirus strains detected in the immunocompromised patient cohort we studied, it appears that most, if not all, noroviruses circulating in nature may have the capacity to establish a chronic infection when a person is unable to mount an effective immune response. Our work is the most comprehensive genetic data set generated to date in which near full-length genomes from noroviruses associated with chronic infection were analyzed by high-resolution next-generation sequencing. Analysis of this data set led to our discovery that certain patients in our cohort were shedding noroviruses that could be subdivided into distinct haplotypes or populations of viruses that were co-evolving independently. The ability to track haplotypes of noroviruses during chronic infection will allow us to fine-tune our understanding of how the virus adapts and maintains itself in the human host, and how selective pressures such as antiviral drugs can affect these distinct populations.
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Affiliation(s)
- Natthawan Chaimongkol
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nathânia Dábilla
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kentaro Tohma
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yuki Matsushima
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison Behrle Yardley
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric A. Levenson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordan A. Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Courtney Ahorrio
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Y. Kim
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Menira Souza
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Stanislav V. Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel I. Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kim Y. Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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3
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Liu F, Lin J, Wang Q, Zhang Y, Shan H. Recovery of Recombinant Canine Distemper Virus That Expresses CPV-2a VP2: Uncovering the Mutation Profile of Recombinant Undergoing 50 Serial Passages In Vitro. Front Cell Infect Microbiol 2022; 11:770576. [PMID: 35096636 PMCID: PMC8795682 DOI: 10.3389/fcimb.2021.770576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Canine distemper and canine parvoviral enteritis are infections caused by the canine distemper virus (CDV) and canine parvovirus type 2 (CPV-2), respectively. They are two common infectious diseases that cause high morbidity and mortality in affected dogs. Combination vaccines have been broadly used to protect dogs from infections of CDV, CPV-2, and other viruses. VP2 is the most abundant protein of the CPV-2 capsid. It elicits potent immunity in animals and, therefore, is widely used for designing subunit antigen-based vaccines. In this study, we rescued a recombinant CDV (QN vaccine strain) using reverse genetics. The recombinant CDV (rCDV-VP2) was demonstrated to express stably the VP2 in cells for at least 33 serial passages in vitro. Unfortunately, a nonsense mutation was initially identified in the VP2 open reading frame (ORF) at passage-34 (P34) and gradually became predominant in rCDV-VP2 quasispecies with passaging. Neither test strip detection nor indirect immunofluorescence assay demonstrated the expression of the VP2 at P50. The P50 rCDV-VP2 was subjected to next-generation sequencing, which totally identified 17 single-nucleotide variations (SNVs), consisting of 11 transitions and 6 transversions. Out of the 17 SNVs, 1 and 9 were identified as nonsense and missense mutations, respectively. Since the nonsense mutation arose in the VP2 ORF as early as P34, an earlier rCDV-VP2 progeny should be selected for the vaccination of animals in future experiments.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Hu Shan, ; Fuxiao Liu,
| | - Jiahui Lin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Hu Shan, ; Fuxiao Liu,
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Jothikumar N, Cromeans T, Shivajothi J, Vinjé J, Murphy J. Development and evaluation of a ligation-free sequence-independent, single-primer amplification (LF-SISPA) assay for whole genome characterization of viruses. J Virol Methods 2022; 299:114346. [PMID: 34740706 PMCID: PMC11075090 DOI: 10.1016/j.jviromet.2021.114346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Molecular identification and characterization of novel or re-emerging infectious pathogens is critical for disease surveillance and outbreak investigations. Next generation sequencing (NGS) using Sequence-Independent, Single-Primer Amplification (SISPA) is being used extensively in sequencing of viral genomes but it requires an expensive library preparation step. We developed a simple, low-cost method that enriches nucleic acids followed by a ligation-free (LF) 2-step Polymerase Chain Reaction (PCR) procedure for library preparation. A pan-chimeric universal primer (JS15N14) containing 15 nucleotides with a random tetradecamer (14N) attached to the 3'-end was designed. The complimentary primer (JS15) was used for nucleic acid enrichment in a first round PCR. A second PCR was designed to create Illumina sequencer-compatible sequencing-ready libraries for NGS. The new LF-SISPA protocol was tested using six RNA and DNA viral genomes (10.8-229.4 kilobases, kb) from an ATCC virome nucleic acid mix (ATCC® MSA-1008™) followed by analysis using One Codex, an online identification tool. In addition, a human stool sample known to be positive for norovirus GII was sequenced, and de novo assembly was performed using the Genome Detective Virus Tool allowing for near complete genome identification in less than 24 h. The LF-SISPA method does not require prior knowledge of target sequences and does not require an expensive enzymatic library preparation kit, thereby providing a simple, fast, low-cost alternative for the identification of unknown viral pathogens.
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Affiliation(s)
- Narayanan Jothikumar
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Theresa Cromeans
- CDC Foundation, USA Contracted to Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | | | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jennifer Murphy
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
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5
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Tohma K, Saito M, Pajuelo MJ, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale. Emerg Microbes Infect 2021; 10:1717-1730. [PMID: 34376124 PMCID: PMC8425682 DOI: 10.1080/22221751.2021.1967706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/08/2021] [Indexed: 11/03/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis. Human noroviruses present >30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Monica J. Pajuelo
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cara J Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | | | - Robert H. Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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6
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Fuentes-Trillo A, Monzó C, Manzano I, Santiso-Bellón C, Andrade JDSRD, Gozalbo-Rovira R, García-García AB, Rodríguez-Díaz J, Chaves FJ. Benchmarking different approaches for Norovirus genome assembly in metagenome samples. BMC Genomics 2021; 22:849. [PMID: 34819031 PMCID: PMC8611953 DOI: 10.1186/s12864-021-08067-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/10/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. RESULTS Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. CONCLUSIONS Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.
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Affiliation(s)
- Azahara Fuentes-Trillo
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | - Carolina Monzó
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | - Iris Manzano
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | | | | | | | - Ana-Bárbara García-García
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain.
- Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Felipe Javier Chaves
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
- Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Sequencing Multiplex S.L., Valencia, Spain
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7
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Liu F, Wang N, Lin J, Wang Q, Huang Y, Zhang Y, Shan H. Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles. Front Cell Infect Microbiol 2021; 11:746926. [PMID: 34604118 PMCID: PMC8481889 DOI: 10.3389/fcimb.2021.746926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 02/05/2023] Open
Abstract
Due to lacking a proofreading mechanism in their RNA-dependent RNA polymerases (RdRp), RNA viruses generally possess high mutation frequencies, making them evolve rapidly to form viral quasispecies during serial passages in cells, especially treated with mutagens, like ribavirin. Canine distemper virus (CDV) belongs to the genus Morbillivirus. Its L protein functions as an RdRp during viral replication. In this study, a recombinant enhanced green fluorescence protein-tagged CDV (rCDV-eGFP) was rescued from its cDNA clone, followed by viral identification and characterization at passage-7 (P7). This recombinant was independently subjected to extra 40 serial passages (P8 to 47) in ribavirin- and non-treated cells. Two viral progenies, undergoing passages in ribavirin- and non-treated VDS cells, were named rCDV-eGFP-R and -N, respectively. Both progenies were simultaneously subjected to next-generation sequencing (NGS) at P47 for comparing their quasispecies diversities with each other. The rCDV-eGFP-R and -N showed 62 and 23 single-nucleotide mutations (SNMs) in individual antigenomes, respectively, suggesting that the ribavirin conferred a mutagenic effect on the rCDV-eGFP-R. The spectrum of 62 SNMs contained 26 missense and 36 silent mutations, and that of 23 SNMs was composed of 17 missense and 6 silent mutations. Neither the rCDV-eGFP-R nor -N exhibited nonsense mutation in individual antigenomes. We speculate that the rCDV-eGFP-R may contain at least one P47 sub-progeny characterized by high-fidelity replication in cells. If such a sub-progeny can be purified from the mutant swarm, its L protein would elucidate a molecular mechanism of CDV high-fidelity replication.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jiahui Lin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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8
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Noroviruses-The State of the Art, Nearly Fifty Years after Their Initial Discovery. Viruses 2021; 13:v13081541. [PMID: 34452406 PMCID: PMC8402810 DOI: 10.3390/v13081541] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022] Open
Abstract
Human noroviruses are recognised as the major global cause of viral gastroenteritis. Here, we provide an overview of notable advances in norovirus research and provide a short recap of the novel model systems to which much of the recent progress is owed. Significant advances include an updated classification system, the description of alternative virus-like protein morphologies and capsid dynamics, and the further elucidation of the functions and roles of various viral proteins. Important milestones include new insights into cell tropism, host and microbial attachment factors and receptors, interactions with the cellular translational apparatus, and viral egress from cells. Noroviruses have been detected in previously unrecognised hosts and detection itself is facilitated by improved analytical techniques. New potential transmission routes and/or viral reservoirs have been proposed. Recent in vivo and in vitro findings have added to the understanding of host immunity in response to norovirus infection, and vaccine development has progressed to preclinical and even clinical trial testing. Ongoing development of therapeutics includes promising direct-acting small molecules and host-factor drugs.
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9
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Liu F, Zou Y, Li L, Liu C, Wu X. Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells. Front Vet Sci 2021; 8:690204. [PMID: 34368277 PMCID: PMC8333274 DOI: 10.3389/fvets.2021.690204] [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: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
Small ruminant morbillivirus (SRMV), formerly known as peste-des-petits-ruminants virus, classified into the genus Morbillivirus in the family Paramyxoviridae. Its L protein functions as the RNA-dependent RNA polymerases (RdRp) during viral replication. Due to the absence of efficient proofreading activity in their RdRps, various RNA viruses reveal high mutation frequencies, making them evolve rapidly during serial passages in cells, especially treated with a certain mutagen, like ribavirin. We have previously rescued a recombinant enhanced green fluorescence protein-tagged SRMV (rSRMV-eGFP) using reverse genetics. In this study, the rSRMV-eGFP was subjected to serial passages in ribavirin-treated cells. Due to the ribavirin-exerted selective pressure, it was speculated that viral progenies would form quasispecies after dozens of passages. Viral progenies at passage-10, -20, -30, -40, and -50 were separately subjected to next-generation sequencing (NGS), consequently revealing a total of 34 single-nucleotide variations, including five synonymous, 21 missense, and one non-sense mutations. The L sequence was found to harbor eight missense mutations during serial passaging. It was speculated that at least one high-fidelity variant was present in viral quasispecies at passage-50. If purified from the population of viral progenies, this putative variant would contribute to clarifying a molecular mechanism in viral high-fidelity replication in vitro.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yanli Zou
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
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10
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Makhaola K, Moyo S, Kebaabetswe LP. Next generation sequencing of near-full length genome of norovirus GII.4 from Botswana. Virus Res 2021; 302:198491. [PMID: 34147552 DOI: 10.1016/j.virusres.2021.198491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Noroviruses are highly diverse, with genotype GII.4 causing most epidemics. This study aimed to investigate the evolutionary dynamics of norovirus genogroup GII strains among acutely infected children under 5 years in Botswana, between 2016 and 2018. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to amplify the whole norovirus genome, followed by next-generation sequencing using Oxford Nanopore technology. Twelve samples were successfully analyzed, with 11 identified as norovirus GII.4 Sydney [P31] and one as GII.4 Sydney [P13]. This study generated the first near-full length norovirus sequences in Botswana (93-95% coverage). Our results show that the norovirus GII.4 strains circulating in Botswana are under evolution through recombination and antigenic drift. Recombination in the GII.4 Sydney [P31] and GII.4 Sydney [P13] strains occurred in the ORF1/ORF2 junction and within ORF1, respectively. This study provides the first description of the GII.4 Sydney [P13] recombinant. Amino acid variation in the immunogenic sites was analyzed. Mutations in epitope A correlate with the emergence of novel norovirus GII.4 strains with altered antigenicity. In this study, we identified 43 unique amino acid substitutions in the VP1 region, with six occurring in epitopes, A (G295N, and E368Q) and E (S40T, N412D, N412K and T413H). The shell subdomain of the GII.4 Sydney [P13] variant was closely related to norovirus GII.17. Lastly, we also observed several mutations in the T cell restricted epitopes of both strains. Our study has made a novel contribution to understanding the evolution of norovirus GII.4 in Botswana.
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Affiliation(s)
- Kgomotso Makhaola
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, MA, Boston, United States
| | - Lemme P Kebaabetswe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana.
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11
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Walker FC, Hassan E, Peterson ST, Rodgers R, Schriefer LA, Thompson CE, Li Y, Kalugotla G, Blum-Johnston C, Lawrence D, McCune BT, Graziano VR, Lushniak L, Lee S, Roth AN, Karst SM, Nice TJ, Miner JJ, Wilen CB, Baldridge MT. Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid. PLoS Pathog 2021; 17:e1009402. [PMID: 33705489 PMCID: PMC7987144 DOI: 10.1371/journal.ppat.1009402] [Citation(s) in RCA: 7] [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: 10/01/2020] [Revised: 03/23/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Interferons (IFNs) are key controllers of viral replication, with intact IFN responses suppressing virus growth and spread. Using the murine norovirus (MNoV) system, we show that IFNs exert selective pressure to limit the pathogenic evolutionary potential of this enteric virus. In animals lacking type I IFN signaling, the nonlethal MNoV strain CR6 rapidly acquired enhanced virulence via conversion of a single nucleotide. This nucleotide change resulted in amino acid substitution F514I in the viral capsid, which led to >10,000-fold higher replication in systemic organs including the brain. Pathogenicity was mediated by enhanced recruitment and infection of intestinal myeloid cells and increased extraintestinal dissemination of virus. Interestingly, the trade-off for this mutation was reduced fitness in an IFN-competent host, in which CR6 bearing F514I exhibited decreased intestinal replication and shedding. In an immunodeficient context, a spontaneous amino acid change can thus convert a relatively avirulent viral strain into a lethal pathogen.
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Affiliation(s)
- Forrest C. Walker
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stefan T. Peterson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rachel Rodgers
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lawrence A. Schriefer
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cassandra E. Thompson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gowri Kalugotla
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Carla Blum-Johnston
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Dylan Lawrence
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Broc T. McCune
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Vincent R. Graziano
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Larissa Lushniak
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanghyun Lee
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alexa N. Roth
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Stephanie M. Karst
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Timothy J. Nice
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jonathan J. Miner
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Craig B. Wilen
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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12
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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13
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Kelly D, Jere KC, Darby AC, Allen DJ, Iturriza-Gómara M. Complete genome characterization of human noroviruses allows comparison of minor alleles during acute and chronic infections. Access Microbiol 2021; 3:000203. [PMID: 34151158 PMCID: PMC8209700 DOI: 10.1099/acmi.0.000203] [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: 11/23/2020] [Accepted: 01/24/2021] [Indexed: 11/18/2022] Open
Abstract
Human noroviruses (HuNoVs) circulate globally, affect all age groups and place a substantial burden upon health services. High genetic diversity leading to antigenic variation plays a significant role in HuNoV epidemiology, driving periodic global emergence of epidemic variants. Studies have suggested that immunocompromised individuals may be a reservoir for such epidemic variants, but studies investigating the diversity and emergence of HuNoV variants in immunocompetent individuals are underrepresented. To address this, we sequenced the genomes of HuNoVs present in samples collected longitudinally from one immunocompetent (acute infection) and one immunocompromised (chronic infection) patient. A broadly reactive HuNoV capture-based method was used to concentrate the virus present in these specimens prior to massively parallel sequencing to recover near complete viral genomes. Using a novel bioinformatics pipeline, we demonstrated that persistent minor alleles were present in both acute and chronic infections, and that minor allele frequencies represented a larger proportion of the population during chronic infection. In acute infection, minor alleles were more evenly spread across the genome, although present at much lower frequencies, and therefore difficult to discern from error. By contrast, in the chronic infection, more minor alleles were present in the minor structural protein. No non-synonymous minor alleles were detected in the major structural protein over the short sampling period of the HuNoV chronic infection, suggesting where immune pressure is variable or non-existent, epidemic variants could emerge over longer periods of infection by random chance.
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Affiliation(s)
- Daniel Kelly
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Present address: Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Khuzwayo C Jere
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Malawi-Liverpool Wellcome Trust - Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Alistair C Darby
- Centre of Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - David J Allen
- Department of Pathogen Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Virus Reference Department, National Infections Service, Public Health England, Colindale, London, UK.,NIHR Health Protection Research Unit Gastrointestinal Infections, Liverpool, UK
| | - Miren Iturriza-Gómara
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit Gastrointestinal Infections, Liverpool, UK
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14
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Rescue of Senecavirus A to uncover mutation profiles of its progenies during 80 serial passages in vitro. Vet Microbiol 2020; 253:108969. [PMID: 33450657 DOI: 10.1016/j.vetmic.2020.108969] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. In this study, a China SVA isolate (CH-LX-01-2016) was rescued from its cDNA clone, and then identified by RT-PCR, indirect immunofluorescence assay and mass spectrometry. The rescued SVA could separately induce typical plaque formations and cytopathic effects in cell monolayers. In order to uncover its evolutionary dynamics, the SVA was subjected to eighty serial passages in vitro. Its progenies per ten passages were analyzed by next-generation sequencing (NGS). The NGS analyses showed that neither sequence-deleting nor -inserting phenotype was detectable in eight progenies, within which a total of forty-one intra-host single-nucleotide variations (SNVs) arose with passaging. Almost all SNVs were identified as the single-nucleotide polymorphism with mixture of two nucleotides. SNVs led to eighteen nonsynonymous mutations, out of which sixteen could directly reflect their own frequencies of amino acid mutation, due to only one SNV occurring in their individual codons. Compared with its parental virus without passaging, the passage-80 SVA progeny had formed a viral quasispecies, as evidenced by a total of twenty-eight SNVs identified in it.
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15
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Socha W, Sztromwasser P, Dunowska M, Jaklinska B, Rola J. Spread of equine arteritis virus among Hucul horses with different EqCXCL16 genotypes and analysis of viral quasispecies from semen of selected stallions. Sci Rep 2020; 10:2909. [PMID: 32076048 PMCID: PMC7031528 DOI: 10.1038/s41598-020-59870-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Equine arteritis virus (EAV) is maintained in the horse populations through persistently infected stallions. The aims of the study were to monitor the spread of EAV among Polish Hucul horses, to analyse the variability of circulating EAVs both between- and within-horses, and to identify allelic variants of the serving stallions EqCXCL16 gene that had been previously shown to strongly correlate with long-term EAV persistence in stallions. Serum samples (n = 221) from 62 horses including 46 mares and 16 stallions were collected on routine basis between December 2010 and May 2013 and tested for EAV antibodies. In addition, semen from 11 stallions was tested for EAV RNA. A full genomic sequence of EAV from selected breeding stallions was determined using next generation sequencing. The proportion of seropositive mares among the tested population increased from 7% to 92% during the study period, while the proportion of seropositive stallions remained similar (64 to 71%). The EAV genomes from different stallions were 94.7% to 99.6% identical to each other. A number (41 to 310) of single nucleotide variants were identified within EAV sequences from infected stallions. Four stallions possessed EqCXCL16S genotype correlated with development of long-term carrier status, three of which were persistent shedders and the shedder status of the remaining one was undetermined. None of the remaining 12 stallions with EqCXCL16R genotype was identified as a persistent shedder.
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Affiliation(s)
- Wojciech Socha
- National Veterinary Research Institute, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Pawel Sztromwasser
- National Veterinary Research Institute, Al. Partyzantow 57, 24-100, Pulawy, Poland.,Medical University of Lodz, Al. Kosciuszki 4, 90-419, Lodz, Poland
| | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Barbara Jaklinska
- Hucul Horse Stud Gladyszow, Regietow 28, 38-315, Uscie Gorlickie, Poland
| | - Jerzy Rola
- National Veterinary Research Institute, Al. Partyzantow 57, 24-100, Pulawy, Poland.
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16
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Zhao L, Duffy S. Gauging genetic diversity of generalists: A test of genetic and ecological generalism with RNA virus experimental evolution. Virus Evol 2019; 5:vez019. [PMID: 31275611 PMCID: PMC6599687 DOI: 10.1093/ve/vez019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Generalist viruses, those with a comparatively larger host range, are considered more likely to emerge on new hosts. The potential to emerge in new hosts has been linked to viral genetic diversity, a measure of evolvability. However, there is no consensus on whether infecting a larger number of hosts leads to higher genetic diversity, or whether diversity is better maintained in a homogeneous environment, similar to the lifestyle of a specialist virus. Using experimental evolution with the RNA bacteriophage phi6, we directly tested whether genetic generalism (carrying an expanded host range mutation) or environmental generalism (growing on heterogeneous hosts) leads to viral populations with more genetic variation. Sixteen evolved viral lineages were deep sequenced to provide genetic evidence for population diversity. When evolved on a single host, specialist and generalist genotypes both maintained the same level of diversity (measured by the number of single nucleotide polymorphisms (SNPs) above 1%, P = 0.81). However, the generalist genotype evolved on a single host had higher SNP levels than generalist lineages under two heterogeneous host passaging schemes (P = 0.001, P < 0.001). RNA viruses’ response to selection in alternating hosts reduces standing genetic diversity compared to those evolving in a single host to which the virus is already well-adapted.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
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17
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van Beek J, de Graaf M, Smits S, Schapendonk CME, Verjans GMGM, Vennema H, van der Eijk AA, Phan MVT, Cotten M, Koopmans M. Whole-Genome Next-Generation Sequencing to Study Within-Host Evolution of Norovirus (NoV) Among Immunocompromised Patients With Chronic NoV Infection. J Infect Dis 2019; 216:1513-1524. [PMID: 29029115 DOI: 10.1093/infdis/jix520] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/22/2017] [Indexed: 01/29/2023] Open
Abstract
Background The genus Norovirus comprises large genetic diversity, and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods Sixty-five fecal samples from 16 immunocompromised patients were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform. Results Patients shed virus for average 352 days (range, 76-716 days). Phylogenetic analysis showed distinct GII.4 variants in 3 of 13 patients (23%). The viral mutation rates were variable between patients but did not differ between various immune status groups. All within-host GII.4 viral populations showed amino acid changes at blocking epitopes over time, and the majority of VP1 amino acid mutations were located at the capsid surface. Conclusions This study found viruses in immunocompromised hosts that are genetically distinct from viruses circulating in the general population, and these patients therefore may contain a reservoir for newly emerging strains. Future studies need to determine whether these new strains are of risk to other immunocompromised patients and the general population.
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Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Saskia Smits
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Viroclinics Biosciences, Rotterdam, Bilthoven, the Netherlands
| | | | | | - Harry Vennema
- Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
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18
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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19
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Petronella N, Ronholm J, Suresh M, Harlow J, Mykytczuk O, Corneau N, Bidawid S, Nasheri N. Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique. BMC Infect Dis 2018; 18:521. [PMID: 30333011 PMCID: PMC6191920 DOI: 10.1186/s12879-018-3419-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples. RESULTS Herein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples. CONCLUSIONS Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses.
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Affiliation(s)
- Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, Ottawa, ON, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada.,Department of Animal Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
| | - Menka Suresh
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Jennifer Harlow
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Oksana Mykytczuk
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Nathalie Corneau
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Sabah Bidawid
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
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20
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Pietsch C, Ennuschat N, Härtel S, Liebert UG. Within-host evolution of virus variants during chronic infection with novel GII.P26-GII.26 norovirus. J Clin Virol 2018; 108:96-102. [PMID: 30268000 DOI: 10.1016/j.jcv.2018.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/29/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Noroviruses are a leading cause of acute gastroenteritis in all age groups. They generally cause a rapidly self-limiting illness. However, chronic norovirus diarrheal disease occurs in immunocompromised individuals, and is accompanied by persistent shedding of infectious norovirus in stool. OBJECTIVES The study aims to characterize a novel GII.P26-GII.26 norovirus strain. Furthermore, it analyses viral mutations arising during chronic infection of an immunocompromised host. STUDY DESIGN Over the course of more than three years, stool samples were obtained from an immunocompromised patient and screened for the presence of norovirus RNA by real-time PCR and norovirus antigen by immunoassay. Viral population kinetics was analyzed by conventional and high-throughput-sequencing. RESULTS Real-time PCR yielded high amounts of norovirus RNA in the stool, but antigen immunoassays failed to detect the virus. The near complete norovirus genome was assigned as novel GII.P26-GII.26 genotype. Conventional as well as high-throughput sequencing pointed to a heterogeneous viral population with low rates of non-synonymous substitutions. Within-host evolution was enhanced in non-structural protein p22 and the N-terminal arm of the capsid protein VP1 but reduced in the viral polymerase RdRp. Intermittent non-synonymous substitutions in the protruding domain of the VP1 reverted fully over time. CONCLUSIONS Confirmation of novel GII.P26-GII.26 norovirus genotypes provides insight into norovirus genetic diversity. The study further illustrates norovirus infection as an important differential diagnosis of recurrent persistent diarrhea in immunocompromised patients. The provided data on within-host evolution contribute to the insight of the mechanisms of viral persistence and pathogenesis in chronic norovirus infections.
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Affiliation(s)
- Corinna Pietsch
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Nora Ennuschat
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Sabine Härtel
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, Leipzig, Germany.
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21
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Oshiki M, Miura T, Kazama S, Segawa T, Ishii S, Hatamoto M, Yamaguchi T, Kubota K, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Kobayashi N, Araki N, Sano D. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters. Front Microbiol 2018; 9:830. [PMID: 29755444 PMCID: PMC5934477 DOI: 10.3389/fmicb.2018.00830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023] Open
Abstract
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan); genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Shinobu Kazama
- Center for Simulation Sciences and Informational Biology, Ochanomizu University, Bunkyô, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Kofu, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, Minneapolis, MN, United States
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
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22
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Nasheri N, Petronella N, Ronholm J, Bidawid S, Corneau N. Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach. Front Microbiol 2017; 8:73. [PMID: 28197136 PMCID: PMC5282449 DOI: 10.3389/fmicb.2017.00073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/11/2017] [Indexed: 01/14/2023] Open
Abstract
Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens.
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Affiliation(s)
- Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada
| | - Sabah Bidawid
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nathalie Corneau
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
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23
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Mauroy A, Taminiau B, Nezer C, Ghurburrun E, Baurain D, Daube G, Thiry E. High-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication. Arch Virol 2016; 162:1019-1023. [PMID: 27942973 DOI: 10.1007/s00705-016-3179-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/16/2016] [Indexed: 01/27/2023]
Abstract
In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in genomic regions encompassing partial coding sequences for non-structural (NS) 1-2, NS5, NS6, NS7 proteins within open reading frame (ORF) 1. In a region encoding a portion of the major capsid protein (VP1) within ORF2 (also including the ORF4 region) and a portion of the minor structural protein (VP2), the mutation rates were estimated to be at least one order of magnitude higher. The VP2 coding region was found to have the highest mutation rate.
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Affiliation(s)
- Axel Mauroy
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animal & Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Bernard Taminiau
- Food Microbiology, Fundamental and Applied Research for Animal & Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | | | - Elsa Ghurburrun
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animal & Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Denis Baurain
- Eukaryotic Phylogenomics, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Georges Daube
- Food Microbiology, Fundamental and Applied Research for Animal & Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animal & Health Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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24
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Cotten M, Koopmans M. Next-generation sequencing and norovirus. Future Virol 2016; 11:719-722. [PMID: 28757893 DOI: 10.2217/fvl-2016-0099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew Cotten
- Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marion Koopmans
- Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
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