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Sobel Leonard A, Mendoza L, McFarland AG, Marques AD, Everett JK, Moncla L, Bushman FD, Odom John AR, Hensley SE. Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status. Virus Evol 2024; 10:veae034. [PMID: 38859985 PMCID: PMC11163376 DOI: 10.1093/ve/veae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at antigenic sites. Because of antigenic drift, influenza vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite the high levels of viral diversity observed across populations, most human studies reveal limited intrahost diversity, leaving the origin of population-level viral diversity unclear. Previous studies show host characteristics, such as immunity, might affect within-host viral evolution. Here we investigate influenza A viral diversity in children aged between 6 months and 18 years. Influenza virus evolution in children is less well characterized than in adults, yet may be associated with higher levels of viral diversity given the lower level of pre-existing immunity and longer durations of infection in children. We obtained influenza isolates from banked influenza A-positive nasopharyngeal swabs collected at the Children's Hospital of Philadelphia during the 2017-18 influenza season. Using next-generation sequencing, we evaluated the population of influenza viruses present in each sample. We characterized within-host viral diversity using the number and frequency of intrahost single-nucleotide variants (iSNVs) detected in each sample. We related viral diversity to clinical metadata, including subjects' age, vaccination status, and comorbid conditions, as well as sample metadata such as virus strain and cycle threshold. Consistent with previous studies, most samples contained low levels of diversity with no clear association between the subjects' age, vaccine status, or health status. Further, there was no enrichment of iSNVs near known antigenic sites. Taken together, these findings are consistent with previous observations that the majority of intrahost influenza virus infection is characterized by low viral diversity without evidence of diversifying selection.
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Affiliation(s)
- Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Lydia Mendoza
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Alexander G McFarland
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Andrew D Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - John K Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Louise Moncla
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
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Connor R, Shakya M, Yarmosh DA, Maier W, Martin R, Bradford R, Brister JR, Chain PSG, Copeland CA, di Iulio J, Hu B, Ebert P, Gunti J, Jin Y, Katz KS, Kochergin A, LaRosa T, Li J, Li PE, Lo CC, Rashid S, Maiorova ES, Xiao C, Zalunin V, Purcell L, Pruitt KD. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 2024; 16:430. [PMID: 38543795 PMCID: PMC10975397 DOI: 10.3390/v16030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 04/01/2024] Open
Abstract
Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.
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Affiliation(s)
- Ryan Connor
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - David A. Yarmosh
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
- BEI Resources, Manassas, VA 20110, USA
| | - Wolfgang Maier
- Galaxy Europe Team, University of Freiburg, 79085 Freiburg, Germany;
| | - Ross Martin
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Rebecca Bradford
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
- BEI Resources, Manassas, VA 20110, USA
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | | | - Julia di Iulio
- Vir Biotechnology Inc., San Francisco, CA 94158, USA; (J.d.I.); (L.P.)
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Philip Ebert
- Eli Lilly and Company, Indianapolis, IN 46225, USA;
| | - Jonathan Gunti
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Yumi Jin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Kenneth S. Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Andrey Kochergin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Tré LaRosa
- Deloitte Consulting LLP, Rosslyn, VA 22209, USA; (C.A.C.); (T.L.)
| | - Jiani Li
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Sujatha Rashid
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
| | - Evguenia S. Maiorova
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Vadim Zalunin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Lisa Purcell
- Vir Biotechnology Inc., San Francisco, CA 94158, USA; (J.d.I.); (L.P.)
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
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3
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Makhsous N, Goya S, Avendaño CC, Rupp J, Kuypers J, Jerome KR, Boeckh M, Waghmare A, Greninger AL. Within-Host Rhinovirus Evolution in Upper and Lower Respiratory Tract Highlights Capsid Variability and Mutation-Independent Compartmentalization. J Infect Dis 2024; 229:403-412. [PMID: 37486790 PMCID: PMC10873175 DOI: 10.1093/infdis/jiad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Rhinovirus (RV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how RV evolves within hosts during infection. METHODS We sequenced RV complete genomes from 12 hematopoietic cell transplant patients with infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL). Metagenomic and amplicon next-generation sequencing were used to track the emergence and evolution of intrahost single nucleotide variants (iSNVs). RESULTS Identical RV intrahost populations in matched NW and BAL specimens indicated no genetic adaptation is required for RV to progress from URT to LRT. Coding iSNVs were 2.3-fold more prevalent in capsid over nonstructural genes. iSNVs modeled were significantly more likely to be found in capsid surface residues, but were not preferentially located in known RV-neutralizing antibody epitopes. Newly emergent, genotype-matched iSNV haplotypes from immunocompromised individuals in 2008-2010 could be detected in Seattle-area community RV sequences in 2020-2021. CONCLUSIONS RV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, RV sequences.
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Affiliation(s)
- Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Stephanie Goya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Carlos C Avendaño
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Jason Rupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Jane Kuypers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Department of Pediatrics, University of Washington, Seattle, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
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4
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Mishra SK, Nelson CW, Zhu B, Pinheiro M, Lee HJ, Dean M, Burdett L, Yeager M, Mirabello L. Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus Evol 2024; 10:veae013. [PMID: 38455683 PMCID: PMC10919477 DOI: 10.1093/ve/veae013] [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: 09/27/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.
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Affiliation(s)
- Sambit K Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Hyo Jung Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
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5
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Torres Ortiz A, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife 2023; 12:e84384. [PMID: 37732733 PMCID: PMC10602588 DOI: 10.7554/elife.84384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low-frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infectious Diseases, Imperial College LondonLondonUnited Kingdom
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Michelle Kendall
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - James Hatcher
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | | | | | | | - Xavier Didelot
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
- Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS TrustLondonUnited Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
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6
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Chung M, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lässig M, Luksza M, Das S, Gresham D, Ghedin E. Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data. mBio 2023; 14:e0104623. [PMID: 37389439 PMCID: PMC10470513 DOI: 10.1128/mbio.01046-23] [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: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023] Open
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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Affiliation(s)
- A. E. Roder
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - K. E. E. Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Knoll
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Khalfan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - B. Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - S. Schultz-Cherry
- Department of Infectious Diseases, St Jude Children Research Hospital, Memphis, Tennessee, USA
| | - S. Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - A. Kreitman
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - C. Mederos
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - J.-H. Youn
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - R. Mercado
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - W. Wang
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - M. Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - D. Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. I. Samanovic
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. J. Mulligan
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - S. Das
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - D. Gresham
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - E. Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
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7
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Makhsous N, Goya S, Avendaño C, Rupp J, Kuypers J, Jerome KR, Boeckh M, Waghmare A, Greninger AL. Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540440. [PMID: 37214809 PMCID: PMC10197658 DOI: 10.1101/2023.05.11.540440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Human rhinovirus (HRV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how HRV evolves within hosts during infection. Methods We sequenced HRV complete genomes from 12 hematopoietic cell transplant patients with prolonged infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL) specimens. Metagenomic (mNGS) and amplicon-based NGS were used to study the emergence and evolution of intra-host single nucleotide variants (iSNVs). Results Identical HRV intra-host populations in matched NW and BAL specimens indicated no genetic adaptation is required for HRV to progress from URT to LRT. Microbial composition between matched NW and BAL confirmed no cross-contamination during sampling procedure. Coding iSNVs were 2.3-fold more prevalent in capsid over non-structural genes, adjusted for length. iSNVs modeled onto HRV capsid structures were significantly more likely to be found in surface residues, but were not preferentially located in known HRV neutralizing antibody epitopes. Newly emergent, serotype-matched iSNV haplotypes from immunocompromised individuals from 2008-2010 could be detected in Seattle-area community HRV sequences from 2020-2021. Conclusion HRV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, HRV sequences.
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Affiliation(s)
- Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Stephanie Goya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Carlos Avendaño
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Jason Rupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Jane Kuypers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
- Department of Medicine, University of Washington, Seattle, 98102, USA
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, 98105, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
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8
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Cereghino C, Roesch F, Carrau L, Hardy A, Ribeiro-Filho HV, Henrion-Lacritick A, Koh C, Marano JM, Bates TA, Rai P, Chuong C, Akter S, Vallet T, Blanc H, Elliott TJ, Brown AM, Michalak P, LeRoith T, Bloom JD, Marques RE, Saleh MC, Vignuzzi M, Weger-Lucarelli J. The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito. PLoS Pathog 2023; 19:e1010491. [PMID: 37018377 PMCID: PMC10109513 DOI: 10.1371/journal.ppat.1010491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/17/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Adaptation to mosquito vectors suited for transmission in urban settings is a major driver in the emergence of arboviruses. To better anticipate future emergence events, it is crucial to assess their potential to adapt to new vector hosts. In this work, we used two different experimental evolution approaches to study the adaptation process of an emerging alphavirus, Mayaro virus (MAYV), to Ae. aegypti, an urban mosquito vector of many other arboviruses. We identified E2-T179N as a key mutation increasing MAYV replication in insect cells and enhancing transmission after escaping the midgut of live Ae. aegypti. In contrast, this mutation decreased viral replication and binding in human fibroblasts, a primary cellular target of MAYV in humans. We also showed that MAYV E2-T179N generates reduced viremia and displays less severe tissue pathology in vivo in a mouse model. We found evidence in mouse fibroblasts that MAYV E2-T179N is less dependent on the Mxra8 receptor for replication than WT MAYV. Similarly, exogenous expression of human apolipoprotein receptor 2 and Mxra8 enhanced WT MAYV replication compared to MAYV E2-T179N. When this mutation was introduced in the closely related chikungunya virus, which has caused major outbreaks globally in the past two decades, we observed increased replication in both human and insect cells, suggesting E2 position 179 is an important determinant of alphavirus host-adaptation, although in a virus-specific manner. Collectively, these results indicate that adaptation at the T179 residue in MAYV E2 may result in increased vector competence-but coming at the cost of optimal replication in humans-and may represent a first step towards a future emergence event.
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Affiliation(s)
- Chelsea Cereghino
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Ferdinand Roesch
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
- UMR 1282 ISP, INRAE Centre Val de Loire, Nouzilly, France
| | - Lucía Carrau
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
- Department of Microbiology, New York University Langone Medical Center, New York, New York, United States of America
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Helder V. Ribeiro-Filho
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Annabelle Henrion-Lacritick
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Cassandra Koh
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Jeffrey M. Marano
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, Virginia, United States of America
| | - Tyler A. Bates
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Christina Chuong
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Bioinformatics and Computational Biology, School of Systems Biology, George Mason University, Fairfax, Virginia, United States of America
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Hervé Blanc
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Truitt J. Elliott
- Program in Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, Virginia, United States of America
- Research and Informatics, University Libraries, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Anne M. Brown
- Program in Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, Virginia, United States of America
| | - Pawel Michalak
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
- Edward Via College of Osteopathic Medicine, Monroe, Louisiana, United States of America
- Center for One Health Research, VA-MD Regional College of Veterinary Medicine, Blacksburg, Virginia, Untied States of Ameria
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
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9
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Fitzmeyer EA, Gallichotte EN, Ebel GD. Scanning barcodes: A way to explore viral populations. PLoS Pathog 2023; 19:e1011291. [PMID: 37079527 PMCID: PMC10118115 DOI: 10.1371/journal.ppat.1011291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Affiliation(s)
- Emily A. Fitzmeyer
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Emily N. Gallichotte
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gregory D. Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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10
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Sun B, Ni M, Liu H, Liu D. Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro. Virus Evol 2023; 9:veac103. [PMID: 37205166 PMCID: PMC10185921 DOI: 10.1093/ve/veac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/04/2022] [Accepted: 03/21/2023] [Indexed: 12/02/2023] Open
Abstract
Analyses of viral inter- and intra-host mutations could better guide the prevention and control of infectious diseases. For a long time, studies on viral evolution have focused on viral inter-host variations. Next-generation sequencing has accelerated the investigations of viral intra-host diversity. However, the theoretical basis and dynamic characteristics of viral intra-host mutations remain unknown. Here, using serial passages of the SA14-14-2 vaccine strain of Japanese encephalitis virus (JEV) as the in vitro model, the distribution characteristics of 1,788 detected intra-host single-nucleotide variations (iSNVs) and their mutated frequencies from 477 deep-sequenced samples were analyzed. Our results revealed that in adaptive (baby hamster kidney (BHK)) cells, JEV is under a nearly neutral selection pressure, and both non-synonymous and synonymous mutations represent an S-shaped growth trend over time. A higher positive selection pressure was observed in the nonadaptive (C6/36) cells, and logarithmic growth in non-synonymous iSNVs and linear growth in synonymous iSNVs were observed over time. Moreover, the mutation rates of the NS4B protein and the untranslated region (UTR) of the JEV are significantly different between BHK and C6/36 cells, suggesting that viral selection pressure is regulated by different cellular environments. In addition, no significant difference was detected in the distribution of mutated frequencies of iSNVs between BHK and C6/36 cells.
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Affiliation(s)
- Bangyao Sun
- School of Medical Laboratory, Weifang Medical University, Baotong West Street, Weifang 261053, China
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Taiping Road 27#, Beijing 100850, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
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11
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Highly pathogenic avian influenza A (H5N1) virus infections in wild carnivores connected to mass mortalities of pheasants in Finland. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105423. [PMID: 36889484 DOI: 10.1016/j.meegid.2023.105423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
Highly pathogenic avian influenza (HPAI) has caused widespread mortality in both wild and domestic birds in Europe during 2020-2022. Virus types H5N8 and H5N1 have dominated the epidemic. Isolated spill-over infections in mammals started to emerge as the epidemic continued. In autumn 2021, HPAI H5N1 caused a series of mass mortality events in farmed and released pheasants (Phasianus colchicus) in a restricted area in southern Finland. Later, in the same area, an otter (Lutra lutra), two red foxes (Vulpes vulpes) and a lynx (Lynx lynx) were found moribund or dead and infected with H5N1 HPAI virus. Phylogenetically, H5N1 strains from pheasants and mammals clustered together. Molecular analyses of the four mammalian virus strains revealed mutations in the PB2 gene segment (PB2-E627K and PB2-D701N) that are known to facilitate viral replication in mammals. This study revealed that avian influenza cases in mammals were spatially and temporally connected with avian mass mortalities suggesting increased infection pressure from birds to mammals.
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12
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Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance. Viruses 2023; 15:v15020477. [PMID: 36851690 PMCID: PMC9961268 DOI: 10.3390/v15020477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/04/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.
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13
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Braun KM, Haddock III LA, Crooks CM, Barry GL, Lalli J, Neumann G, Watanabe T, Imai M, Yamayoshi S, Ito M, Moncla LH, Koelle K, Kawaoka Y, Friedrich TC. Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals. Virus Evol 2023; 9:vead004. [PMID: 36814938 PMCID: PMC9939568 DOI: 10.1093/ve/vead004] [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: 05/13/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
H7N9 avian influenza viruses (AIVs) have caused over 1,500 documented human infections since emerging in 2013. Although wild-type H7N9 AIVs can be transmitted by respiratory droplets in ferrets, they have not yet caused widespread outbreaks in humans. Previous studies have revealed molecular determinants of H7N9 AIV host switching, but little is known about potential evolutionary constraints on this process. Here, we compare patterns of sequence evolution for H7N9 AIV and mammalian H1N1 viruses during replication and transmission in ferrets. We show that three main factors-purifying selection, stochasticity, and very narrow transmission bottlenecks-combine to severely constrain the ability of H7N9 AIV to effectively adapt to mammalian hosts in isolated, acute spillover events. We find rare evidence of natural selection favoring new, potentially mammal-adapting mutations within ferrets but no evidence of natural selection acting during transmission. We conclude that human-adapted H7N9 viruses are unlikely to emerge during typical spillover infections. Our findings are instead consistent with a model in which the emergence of a human-transmissible virus would be a rare and unpredictable, though highly consequential, 'jackpot' event. Strategies to control the total number of spillover infections will limit opportunities for the virus to win this evolutionary lottery.
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Affiliation(s)
| | | | - Chelsea M Crooks
- AIDS Vaccine Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 585 Science Dr. Madison, WI 53711, USA
| | - Gabrielle L Barry
- AIDS Vaccine Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 585 Science Dr. Madison, WI 53711, USA
| | - Joseph Lalli
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall Madison, WI 53706, US
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 575 Science Dr. Madison, WI 53711, USA
| | - Tokiko Watanabe
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka Suita City, Osaka 565-0871, Japan,Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-8 Yamadaoka Suita City, Osaka 565-0871, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1 Chome-21-1 Toyama Shinjuku City, Tokyo 162-8655, Japan
| | | | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan
| | | | | | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, 575 Science Dr. Madison, WI 53711, USA,Division of Virology, Institute of Medical Science, University of Tokyo, 4 Chome-6-1 Shirokanedai Minato City, Tokyo 108-0071, Japan,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1 Chome-21-1 Toyama Shinjuku City, Tokyo 162-8655, Japan
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14
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Walter KS, Kim E, Verma R, Altamirano J, Leary S, Carrington YJ, Jagannathan P, Singh U, Holubar M, Subramanian A, Khosla C, Maldonado Y, Andrews JR. Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference. Open Forum Infect Dis 2023; 10:ofad001. [PMID: 36751652 PMCID: PMC9898879 DOI: 10.1093/ofid/ofad001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023] Open
Abstract
Background The limited variation observed among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference. Methods We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage. Results Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0-40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02-1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28-.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23-1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants. Conclusions Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.
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Affiliation(s)
- Katharine S Walter
- Correspondence: Katharine S. Walter, PhD, Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City, UT 84108, USA ()
| | - Eugene Kim
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Renu Verma
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan Altamirano
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - Sean Leary
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Yuan J Carrington
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Prasanna Jagannathan
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Aruna Subramanian
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Chaitan Khosla
- Stanford ChEM-H, Stanford University, Stanford, California, USA,Department of Chemistry and Chemical Engineering, Stanford University, Stanford, California, USA
| | - Yvonne Maldonado
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA,Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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15
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Kimbrel J, Moon J, Avila-Herrera A, Martí JM, Thissen J, Mulakken N, Sandholtz SH, Ferrell T, Daum C, Hall S, Segelke B, Arrildt KT, Messenger S, Wadford DA, Jaing C, Allen JE, Borucki MK. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 2022; 14:v14122775. [PMID: 36560780 PMCID: PMC9788161 DOI: 10.3390/v14122775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/23/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic analysis of intra-host viral populations provides unique insight into pre-emergent mutations that may contribute to the genotype of future variants. Clinical samples positive for SARS-CoV-2 collected in California during the first months of the pandemic were sequenced to define the dynamics of mutation emergence as the virus became established in the state. Deep sequencing of 90 nasopharyngeal samples showed that many mutations associated with the establishment of SARS-CoV-2 globally were present at varying frequencies in a majority of the samples, even those collected as the virus was first detected in the US. A subset of mutations that emerged months later in consensus sequences were detected as subconsensus members of intra-host populations. Spike mutations P681H, H655Y, and V1104L were detected prior to emergence in variant genotypes, mutations were detected at multiple positions within the furin cleavage site, and pre-emergent mutations were identified in the nucleocapsid and the envelope genes. Because many of the samples had a very high depth of coverage, a bioinformatics pipeline, "Mappgene", was established that uses both iVar and LoFreq variant calling to enable identification of very low-frequency variants. This enabled detection of a spike protein deletion present in many samples at low frequency and associated with a variant of concern.
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Affiliation(s)
- Jeffrey Kimbrel
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Joseph Moon
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | | | - James Thissen
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Nisha Mulakken
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Tyshawn Ferrell
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Sara Hall
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Brent Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Sharon Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Crystal Jaing
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Correspondence:
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16
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Camiolo S, Hughes J, Baldanti F, Furione M, Lilleri D, Lombardi G, Angelini M, Gerna G, Zavattoni M, Davison AJ, Suárez NM. Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus Evol 2022; 8:veac114. [PMID: 37091479 PMCID: PMC10120596 DOI: 10.1093/ve/veac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding the intrahost evolution of viral populations has implications in pathogenesis, diagnosis, and treatment and has recently made impressive advances from developments in high-throughput sequencing. However, the underlying analyses are very sensitive to sources of bias, error, and artefact in the data, and it is important that these are addressed adequately if robust conclusions are to be drawn. The key factors include (1) determining the number of viral strains present in the sample analysed; (2) monitoring the extent to which the data represent these strains and assessing the quality of these data; (3) dealing with the effects of cross-contamination; and (4) ensuring that the results are reproducible. We investigated these factors by generating sequence datasets, including biological and technical replicates, directly from clinical samples obtained from a small cohort of patients who had been infected congenitally with the herpesvirus human cytomegalovirus, with the aim of developing a strategy for identifying high-confidence intrahost variants. We found that such variants were few in number and typically present in low proportions and concluded that human cytomegalovirus exhibits a very low level of intrahost variability. In addition to clarifying the situation regarding human cytomegalovirus, our strategy has wider applicability to understanding the intrahost variability of other viruses.
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Affiliation(s)
- Salvatore Camiolo
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Joseph Hughes
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, School of Infection and Immunity, University of Pavia, Pavia 27100, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Milena Furione
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Daniele Lilleri
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Giuseppina Lombardi
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Micol Angelini
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Giuseppe Gerna
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Maurizio Zavattoni
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Andrew J Davison
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nicolás M Suárez
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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17
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Li C, Culhane MR, Schroeder DC, Cheeran MCJ, Galina Pantoja L, Jansen ML, Torremorell M. Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs. eLife 2022; 11:78618. [PMID: 36052992 PMCID: PMC9439680 DOI: 10.7554/elife.78618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Although vaccination is broadly used in North American swine breeding herds, managing swine influenza is challenging primarily due to the continuous evolution of influenza A virus (IAV) and the ability of the virus to transmit among vaccinated pigs. Studies that have simultaneously assessed the impact of vaccination on the emergence of IAV reassortment and genetic variation in pigs are limited. Here, we directly sequenced 28 bronchoalveolar lavage fluid (BALF) samples collected from vaccinated and unvaccinated pigs co-infected with H1N1 and H3N2 IAV strains, and characterized 202 individual viral plaques recovered from 13 BALF samples. We identified 54 reassortant viruses that were grouped in 17 single and 16 mixed genotypes. Notably, we found that prime-boost vaccinated pigs had less reassortant viruses than nonvaccinated pigs, likely due to a reduction in the number of days pigs were co-infected with both challenge viruses. However, direct sequencing from BALF samples revealed limited impact of vaccination on viral variant frequency, evolutionary rates, and nucleotide diversity in any IAV coding regions. Overall, our results highlight the value of IAV vaccination not only at limiting virus replication in pigs but also at protecting public health by restricting the generation of novel reassortants with zoonotic and/or pandemic potential. Swine influenza A viruses cause severe illness among pigs and financial losses on pig farms worldwide. These viruses can also infect humans and have caused deadly human pandemics in the past. Influenza A viruses are dangerous because viruses can be transferred between humans, birds and pigs. These co-infections can allow the viruses to swap genetic material. Viral genetic exchanges can result in new virus strains that are more dangerous or that can infect other types of animals more easily. Farmers vaccinate their pigs to control the swine influenza A virus. The vaccines are regularly updated to match circulating virus strains. But the virus evolves rapidly to escape vaccine-induced immunity, and infections are common even in vaccinated pigs. Learning about how vaccination affects the evolution of influenza A viruses in pigs could help scientists prevent outbreaks on pig farms and avoid spillover pandemics in humans. Li et al. show that influenza A viruses are less likely to swap genetic material in vaccinated and boosted pigs than in unvaccinated animals. In the experiments, Li et al. collected swine influenza A samples from the lungs of pigs that had received different vaccination protocols. Next, Li et al. used next-generation sequencing to identify new mutations in the virus or genetic swaps among different strains. In pigs infected with both the H1N1 and H3N2 strains of influenza, the two viruses began trading genes within a week. But less genetic mixing occurred in vaccinated and boosted pigs because they spent less time infected with both viruses than in unvaccinated pigs. The vaccination status of the pig did not have much effect on how many new mutations occurred in the viruses. The experiments show that vaccinating and boosting pigs against influenza A viruses may protect against genetic swapping among influenza viruses. If future studies on pig farms confirm the results, the information gleaned from the study could help scientists improve farm vaccine protocols to further reduce influenza risks to animals and people.
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Affiliation(s)
- Chong Li
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Marie R Culhane
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Declan C Schroeder
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Maxim C-J Cheeran
- College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
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18
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [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: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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19
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.05.05.442873. [PMID: 36656775 PMCID: PMC9836620 DOI: 10.1101/2021.05.05.442873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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20
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Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat. Virus Evol 2022; 8:veac052. [PMID: 35799885 PMCID: PMC9257191 DOI: 10.1093/ve/veac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here, we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting that viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.
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Affiliation(s)
- William W Hannon
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA,Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | | | - Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | | | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
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21
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Ortiz AT, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.07.495142. [PMID: 35702156 PMCID: PMC9196117 DOI: 10.1101/2022.06.07.495142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
| | - Michelle Kendall
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Rachel Williams
- UCL Genomics, Institute of Child Health, UCL, London WC1N 1EH
| | | | | | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
- Department of Virology, East South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London E12ES
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
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22
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Low Pathogenicity H7N3 Avian Influenza Viruses Have Higher Within-Host Genetic Diversity Than a Closely Related High Pathogenicity H7N3 Virus in Infected Turkeys and Chickens. Viruses 2022; 14:v14030554. [PMID: 35336961 PMCID: PMC8951284 DOI: 10.3390/v14030554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Within-host viral diversity offers a view into the early stages of viral evolution occurring after a virus infects a host. In recent years, advances in deep sequencing have allowed for routine identification of low-frequency variants, which are important sources of viral genetic diversity and can potentially emerge as a major virus population under certain conditions. We examined within-host viral diversity in turkeys and chickens experimentally infected with closely related H7N3 avian influenza viruses (AIVs), specifically one high pathogenicity AIV (HPAIV) and two low pathogenicity AIV (LPAIVs) with different neuraminidase protein stalk lengths. Consistent with the high mutation rates of AIVs, an abundance of intra-host single nucleotide variants (iSNVs) at low frequencies of 2–10% was observed in all samples collected. Furthermore, a small number of common iSNVs were observed between turkeys and chickens, and between directly inoculated and contact-exposed birds. Notably, the LPAIVs have significantly higher iSNV diversities and frequencies of nonsynonymous changes than the HPAIV in both turkeys and chickens. These findings highlight the dynamics of AIV populations within hosts and the potential impact of genetic changes, including mutations in the hemagglutinin gene that confers the high pathogenicity pathotype, on AIV virus populations and evolution.
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23
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Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.. [PMID: 35169803 PMCID: PMC8845427 DOI: 10.1101/2022.02.09.479546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a SARS-CoV-2 outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.
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24
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Goossens SN, Heupink TH, De Vos E, Dippenaar A, De Vos M, Warren R, Van Rie A. Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data. Brief Bioinform 2021; 23:6484510. [PMID: 34962257 PMCID: PMC8769888 DOI: 10.1093/bib/bbab541] [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: 09/14/2021] [Revised: 11/05/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
The study of genetic minority variants is fundamental to the understanding of complex processes such as evolution, fitness, transmission, virulence, heteroresistance and drug tolerance in Mycobacterium tuberculosis (Mtb). We evaluated the performance of the variant calling tool LoFreq to detect de novo as well as drug resistance conferring minor variants in both in silico and clinical Mtb next generation sequencing (NGS) data. The in silico simulations demonstrated that LoFreq is a conservative variant caller with very high precision (≥96.7%) over the entire range of depth of coverage tested (30x to1000x), independent of the type and frequency of the minor variant. Sensitivity increased with increasing depth of coverage and increasing frequency of the variant, and was higher for calling insertion and deletion (indel) variants than for single nucleotide polymorphisms (SNP). The variant frequency limit of detection was 0.5% and 3% for indel and SNP minor variants, respectively. For serial isolates from a patient with DR-TB; LoFreq successfully identified all minor Mtb variants in the Rv0678 gene (allele frequency as low as 3.22% according to targeted deep sequencing) in whole genome sequencing data (median coverage of 62X). In conclusion, LoFreq can successfully detect minor variant populations in Mtb NGS data, thus limiting the need for filtering of possible false positive variants due to sequencing error. The observed performance statistics can be used to determine the limit of detection in existing whole genome sequencing Mtb data and guide the required depth of future studies that aim to investigate the presence of minor variants.
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Affiliation(s)
- Sander N Goossens
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Tim H Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Rob Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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25
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Van Poelvoorde LAE, Delcourt T, Coucke W, Herman P, De Keersmaecker SCJ, Saelens X, Roosens NHC, Vanneste K. Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing. Front Microbiol 2021; 12:747458. [PMID: 34721349 PMCID: PMC8548777 DOI: 10.3389/fmicb.2021.747458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by SARS-CoV-2, constitutes a tremendous global health issue. Continuous monitoring of the virus has become a cornerstone to make rational decisions on implementing societal and sanitary measures to curtail the virus spread. Additionally, emerging SARS-CoV-2 variants have increased the need for genomic surveillance to detect particular strains because of their potentially increased transmissibility, pathogenicity and immune escape. Targeted SARS-CoV-2 sequencing of diagnostic and wastewater samples has been explored as an epidemiological surveillance method for the competent authorities. Currently, only the consensus genome sequence of the most abundant strain is taken into consideration for analysis, but multiple variant strains are now circulating in the population. Consequently, in diagnostic samples, potential co-infection(s) by several different variants can occur or quasispecies can develop during an infection in an individual. In wastewater samples, multiple variant strains will often be simultaneously present. Currently, quality criteria are mainly available for constructing the consensus genome sequence, and some guidelines exist for the detection of co-infections and quasispecies in diagnostic samples. The performance of detection and quantification of low-frequency variants using whole genome sequencing (WGS) of SARS-CoV-2 remains largely unknown. Here, we evaluated the detection and quantification of mutations present at low abundances using the mutations defining the SARS-CoV-2 lineage B.1.1.7 (alpha variant) as a case study. Real sequencing data were in silico modified by introducing mutations of interest into raw wild-type sequencing data, or by mixing wild-type and mutant raw sequencing data, to construct mixed samples subjected to WGS using a tiling amplicon-based targeted metagenomics approach and Illumina sequencing. As anticipated, higher variation and lower sensitivity were observed at lower coverages and allelic frequencies. We found that detection of all low-frequency variants at an abundance of 10, 5, 3, and 1%, requires at least a sequencing coverage of 250, 500, 1500, and 10,000×, respectively. Although increasing variability of estimated allelic frequencies at decreasing coverages and lower allelic frequencies was observed, its impact on reliable quantification was limited. This study provides a highly sensitive low-frequency variant detection approach, which is publicly available at https://galaxy.sciensano.be, and specific recommendations for minimum sequencing coverages to detect clade-defining mutations at certain allelic frequencies. This approach will be useful to detect and quantify low-frequency variants in both diagnostic (e.g., co-infections and quasispecies) and wastewater [e.g., multiple variants of concern (VOCs)] samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Wim Coucke
- Quality of Laboratories, Sciensano, Brussels, Belgium
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, Brussels, Belgium
| | | | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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26
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Li J, Yang Z, Mao LF, Chen RH, Yu XF, Yang XH, Zhang GZ, Wang HQ, Chen SC, Zhao G. Reverse transcription recombinase-aided amplification assay for rapid detection of the influenza A(H1N1)pdm09 H275Y mutation that confers oseltamivir resistance. Mol Cell Probes 2021; 60:101771. [PMID: 34560257 DOI: 10.1016/j.mcp.2021.101771] [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: 02/05/2021] [Revised: 05/02/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
The emergence of the influenza A(H1N1)pdm09 virus with the NA-H275Y mutation, which confers oseltamivir resistance, must be monitored, especially in patients undergoing neuraminidase inhibitor treatment. In this study, we developed a reverse transcription recombinase-aided amplification assay that has high sensitivity (detection limit: 1.0 × 101 copies/μL) and specificity for detecting the oseltamivir-resistant H275Y mutation; the assay is performed within 30 min at a constant temperature of 39° Celsius using an isothermal device. This method is suitable for the clinical application of targeted testing, thereby providing technical support for precision medicine in individual drug applications for patients with severe infection or immunosuppression.
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Affiliation(s)
- Jun Li
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Zi Yang
- Dali University, Yunnan, 671003, China
| | - Ling-Feng Mao
- Hangzhou Baocheng Biotechnology Co., Ltd., Zhejiang, 310052, China
| | - Ren-Hua Chen
- Department of Infectious Diseases, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Xin-Fen Yu
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Xu-Hui Yang
- Department of Infectious Diseases, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Guo-Zhong Zhang
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Hao-Qiu Wang
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Shu-Chang Chen
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Gang Zhao
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China.
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27
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Japanese encephalitis virus live attenuated vaccine strains display altered immunogenicity, virulence and genetic diversity. NPJ Vaccines 2021; 6:112. [PMID: 34475404 PMCID: PMC8413339 DOI: 10.1038/s41541-021-00371-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
Japanese encephalitis virus (JEV) is the etiological agent of Japanese encephalitis (JE). The most commonly used vaccine used to prevent JE is the live-attenuated strain SA14-14-2, which was generated by serial passage of the wild-type (WT) JEV strain SA14. Two other vaccine candidates, SA14-5-3 and SA14-2-8 were derived from SA14. Both were shown to be attenuated but lacked sufficient immunogenicity to be considered effective vaccines. To better contrast the SA14-14-2 vaccine with its less-immunogenic counterparts, genetic diversity, ribavirin sensitivity, mouse virulence and mouse immunogenicity of the three vaccines were investigated. Next generation sequencing demonstrated that SA14-14-2 was significantly more diverse than both SA14-5-3 and SA14-2-8, and was slightly less diverse than WT SA14. Notably, WT SA14 had unpredictable levels of diversity across its genome whereas SA14-14-2 is highly diverse, but genetic diversity is not random, rather the virus only tolerates variability at certain residues. Using Ribavirin sensitivity in vitro, it was found that SA14-14-2 has a lower fidelity replication complex compared to SA14-5-3 and SA14-2-8. Mouse virulence studies showed that SA14-2-8 was the most virulent of the three vaccine strains while SA14-14-2 had the most favorable combination of safety (virulence) and immunogenicity for all vaccines tested. SA14-14-2 contains genetic diversity and sensitivity to the antiviral Ribavirin similar to WT parent SA14, and this genetic diversity likely explains the (1) differences in genomic sequences reported for SA14-14-2 and (2) the encoding of major attenuation determinants by the viral E protein.
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28
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Lin GL, Drysdale SB, Snape MD, O’Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Bonsall D, Ansari MA, Öner D, Aerssens J, Butler C, Bont L, Openshaw P, Martinón-Torres F, Nair H, Bowden R, Golubchik T, Pollard AJ. Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus. Nat Commun 2021; 12:5125. [PMID: 34446722 PMCID: PMC8390747 DOI: 10.1038/s41467-021-25265-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children globally, but little is known about within-host RSV diversity. Here, we characterised within-host RSV populations using deep-sequencing data from 319 nasopharyngeal swabs collected during 2017-2020. RSV-B had lower consensus diversity than RSV-A at the population level, while exhibiting greater within-host diversity. Two RSV-B consensus sequences had an amino acid alteration (K68N) in the fusion (F) protein, which has been associated with reduced susceptibility to nirsevimab (MEDI8897), a novel RSV monoclonal antibody under development. In addition, several minor variants were identified in the antigenic sites of the F protein, one of which may confer resistance to palivizumab, the only licensed RSV monoclonal antibody. The differences in within-host virus populations emphasise the importance of monitoring for vaccine efficacy and may help to explain the different prevalences of monoclonal antibody-escape mutants between the two subgroups.
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Affiliation(s)
- Gu-Lung Lin
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simon B. Drysdale
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK ,grid.4464.20000 0001 2161 2573Present Address: Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George’s, University of London, London, UK
| | - Matthew D. Snape
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O’Connor
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anthony Brown
- grid.4991.50000 0004 1936 8948Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Esther Mellado-Gomez
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M. Azim Ansari
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deniz Öner
- grid.419619.20000 0004 0623 0341Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jeroen Aerssens
- grid.419619.20000 0004 0623 0341Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christopher Butler
- grid.4991.50000 0004 1936 8948Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Louis Bont
- grid.7692.a0000000090126352Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands ,ReSViNET Foundation, Zeist, Netherlands
| | - Peter Openshaw
- grid.7445.20000 0001 2113 8111National Heart and Lung Institute, Imperial College London, London, UK
| | - Federico Martinón-Torres
- grid.411048.80000 0000 8816 6945Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain ,grid.488911.d0000 0004 0408 4897Genetics, Vaccines, Infectious Diseases, and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Harish Nair
- grid.4305.20000 0004 1936 7988Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Rory Bowden
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.1042.7Present Address: Division of Advanced Technology and Biology, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | | | - Tanya Golubchik
- grid.4991.50000 0004 1936 8948Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J. Pollard
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
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29
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Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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30
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Braun KM, Moreno GK, Wagner C, Accola MA, Rehrauer WM, Baker DA, Koelle K, O’Connor DH, Bedford T, Friedrich TC, Moncla LH. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks. PLoS Pathog 2021; 17:e1009849. [PMID: 34424945 PMCID: PMC8412271 DOI: 10.1371/journal.ppat.1009849] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/02/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Molly A. Accola
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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31
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Berry IM, Melendrez MC, Pollett S, Figueroa K, Buddhari D, Klungthong C, Nisalak A, Panciera M, Thaisomboonsuk B, Li T, Vallard TG, Macareo L, Yoon IK, Thomas SJ, Endy T, Jarman RG. Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand. Emerg Infect Dis 2021; 27:1637-1644. [PMID: 34013878 PMCID: PMC8153871 DOI: 10.3201/eid2706.204323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dengue control approaches are best informed by granular spatial epidemiology of these viruses, yet reconstruction of inter- and intra-household transmissions is limited when analyzing case count, serologic, or genomic consensus sequence data. To determine viral spread on a finer spatial scale, we extended phylogenomic discrete trait analyses to reconstructions of house-to-house transmissions within a prospective cluster study in Kamphaeng Phet, Thailand. For additional resolution and transmission confirmation, we mapped dengue intra-host single nucleotide variants on the taxa of these time-scaled phylogenies. This approach confirmed 19 household transmissions and revealed that dengue disperses an average of 70 m per day between households in these communities. We describe an evolutionary biology framework for the resolution of dengue transmissions that cannot be differentiated based on epidemiologic and consensus genome data alone. This framework can be used as a public health tool to inform control approaches and enable precise tracing of dengue transmissions.
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32
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Fuhrmann L, Jablonski KP, Beerenwinkel N. Quantitative measures of within-host viral genetic diversity. Curr Opin Virol 2021; 49:157-163. [PMID: 34153841 DOI: 10.1016/j.coviro.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022]
Abstract
The genetic diversity of virus populations within their hosts is known to influence disease progression, treatment outcome, drug resistance, cell tropism, and transmission risk, and the study of dynamic changes of genetic heterogeneity can provide insights into the evolution of viruses. Several measures to quantify within-host genetic diversity capturing different aspects of diversity patterns in a sample or population are used, based on incidence, relative frequencies, pairwise distances, or phylogenetic trees. Here, we review and compare several of these measures.
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Affiliation(s)
- Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
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33
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Valesano AL, Rumfelt KE, Dimcheff DE, Blair CN, Fitzsimmons WJ, Petrie JG, Martin ET, Lauring AS. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. PLoS Pathog 2021; 17:e1009499. [PMID: 33826681 PMCID: PMC8055005 DOI: 10.1371/journal.ppat.1009499] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.
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Affiliation(s)
- Andrew L. Valesano
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kalee E. Rumfelt
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Derek E. Dimcheff
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher N. Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William J. Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joshua G. Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Emily T. Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Adam S. Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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34
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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35
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 11/08/2023] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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36
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Fung CK, Li T, Pollett S, Alera MT, Yoon IK, Hang J, Macareo L, Srikiatkhachorn A, Ellison D, Rothman AL, Fernandez S, Jarman RG, Maljkovic Berry I. Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies. J Gen Virol 2021; 102:001553. [PMID: 33591246 PMCID: PMC8515859 DOI: 10.1099/jgv.0.001553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
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Affiliation(s)
| | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - In-Kyu Yoon
- Coalition for Epidemic Preparedness Innovations, Washington, DC, USA
| | - Jun Hang
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Louis Macareo
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of Rhode Island, Kingston, RI, USA
| | - Damon Ellison
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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37
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Valesano AL, Rumfelt KE, Dimcheff DE, Blair CN, Fitzsimmons WJ, Petrie JG, Martin ET, Lauring AS. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.19.427330. [PMID: 33501443 PMCID: PMC7836113 DOI: 10.1101/2021.01.19.427330] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.
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Affiliation(s)
- Andrew L. Valesano
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Kalee E. Rumfelt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Derek E. Dimcheff
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christopher N. Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - William J. Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua G. Petrie
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Emily T. Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S. Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
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38
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The Early Evolution of Oral Poliovirus Vaccine Is Shaped by Strong Positive Selection and Tight Transmission Bottlenecks. Cell Host Microbe 2020; 29:32-43.e4. [PMID: 33212020 PMCID: PMC7815045 DOI: 10.1016/j.chom.2020.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023]
Abstract
The emergence of circulating vaccine-derived polioviruses through evolution of the oral polio vaccine (OPV) poses a significant obstacle to polio eradication. Understanding the early genetic changes that occur as OPV evolves and transmits is important for preventing future outbreaks. Here, we use deep sequencing to define the evolutionary trajectories of type 2 OPV in a vaccine trial. By sequencing 497 longitudinal stool samples from 271 OPV2 recipients and household contacts, we were able to examine the extent of convergent evolution in vaccinated individuals and the amount of viral diversity that is transmitted. In addition to rapid reversion of key attenuating mutations, we identify strong selection at 19 sites across the genome. We find that a tight transmission bottleneck limits the onward transmission of these early adaptive mutations. Our results highlight the distinct evolutionary dynamics of live attenuated virus vaccines and have important implications for the success of next-generation OPV.
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39
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Gelbart M, Harari S, Ben-Ari Y, Kustin T, Wolf D, Mandelboim M, Mor O, Pennings PS, Stern A. Drivers of within-host genetic diversity in acute infections of viruses. PLoS Pathog 2020; 16:e1009029. [PMID: 33147296 PMCID: PMC7668575 DOI: 10.1371/journal.ppat.1009029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 10/04/2020] [Indexed: 12/01/2022] Open
Abstract
Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs. The few days or weeks following infection with a virus, termed acute infection, are critical for virus establishment. Here we sought to characterize what leads to differences in the genetic diversity of different viruses sampled during acute infection. We performed ultra-deep sequencing of hundreds to thousands viral genomes from forty-three samples spanning three pathogenic human viruses: HIV, RSV and CMV. We found major differences in the genetic diversity of these different viruses, and in different patients infected with the same virus. We investigated the factors responsible for these differences. We found that the DNA virus CMV was less diverse, most likely since it has a lower mutation rate than the RNA viruses HIV and RSV. We also found that the samples with the highest genetic diversity, which included one CMV sample and two HIV samples, bore evidence for multiple genotype infection. In other words, patients from whom these samples were taken were infected with two different “strains” of the virus. Finally, we also found evidence that viral genomes of HIV, and in particular RSV, are edited by the innate immune system of the host, leading to the presence of defective virus genomes.
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Affiliation(s)
- Maoz Gelbart
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ya’ara Ben-Ari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Lautenberg Center for General and Tumor Immunology, IMRIC, the Faculty of Medicine, the Hebrew University, Jerusalem, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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40
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Maclot F, Candresse T, Filloux D, Malmstrom CM, Roumagnac P, van der Vlugt R, Massart S. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Front Microbiol 2020; 11:578064. [PMID: 33178159 PMCID: PMC7596190 DOI: 10.3389/fmicb.2020.578064] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 01/08/2023] Open
Abstract
The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
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Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - Carolyn M Malmstrom
- Department of Plant Biology and Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI, United States
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - René van der Vlugt
- Laboratory of Virology, Wageningen University and Research Centre (WUR-PRI), Wageningen, Netherlands
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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41
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The Genetic Diversification of a Single Bluetongue Virus Strain Using an In Vitro Model of Alternating-Host Transmission. Viruses 2020; 12:v12091038. [PMID: 32961886 PMCID: PMC7551957 DOI: 10.3390/v12091038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Bluetongue virus (BTV) is an arbovirus that has been associated with dramatic epizootics in both wild and domestic ruminants in recent decades. As a segmented, double-stranded RNA virus, BTV can evolve via several mechanisms due to its genomic structure. However, the effect of BTV’s alternating-host transmission cycle on the virus’s genetic diversification remains poorly understood. Whole genome sequencing approaches offer a platform for investigating the effect of host-alternation across all ten segments of BTV’s genome. To understand the role of alternating hosts in BTV’s genetic diversification, a field isolate was passaged under three different conditions: (i) serial passages in Culicoides sonorensis cells, (ii) serial passages in bovine pulmonary artery endothelial cells, or (iii) alternating passages between insect and bovine cells. Aliquots of virus were sequenced, and single nucleotide variants were identified. Measures of viral population genetics were used to quantify the genetic diversification that occurred. Two consensus variants in segments 5 and 10 occurred in virus from all three conditions. While variants arose across all passages, measures of genetic diversity remained largely similar across cell culture conditions. Despite passage in a relaxed in vitro system, we found that this BTV isolate exhibited genetic stability across passages and conditions. Our findings underscore the valuable role that whole genome sequencing may play in improving understanding of viral evolution and highlight the genetic stability of BTV.
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42
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Lumby CK, Zhao L, Breuer J, Illingworth CJR. A large effective population size for established within-host influenza virus infection. eLife 2020; 9:e56915. [PMID: 32773034 PMCID: PMC7431133 DOI: 10.7554/elife.56915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
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Affiliation(s)
- Casper K Lumby
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Lei Zhao
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Judith Breuer
- Great Ormond Street HospitalLondonUnited Kingdom
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of CambridgeCambridgeUnited Kingdom
- Department of Computer Science, Institute of Biotechnology, University of HelsinkiHelsinkiFinland
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43
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Lu IN, Muller CP, He FQ. Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies. Virus Res 2020; 283:197963. [PMID: 32278821 PMCID: PMC7144618 DOI: 10.1016/j.virusres.2020.197963] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze and quantify the exceptionally-high diversity within viral quasispecies, and many low-frequency drug- or vaccine-resistant mutations of therapeutic importance have been discovered. Although many works have intensively discussed the latest NGS approaches and applications in general, none of them has focused on applying NGS in viral quasispecies studies, mostly due to the limited ability of current NGS technologies to accurately detect and quantify rare viral variants. Here, we summarize several error-correction strategies that have been developed to enhance the detection accuracy of minority variants. We also discuss critical considerations for preparing a sequencing library from viral RNAs and for analyzing NGS data to unravel the mutational landscape.
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Affiliation(s)
- I-Na Lu
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, D-45147 Essen, Germany; Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark.
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Laboratoire National de Santé, L-3583 Dudelange, Luxembourg
| | - Feng Q He
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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44
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Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [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: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
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Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
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45
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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46
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Abstract
Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.
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Affiliation(s)
- Katherine S Xue
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jesse D Bloom
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA
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47
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Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. J Virol 2020; 94:JVI.01710-19. [PMID: 31801858 DOI: 10.1128/jvi.01710-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Influenza B virus (IBV) undergoes seasonal antigenic drift more slowly than influenza A virus, but the reasons for this difference are unclear. While the evolutionary dynamics of influenza viruses play out globally, they are fundamentally driven by mutation, reassortment, drift, and selection at the level of individual hosts. These processes have recently been described for influenza A virus, but little is known about the evolutionary dynamics of IBV during individual infections and transmission events. Here, we define the within-host evolutionary dynamics of IBV by sequencing virus populations from naturally infected individuals enrolled in a prospective, community-based cohort over 8,176 person-seasons of observation. Through analysis of high depth-of-coverage sequencing data from samples from 91 individuals with influenza B, we find that IBV accumulates lower genetic diversity than previously observed for influenza A virus during acute infections. Consistent with studies of influenza A viruses, the within-host evolution of IBVs is characterized by purifying selection and the general absence of widespread positive selection of within-host variants. Analysis of shared genetic diversity across 15 sequence-validated transmission pairs suggests that IBV experiences a tight transmission bottleneck similar to that of influenza A virus. These patterns of local-scale evolution are consistent with the lower global evolutionary rate of IBV.IMPORTANCE The evolution of influenza virus is a significant public health problem and necessitates the annual evaluation of influenza vaccine formulation to keep pace with viral escape from herd immunity. Influenza B virus is a serious health concern for children, in particular, yet remains understudied compared to influenza A virus. Influenza B virus evolves more slowly than influenza A virus, but the factors underlying this are not completely understood. We studied how the within-host diversity of influenza B virus relates to its global evolution by sequencing viruses from a community-based cohort. We found that influenza B virus populations have lower within-host genetic diversity than influenza A virus and experience a tight genetic bottleneck during transmission. Our work provides insights into the varying dynamics of influenza viruses in human infection.
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48
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Xue KS, Bloom JD. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nat Genet 2020; 51:1298-1301. [PMID: 30804564 DOI: 10.1038/s41588-019-0349-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Katherine S Xue
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jesse D Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
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49
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Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread. J Virol 2019; 94:JVI.01162-19. [PMID: 31619551 DOI: 10.1128/jvi.01162-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 12/27/2022] Open
Abstract
Canine parvovirus (CPV) is a highly successful pathogen that has sustained pandemic circulation in dogs for more than 40 years. Here, integrating full-genome and deep-sequencing analyses, structural information, and in vitro experimentation, we describe the macro- and microscale features that accompany CPV's evolutionary success. Despite 40 years of viral evolution, all CPV variants are more than ∼99% identical in nucleotide sequence, with only a limited number (<40) of substitutions becoming fixed or widespread during this time. Notably, most substitutions in the major capsid protein (VP2) gene are nonsynonymous, altering amino acid residues that fall within, or adjacent to, the overlapping receptor footprint or antigenic regions, suggesting that natural selection has channeled much of CPV evolution. Among the limited number of variable sites, CPV genomes exhibit complex patterns of variation that include parallel evolution, reversion, and recombination, compromising phylogenetic inference. At the intrahost level, deep sequencing of viral DNA in original clinical samples from dogs and other host species sampled between 1978 and 2018 revealed few subconsensus single nucleotide variants (SNVs) above ∼0.5%, and experimental passages demonstrate that substantial preexisting genetic variation is not necessarily required for rapid host receptor-driven adaptation. Together, these findings suggest that although CPV is capable of rapid host adaptation, a relatively low mutation rate, pleiotropy, and/or a lack of selective challenges since its initial emergence have inhibited the long-term accumulation of genetic diversity. Hence, continuously high levels of inter- and intrahost diversity are not necessarily required for virus host adaptation.IMPORTANCE Rapid mutation rates and correspondingly high levels of intra- and interhost diversity are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little known about evolutionary processes in viruses with single-stranded DNA (ssDNA) genomes. Here, we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intrahost evolutionary processes of an ssDNA virus that emerged to cause a pandemic in a new host animal. Our analysis reveals that successful host jumping and sustained transmission does not necessarily depend on a high level of intrahost diversity nor result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of the biology and ecology of a virus are relevant when considering their adaptability.
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Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. J Virol 2019; 93:e01039-19. [PMID: 31511393 PMCID: PMC6854484 DOI: 10.1128/jvi.01039-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/09/2019] [Indexed: 12/19/2022] Open
Abstract
Influenza A viruses have regularly jumped to new host species to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here, we examine the processes of influenza A virus infection and evolution in mice by comparing single nucleotide variations of a human H1N1 pandemic virus, a seasonal H3N2 virus, and an H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with those seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full-genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear evidence for adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc.IMPORTANCE Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts, we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and that the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not affect influenza virus evolution in this model. Overall, our results show that while mice provide a useful animal model for influenza virus pathology, host passage evolution will vary depending on the specific virus tested.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen N Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brynn K Alford-Lawrence
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Grace Hood
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- College of Veterinary Medicine, University of Queensland, Gatton, Queensland, Australia
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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