دورية أكاديمية
أعرض في EDS

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections.

التفاصيل البيبلوغرافية
العنوان: Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections.
المؤلفون: VanInsberghe D; Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America.; Department of Biology, Emory University, Atlanta, Georgia, United States of America., McBride DS; Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America., DaSilva J; Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America., Stark TJ; Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America., Lau MSY; Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America., Shepard SS; Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America., Barnes JR; Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America., Bowman AS; Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America., Lowen AC; Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America.; Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America., Koelle K; Department of Biology, Emory University, Atlanta, Georgia, United States of America.; Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America.
المصدر: PLoS pathogens [PLoS Pathog] 2024 Apr 16; Vol. 20 (4), pp. e1012131. Date of Electronic Publication: 2024 Apr 16 (Print Publication: 2024).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238921 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7374 (Electronic) Linking ISSN: 15537366 NLM ISO Abbreviation: PLoS Pathog Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science, c2005-
مواضيع طبية MeSH: Orthomyxoviridae Infections*/virology , Genetic Drift* , Swine Diseases*/virology, Animals ; Swine ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A virus/genetics ; Influenza A Virus, H1N1 Subtype/genetics ; Genetic Variation ; Evolution, Molecular ; Selection, Genetic ; Phylogeny
مستخلص: Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype swine IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intrahost Single Nucleotide Variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
التعليقات: Update of: bioRxiv. 2023 Oct 25;:. (PMID: 37961583)
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معلومات مُعتمدة: 75N93021C00016 United States AI NIAID NIH HHS; 75N93021C00017 United States AI NIAID NIH HHS; R01 GM124280 United States GM NIGMS NIH HHS; U38 OT000143 United States OT OSTLTS CDC HHS
تواريخ الأحداث: Date Created: 20240416 Date Completed: 20240426 Latest Revision: 20240503
رمز التحديث: 20240503
مُعرف محوري في PubMed: PMC11051653
DOI: 10.1371/journal.ppat.1012131
PMID: 38626244
قاعدة البيانات: MEDLINE
الوصف
تدمد:1553-7374
DOI:10.1371/journal.ppat.1012131