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Kim G, Shin HM, Kim HR, Kim Y. Effects of Host and Pathogenicity on Mutation Rates in Avian Influenza A Viruses. Virus Evol 2022; 8:veac013. [PMID: 35295747 PMCID: PMC8922178 DOI: 10.1093/ve/veac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/11/2022] [Accepted: 02/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mutation is the primary determinant of genetic diversity in influenza viruses. The rate of mutation, measured in an absolute time-scale, is likely to be dependent on the rate of errors in copying RNA sequences per replication and the number of replications per unit time. Conditions for viral replication are probably different among host taxa, potentially generating the host-specificity of the viral mutation rate, and possibly between highly and low pathogenic viruses. This study investigated whether mutation rates per year in avian influenza A viruses depend on host taxa and pathogenicity. We inferred mutation rates from the rates of synonymous substitutions, which are assumed to be neutral and thus equal to mutation rates, at four segments that code internal viral proteins (PB2, PB1, PA, NP). On the phylogeny of all avian viral sequences for each segment, multiple distinct subtrees (clades) were identified that represent viral subpopulations, which are likely to have evolved within particular host taxa. Using simple regression analysis, we found that mutation rates were significantly higher in viruses infecting chickens than domestic ducks, and in those infecting wild shorebirds than wild ducks. Host-dependency of the substitution rate was also confirmed by Bayesian phylogenetic analysis. However, we did not find evidence that the mutation rate is higher in highly pathogenic than in low pathogenic viruses. We discuss these results considering viral replication rate as the major determinant of mutation rate per unit time.
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Affiliation(s)
- Gwanghun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyun Mu Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Hang-Rae Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Yuseob Kim
- Division of EcoScience and Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
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