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Guo F, Yang J, Pan J, Liang X, Shen X, Irwin DM, Chen RA, Shen Y. Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective. Front Microbiol 2020; 11:1615. [PMID: 32760376 PMCID: PMC7372903 DOI: 10.3389/fmicb.2020.01615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/19/2020] [Indexed: 12/21/2022] Open
Abstract
The H1N1/pdm2009 virus is a new triple-reassortant virus. While Eurasian avian-like and triple-reassortant swine influenza viruses are the direct ancestors of H1N1/pdm2009, the classic swine influenza virus facilitate the spectrum of influenza A diversity in pig population when the reassortant events occurred during 1998 to April 2009. The factors that facilitate the final formation of this gene constellation for H1N1/pdm2009 virus from this complex gene pool remain unknown. Since a novel successful virus should efficiently replicate and transmit in their hosts, in this study, we estimated the adaptability of the codon usage patterns of the pool of genes from these lineages of swine influenza viruses to the human expression system. We found that the MP and NA genes of Eurasian avian-like swine influenza viruses, and the PB2, PB1 and PA genes of triple-reassortant swine influenza viruses were best adapted to the human codon usage pattern. As these genes participated in the development of H1N1/pdm2009, they might help in viral replication and strengthen its competitiveness during its emergence. After its emergence in the human population, a gradual optimization of codon usage patterns between 2009 and 2019 to the human codon usage for the H1N1/pdm2009 genes was detected. This reveals that ongoing adaptive evolution, after its original incursion, occurred to further increase the adaptability of overall gene cassette to human expression system.
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Affiliation(s)
- Fucheng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinjin Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Junbin Pan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xianghui Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Rui-Ai Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Enterprise Key Laboratory of Biotechnology R&D of Veterinary Biological Products, Zhaoqing, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Codon usage bias of H3N8 equine influenza virus - An evolutionary perspective. J Infect 2020; 80:671-693. [PMID: 31958543 DOI: 10.1016/j.jinf.2020.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 01/16/2023]
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Better fit of codon usage of the polymerase and nucleoprotein genes to the chicken host for H7N9 than H9N2 AIVs. J Infect 2019; 79:174-187. [PMID: 31125636 DOI: 10.1016/j.jinf.2019.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
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