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Article

Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus

College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(19), 7129; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197129
Received: 29 August 2020 / Revised: 23 September 2020 / Accepted: 24 September 2020 / Published: 27 September 2020
(This article belongs to the Section Molecular Genetics and Genomics)
Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus. View Full-Text
Keywords: H7N9; codon usage bias; HA gene; NA gene; host specificity H7N9; codon usage bias; HA gene; NA gene; host specificity
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MDPI and ACS Style

Sun, J.; Zhao, W.; Wang, R.; Zhang, W.; Li, G.; Lu, M.; Shao, Y.; Yang, Y.; Wang, N.; Gao, Q.; Su, S. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. Int. J. Mol. Sci. 2020, 21, 7129. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197129

AMA Style

Sun J, Zhao W, Wang R, Zhang W, Li G, Lu M, Shao Y, Yang Y, Wang N, Gao Q, Su S. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. International Journal of Molecular Sciences. 2020; 21(19):7129. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197129

Chicago/Turabian Style

Sun, Jiumeng, Wen Zhao, Ruyi Wang, Wenyan Zhang, Gairu Li, Meng Lu, Yuekun Shao, Yichen Yang, Ningning Wang, Qi Gao, and Shuo Su. 2020. "Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus" International Journal of Molecular Sciences 21, no. 19: 7129. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197129

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