Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective.

Fucheng Guo,Junbin Pan,David M Irwin,Jinjin Yang,Xianghui Liang,Rui-Ai Chen,Xuejuan Shen,Yongyi Shen

doi:10.3389/fmicb.2020.01615

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.

Highlights

The H1N1/pdm2009 virus was first isolated from humans in North America in April 2009 (Smith et al, 2009)
The H1N1/pdm2009 virus has replaced the previous human seasonal H1N1 and has circulated as a seasonal virus, posing a substantial risk to human populations. This virus is the product of reassortments among multiple swine influenza virus lineages: its NA and M genes were derived from the Eurasian avian-like swine H1N1 influenza virus (EAsw SIV), while its other genes were from the triple-reassortant (TRsw) SIV with PB2 and PA derived from avian H1N1, PB1 from human H3N2, and HA, NP, NS, NA, and M from classical swine (Csw) H1N1 (Newman et al, 2008; Smith et al, 2009)
In Asia, the circulation of SIVs is more complex than it is elsewhere. Apart from these viruses that circulated in North American and European countries, several other lineages have been found only in Asia, such as Csw SIVs and human-origin H3N2 viruses circulating in pigs

Summary

Introduction

The H1N1/pdm2009 virus was first isolated from humans in North America in April 2009 (Smith et al, 2009). The H1N1/pdm2009 virus has replaced the previous human seasonal H1N1 and has circulated as a seasonal virus, posing a substantial risk to human populations. This virus is the product of reassortments among multiple swine influenza virus lineages: its NA and M genes were derived from the Eurasian avian-like swine H1N1 influenza virus (EAsw SIV), while its other genes were from the triple-reassortant (TRsw) SIV with PB2 and PA derived from avian H1N1, PB1 from human H3N2, and HA, NP, NS, NA, and M from classical swine (Csw) H1N1 (Newman et al, 2008; Smith et al, 2009). In Asia, Csw H1N1 SIVs viruses continue to cause endemics in southern China and Southeast Asia later than 2005, in addition to other identified viruses like human H3N2, EAsw H1N1 and North American TRsw SIVs (Qi et al, 2009)

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Results

Conclusion