Reassortment Network of Influenza A Virus.

Xingfei Gong,Mingda Hu,Hongguang Ren,Junjie Yue,Long Liang,Boqian Wang,Haoyi Yang,Yuan Jin,Wei Chen

doi:10.3389/fmicb.2021.793500

Xingfei Gong, Mingda Hu + Show 7 more

Open Access

https://doi.org/10.3389/fmicb.2021.793500

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Abstract

Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments. Genetic exchange through reassortment of the segmented genomes often endows IAVs with new genetic characteristics, which may affect transmissibility and pathogenicity of the viruses. However, a comprehensive understanding of the reassortment history of IAVs remains lacking. To this end, we assembled 40,296 whole-genome sequences of IAVs for analysis. Using a new clustering method based on Mean Pairwise Distances in the phylogenetic trees, we classified each segment of IAVs into clades. Correspondingly, reassortment events among IAVs were detected by checking the segment clade compositions of related genomes under specific environment factors and time period. We systematically identified 1,927 possible reassortment events of IAVs and constructed their reassortment network. Interestingly, minimum spanning tree of the reassortment network reproved that swine act as an intermediate host in the reassortment history of IAVs between avian species and humans. Moreover, reassortment patterns among related subtypes constructed in this study are consistent with previous studies. Taken together, our genome-wide reassortment analysis of all the IAVs offers an overview of the leaping evolution of the virus and a comprehensive network representing the relationships of IAVs.

Highlights

Influenza A Virus (IAV) is a highly infectious viral pathogen that causes seasonal epidemics, occasional pandemics, and zoonotic outbreaks, which may lead to substantial human morbidity and mortality and a considerable financial burden worldwide (Liu et al, 2020)
In order to verify the correctness of our clustering method, we used the unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses (WHO, 2011) to cluster HA segments of H5N1 viruses in the database and compared with our result
We marked the clustering results of the two methods on the phylogenetic tree, which was shown in Supplementary Figure 11

Summary

Introduction

Influenza A Virus (IAV) is a highly infectious viral pathogen that causes seasonal epidemics, occasional pandemics, and zoonotic outbreaks, which may lead to substantial human morbidity and mortality and a considerable financial burden worldwide (Liu et al, 2020). It has been more than 100 years since the Spanish flu (H1N1) virus caused the first recorded influenza pandemic, which is considered to be the most lethal natural event in modern history (Smith, 2011; Liu et al, 2018). The WHO estimated that seasonal influenza viruses infect 5–15% of the human population each year, causing approximately 500,000 deaths worldwide (Stohr, 2002)

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