Scoring amino acid mutation to predict pandemic risk of avian influenza virus

Xiaoli Qiang,Zheng Kou

doi:10.1186/s12859-019-2770-0

Abstract

BackgroundAvian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. The pandemic risk of avian influenza viruses should be analyzed and a prediction model should be constructed for virology applications.ResultsThe 178 signature positions in 11 viral proteins were firstly screened as features by the scores of five amino acid factors and their random forest rankings. The Supporting Vector Machine algorithm achieved well performance. The most important amino acid factor (Factor 5) and the minimal range of signature positions (63 amino acid residues) were also explored. Moreover, human-origin avian influenza viruses with three or four genome segments from human virus had pandemic risk with high probability.ConclusionUsing machine learning methods, the present paper scores the amino acid mutations and predicts pandemic risk with well performance. Although long evolution distances between avian and human viruses suggest that avian influenza virus in nature still need time to fix among human host, it should be notable that there are high pandemic risks for H7N9 and H9N2 avian viruses.

Highlights

Avian influenza virus can directly cross species barriers and infect humans with high fatality
The importance score at each position in the 11 viral proteins was computed by the random forest (RF) model to screening the signature positions
The signature positions were founded and the initial amino acid mutation set was generated for further machine learning

Summary

Introduction

Avian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. Influenza A virus contains eight segments of single-strand negative RNA. According to the antigenic characteristics of HA and NA, avian influenza A virus has 16 subtypes HA and nine subtypes. Since the mutation rates of viral genome were fast, the phenotype of antigen, drug-resistance, and virulence changed in a relative short time. Segmental pattern facilitates the reassortment of viral genome and promote fast change of phenotypes [1]. Avian influenza virus (AIV) could across the species barrier and infect human fatally, which caused huge loss of economy and attracted extensive attention of the society.

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Conclusion