Abstract

Influenza A virus is a segmented RNA virus whose genome consists of 8 single-stranded negative-sense RNA segments. This unique genetic structure allows viruses to exchange their segments through reassortment when they infect the same host cell. Studying the determination and nature of influenza A virus reassortment is critical to understanding the generation of pandemic strains and the spread of viruses across species. Reassortment detection is the first step in influenza A virus reassortment research. Several methods for automatic detection of reassortment have been proposed, which can be roughly divided into two categories: phylogenetic methods and distance methods. In this article, we proposed a reassortment detection method that does not require multiple sequence alignment and phylogenetic analysis. We extracted the codon features from the segment sequence and expressed the sequence as a feature vector, and then used the clustering method of self-organizing map to cluster the sequence for each segment. Based on the clustering results and the epidemiological information of the virus, the reassortment detection was implemented. We used this method to perform reassortment detection on the collected 7,075 strains from Asia and identified 516 reassortment events. We also conducted a statistical analysis of the identified reassortment events and found conclusions consistent with previous studies. Our method will provide new insights for automating reassortment detection tasks and understanding the reassortment patterns of influenza A viruses.

Highlights

  • Annual epidemics and occasional pandemics caused by the influenza A virus (IAV) are important threats to human health

  • Based on the feature vectors extracted from each sequence, we represented the IAV genome as a 488-dimensional feature vector composed of eight segment feature vectors

  • It should be noted that swine is a mixed vessel, which connected the genome of the avian influenza virus and the genome of the human infected influenza virus (Figure 3B)

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Summary

Introduction

Annual epidemics and occasional pandemics caused by the influenza A virus (IAV) are important threats to human health. When multiple influenza A viruses infect the same host cell, due to the genome characteristics of segmented viruses, the genomes of multiple viruses may exchange their segments, resulting in progeny viruses with new genome combinations [2]. Reassortment plays an important but undefined role in the cross-species transmission of influenza A virus [3].

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