Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.

Yuanlin Ma,Xianhua Xie,Vo V. Anh,Guosheng Han,Runbin Tang,Zuguo Yu

doi:10.3390/e22020255

Abstract

HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time. In this study, we propose a new and effective alignment-free method for the phylogenetic analysis of HIV-1 viruses using complete genome sequences. Our method combines the position distribution information and the counts of the k-mers together. We also propose a metric to determine the optimal k value. We name our method the Position-Weighted k-mers (PWkmer) method. Validation and comparison with the Robinson–Foulds distance method and the modified bootstrap method on a benchmark dataset show that our method is reliable for the phylogenetic analysis of HIV-1 viruses. PWkmer can resolve within-group variations for different known subtypes of Group M of HIV-1 viruses. This method is simple and computationally fast for whole genome phylogenetic analysis.

Highlights

Human Immunodeficiency Viruses (HIVs) are retroviruses which are the causative agents of the global pandemic of Acquired Immunodeficiency Syndrome (AIDS) [1]
We present a new alignment-free method based on position-weighted k-mers to capture the subtle variations from the complete genome sequences of HIV-1 viruses
Subtyping of HIV-1 Based on Position-Weighted k-mers (PWkmer) Feature for Complete Genome Sequences

Summary

Introduction

Human Immunodeficiency Viruses (HIVs) are retroviruses which are the causative agents of the global pandemic of Acquired Immunodeficiency Syndrome (AIDS) [1]. HIV-1 viruses are divided into a major group (Group M) and two or more minor groups, namely Groups N, O, and possibly Group P. The subtypes A and F are further divided into sub-subtypes (A1, A2) and (F1, F2) based on differential phylogenetic clustering, respectively. Two or more HIV-1 subtypes can recombine and form Circulating Recombinant Forms (CRFs) [3]. Classification of HIV-1 strains into subtypes, sub-subtypes, and CRFs is a complex issue, which leads to major problems in the development of vaccines against HIV-1. These problems include high genetic variation, the fast evolution of different variants, and sequence diversity. The first task to solve these problems is how Entropy 2020, 22, 255; doi:10.3390/e22020255 www.mdpi.com/journal/entropy

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