Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification

Nathalie Désiré,Lorenzo Cerutti,Anne-Geneviève Marcelin,Stéphane Hué,Marine Perrier,Stefan Emler,Diane Descamps,Quentin Le Hingrat,Benoit Visseaux,Vincent Calvez

doi:10.1186/s12977-018-0461-y

Abstract

BackgroundThe large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes.ResultsAll HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes.ConclusionsWith this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.

Highlights

The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity
HIV-1 presents an extraordinary degree of genetic diversity and has been classified, based on phylogenetic clustering, into groups, subtypes and sub-subtypes
Sequence data All HIV-1 groups M, N, O and P near full-genome sequences with available subtype information were downloaded from the Los Alamos National Laboratory (LANL) database on June 2016

Summary

Introduction

The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. While groups correspond to distinct lineages independently introduced into the human population from non-human apes, subtypes and sub-subtypes results from postintroduction founder events and further diversification. HIV subtypes can present different antiretroviral drug or vaccine response [4,5,6] [7, 8], disease progression [9,10,11] or transmission rates [12,13,14] All of these observations rely on an up-to-date and representative classification system, reflecting as best as possible the true and constantly evolving diversity of HIV-1 strains. Since HIV-1 is rapidly and continuously evolving, it is important to keep track of the diversification of the virus on a regular basis

Methods

Results

Conclusion