Abstract
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics. Here we describe the development and implementation of approaches for HIV-1 NGS analysis in a southern Indian cohort. Plasma samples (n = 20) were obtained from HIV-1-confirmed individuals living in and around the city of Bengaluru. Near full-length genome recovery was obtained for 9 Indian HIV-1 patients, with recovery of full-length gag and env genes for 10 and 2 additional subjects, respectively. Phylogenetic analyses indicate the majority of sequences to be represented by subtype C viruses branching within a monophyletic clade, comprising viruses from India, Nepal, Myanmar and China and closely related to a southern African cluster, with a low prevalence of the A1C recombinant form also present. Development of algorithms for bespoke recovery and analysis at a local level will further aid clinical management of HIV-1 infected Indian subjects and delineate the progress of the HIV-1 pandemic in this and other geographical regions.
Highlights
Characterising the genetic composition of HIV-1 circulating in different geographical locales represents a significant undertaking, with implications for vaccine design, treatment efficacy regimes and understanding the molecular epidemiology of transmitted variants in target populations, with group M subtypes (A-K) and circulating recombinant forms (CRFs) comprising the majority of the genotypes in global circulation
We describe modifications of the whole genome amplification protocol described by Gall et al [4] applied to clinically-relevant plasma viruses and a bioinformatics framework in the form of a bespoke pipeline, to amplify HIV-1 genomes from Indian clinical isolates and assemble them reliably post-next generation sequencing (NGS) sequencing
We describe a phylogenetic analysis of these Indian HIV-1 sequences using this pipeline for the first time, as either whole genome sequences or gag genes to determine the relationship with the diversity of HIV-1 clade C infections worldwide
Summary
Characterising the genetic composition of HIV-1 circulating in different geographical locales represents a significant undertaking, with implications for vaccine design, treatment efficacy regimes and understanding the molecular epidemiology of transmitted variants in target populations, with group M subtypes (A-K) and circulating recombinant forms (CRFs) comprising the majority of the genotypes in global circulation. HIV-1 clade C infections represent approximately half of the total HIV-1 infections worldwide, being the majority variant in Southern Africa and the Indian subcontinent [1]. Whole genome recovery of HIV-1 RNA from plasma using a pan-HIV-1 amplification strategy and generation sequencing (NGS) and bioinformatics analyses has been reported [2,3,4], providing fresh insight on HIV-1 variation by taking into account many under-represented HIV-1 variants and recombinant forms in a given host. We describe a phylogenetic analysis of these Indian HIV-1 sequences using this pipeline for the first time, as either whole genome sequences or gag genes to determine the relationship with the diversity of HIV-1 clade C infections worldwide
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