HIV-2 Surveillance with Next-Generation Sequencing Reveals Mutations in a Cytotoxic Lymphocyte-Restricted Epitope Involved in Long-Term Nonprogression

Abstract

HIV-2 exhibits a natural history of infection distinct from HIV-1. Primarily found in West Africa and in only 10%-20% of HIV infections in this region, patients with HIV-2 typically exhibit a slower progression to AIDS, lower viral loads, and decreased rates of transmission. Here, we used next-generation sequencing to determine the sequence and phylogenetic classification of nine HIV-2 genomes. We identified a patient with a series of mutations in an invariant cytotoxic lymphocyte (CTL)-restricted gag epitope required for retroviral structure and replication and implicated in long-term nonprogression to AIDS. The presence of wild-type sequence argues these mutations are involved in immune escape, whereas its reversion to a sequence seen only in the sooty mangabey reservoir suggests an alternate means of controlling infection. Surveillance and molecular characterization of circulating strains are essential for continued development of monitoring tools and may provide greater insight into the reduced pathogenicity of HIV-2.

Universal Target Capture of HIV Sequences From NGS Libraries

“…We continued to evaluate the probe set for the ability to capture HIV-1 groups O and N and HIV-2A sequences from virus isolate-generated libraries. Complete coverage was previously obtained in each case, with HIV-SMART libraries comprised of 3.8% (LA34; group O) and 10.0% (LA28; group N) HIV reads and randomly primed Ovation Single Cell libraries with 1.33% (LA38; HIV-2A) HIV reads (Berg et al, 2016 ; Yamaguchi et al, 2017 ). Here, cDNA libraries of each isolate were remade by random priming in this study and once again, 100% coverage was achieved for all three strains with a post-Nextera HIV-xGen enrichment, confirming that probes adequately covering these diverse groups were present and functional.…”

“…By contrast, metagenomic approaches using random priming permit an assessment of the full extent of sequence diversity in strains and can be applied to surveillance. Complete genomes of HIV and co-infecting viruses can be obtained directly from patient specimens, provided viral loads are high enough (Luk et al, 2015 ; Yamaguchi et al, 2017 ). To increase sensitivity, the HIV-SMART method utilizes reverse primers in conserved sequences of HIV fused to a tag to facilitate combined virus-specific priming and amplification (Berg et al, 2016 ; Rodgers et al, 2017a ).…”

Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma

“…We show a broad applicability of this method, presenting data from both lab-adapted isolates and patient plasma samples. To our knowledge, only one previous study has used a next-generation sequencing approach to determine the full genome of HIV-2 (35). However, we used HIV-2 isolates propagated in cell culture prior to library preparation and aligned the generated sequence reads to a common reference strain (HIV-2 BEN).…”