New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men

Abstract

Background: HIV-1 circulating recombinant forms (CRF) containing subtype B are uncommon in sub-Saharan Africa. Prevalent infections observed during enrollment of a prospective study of men who have sex with men (MSM) from Lagos, Nigeria, revealed the presence of a family of subtype B and CRF02_AG recombinants. This report describes the HIV-1 genetic diversity within a high-risk, high-prevalence, and previously undersampled cohort of Nigerian MSM. Methods: Between 2013 and 2016, 672 MSM were enrolled at the Lagos site of the TRUST/RV368 study. Prevalent HIV-1 infections were initially characterized by pol sequencing and phylogenetic subtyping analysis. Samples demonstrating the presence of subtype B were further characterized by near full-length sequencing, phylogenetic, and Bayesian analyses. Results: Within this cohort, HIV-1 prevalence was 59%. The major subtype was CRF02_AG (57%), followed by CRF02/B recombinants (15%), subtype G (13%), and smaller amounts of A1, B, and other recombinants. Nine clusters of closely related pol sequences indicate ongoing transmission events within this cohort. Among the CRF02_AG/B, a new CRF was identified and termed CRF95_02B. Shared risk factors and Bayesian phylogenetic inference of the new CRF95_02B and the similarly structured CRF56_cpx indicate a Nigerian or West African origin of CRF56_cpx before its observation in France. Conclusion: With high HIV-1 prevalence, new strains, and multiple transmission networks, this cohort of Nigerian MSM represents a previously hidden reservoir of HIV-1 strains, including the newly identified CRF95_02B and closely related CRF56_cpx. These strains will need to be considered during vaccine selection and development to optimize the design of a globally effective HIV-1 vaccine.

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

“…These two sequences, MH654876 and MH654941, were the top two hits in the BLAST results, with 95% and 94% genetic similarity, respectively. Both samples were collected in Nigeria as part of a prospective observational cohort study focusing on MSM, and the collection dates were September 2015 for MH654876 and May 2014 for MH654941 [ 30 ]. The aligned partial sequences covered the 3’ end of the first fragment, the second fragment, and the 5’ end of the third fragment of the CRF91_cpx strain.…”

Transmitted, Pre-treatment and Acquired Antiretroviral Drug Resistance among Men who have Sex with Men and Transgender Women Living with HIV in Nigeria

“…Plasma samples with HIV RNA ≥1000 copies/mL at either enrollment or the first visit after HIV seroconversion underwent retrospective viral RNA extraction, cDNA generation, and near-endpoint dilution prior to PCR amplification, purification, and sequencing with an ABI 3730XL capillary sequencer [12]. HIV subtype was determined by evaluating Pol sequences and achieving a consensus assignment [12]. Pol sequences were evaluated for major mutations conferring resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) using the IAS-USA 2017 Update of the Drug Resistance Mutations in HIV [13].…”

“…HIV RNA was measured via nucleic acid amplification using the COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test, v2.0 (Roche Molecular Diagnostics, Pleasanton, CA, USA). Plasma samples with HIV RNA ≥1,000 copies/ml at either enrolment or the first visit after HIV seroconversion underwent retrospective viral RNA extraction, cDNA generation, and near-endpoint dilution prior to PCR amplification, purification and sequencing with an ABI 3730XL capillary sequencer [12]. HIV subtype was determined by evaluating Pol sequences and achieving a consensus assignment [12].…”

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens

“…Previously under-sampled regions can reveal unexpected patterns of change. For example, a CRF02/B recombinant form was found to be commonly circulating in Nigeria, an unexpected finding since B clade variants have rarely been sampled in Africa (Billings et al, 2019). One of the more unfortunate recent trends evident in Figure 5 is that CRF01 viruses, which once had a more limited distribution focused in Southeast Asia, are now more commonly sampled in China and Australia.…”