New subtype B containing HIV-1 circulating recombinant of sub-Saharan Africa origin in Nigerian men who have sex with men
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 via 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_02/B. 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 prior to 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 in order to optimize the design of a globally effective HIV-1 vaccine.
Billings, Erik, Gustavo H. Kijak, Eric Sanders-Buell, Nicaise Ndembi, Anne Marie O'Sullivan, Sylvia Adebajo, Afoke Kokogho, Mark Milazzo, Kara Lombardi, Stefan Baral, Rebecca G. Nowak, Habib O. Ramadhani, Robert Gramzinski, Merlin L. Robb, Nelson L. Michael, Manhattan E. Charurat, Julie Ake, Trevor A. Crowell, Sodsai Tovanabutra for the MHRP Viral Sequencing Core and the TRUST/RV368 Study Group. 2019. "New subtype B containing HIV-1 circulating recombinant of sub-Saharan Africa origin in Nigerian men who have sex with men," Journal of Acquired Immune Deficiency Syndromes 81(5): 578–584.