The evolution of HIV‐1 group M genetic variability in Southern Cameroon is characterized by several emerging recombinant forms of CRF02_AG and viruses with drug resistance mutations

Abstract

The HIV epidemic in Cameroon is marked by a broad genetic diversity dominated by Circulating Recombinant Forms (CRFs). Studies performed more than a decade ago in urban settings of Southern Cameroon revealed a dominance of the CRF02_AG and clade A variants in >90% of the infected subjects; however, little is known about the evolving viral variants circulating in this region. To document circulating HIV viral diversity, four regions of the viral genome (gag, PR, reverse transcriptase, env) in 116 HIV-1 positive individuals in Limbe, Southern Cameroon, were PCR-amplified. Sequences obtained at the RT and protease regions were analyzed for mutations that conferred drug resistance using the Stanford Drug Resistance Database. The present study reveals a broad genetic diversity characterized by several unique recombinant forms (URF) accounting for 36% of infections, 48.6% of patients infected with CRF02_AG, and the emergence of CRF22_01A1 in 7.2% of patients. Three out of 15 (20%) treated patients and 13 out of 93 (13.9%) drug naïve patients harbor drug resistance mutations to RT inhibitors, while 3.2% of drug naïve patients harbor drug resistance mutations associated with protease inhibitors. The high proportion (13.9%) of drug resistance mutations among the drug naïve patients reveals the ongoing transmission of these viruses in this region of Cameroon and highlights the need for drug resistance testing before starting treatment for patients infected with HIV-1.

Near full genome characterization of HIV‐1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns

“…Plasma samples from 18 Cameroonian study participants at ART‐naïve time points were selected for the current study (Table ). All study participants were infected with HIV‐1 M URFs based on partial genome sequencing ; no further biological selection criteria were applied. The study included participants from both genders, between 20 and 70 years of age, and at different stages of HIV‐1 infection.…”

“…It underlined the necessity of performing NFGS in order to achieve accurate HIV surveillance, subtyping and genotypic analyses. The URFs were composed of pure (sub‐)subtypes A (A1), F (F2) and G, and recombinant forms CRF02_AG, CRF01_AE and CRF22_01A1, thus, URFs appeared to have taken up key circulating strains in Cameroon . Notably, 16/18 URFs contained CRF02_AG sequences and 13/18 URFs contained F2 sequences.…”

“…They were shipped from the MDC under regulatory guidelines of transfer on biological samples to NYUSoM, where plasma was separated from peripheral blood mononuclear cells through Ficoll gradient centrifugation (Histopaque, Sigma‐Aldrich, St. Louis, MO, USA), and stored at −80°C. Eighteen URFs were selected based on previously published work from our group using partial genome sequencing (total of 509 participants) . Inclusion criteria were genetic evidence of URF infection and available plasma volumes ≥500 μL.…”

“…The predominant lineage is the recombinant CRF02_AG, which accounts for more than half of infections . Also, circulating virus lineages include virtually every known HIV‐1 group M (HIV‐1 M) pure subtype, many CRFs, and a variety of URFs composed of pure, CRF and/or non‐classifiable sequences making this country a unique source of rare and emerging HIV‐1 M viral variants . The range of subtypes and the extent of viral diversity within a geographical region considerably impact HIV diagnosis, treatment and prevention .…”

“…As part of our ongoing molecular surveillance efforts in Cameroon, our laboratories have in recent years identified and characterized two CRFs (CRF_36cpx and CRF_37cpx) , and we have monitored a steady increase in URFs . Through the application of a robust and versatile near full genome (NFG) amplification and sequencing technique , the current study characterized 18 near‐full genomes of HIV‐1 M recombinants.…”