Characterization of HIV-1 gag and nef in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic

Abstract

Background: Cameroon, in west central Africa, has an extraordinary degree of HIV diversity, presenting a major challenge for the development of an effective HIV vaccine. Given the continuing need to closely monitor the emergence of new HIV variants in the country, we analyzed HIV-1 genetic diversity in 59 plasma samples from HIV-infected Cameroonian blood donors. Full length HIV gag and nef sequences were generated and phylogenetic analyses were performed.

Findings: All gag and nef sequences clustered within HIV-1M. Circulating recombinant form CRF02_AG predominated, accounting for 50% of the studied infections, followed by clade G (11%), clade D and CRF37_cpx (4% each), and clades A, F, CRF01_AE and CRF36_cpx (2% each). In addition, 22% of the studied viruses apparently had nef and gag genes from viruses belonging to different clades, with the majority (8/10) having either a nef or gag gene derived from CRF02_AG. Interestingly, five gag sequences (10%) and three (5%) nef sequences were neither obviously recombinant nor easily classifiable into any of the known HIV-1M clades.

Conclusion: This suggests the widespread existence of highly divergent HIV lineages in Cameroon. While the genetic complexity of the Cameroonian HIV-1 epidemic has potentially serious implications for the design of biomedical interventions, detailed analyses of divergent Cameroonian HIV-1M lineages could be crucial for dissecting the earliest evolutionary steps in the emergence of HIV-1M.

Figure 1

Maximum likelihood trees indicating the phylogenetic relationships between 727 gag (A) and 628 nef (B) sequences of HIV-1. The trees were constructed from these sequences with 100 boostrap replicates following removal of recombinant sequence fragments by a blinded fully exploratory screen for recombination using RDP3. Black squares at the end of the branches represent the gag and nef sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. The gag tree was rooted using HIV-1 group N, O, P and SIV CPZ isolates, while the nef tree was rooted with HIV-1 group N, O and P isolates. Solid and open circles indicate branches with greater than 70% and 50% bootstrap support, respectively. The arrow in the nef tree indicates an outlier of both clades G and CRF02_AG.

Figure 2

Pie chart summarizing the distribution of HIV-1 Group M clades and recombinant forms from full length gag and nef gene sequencing (n=46). Intergene recombinants are detailed in the right panel. The 13 samples that were typed in only one of the genes were excluded from this analysis.