HIV-1 recombinants with multiple parental strains in low-prevalence, remote regions of Cameroon: evolutionary relics?

Abstract

Background: The HIV pandemic disseminated globally from Central West Africa, beginning in the second half of the twentieth century. To elucidate the virologic origins of the pandemic, a cross-sectional study was conducted of the genetic diversity of HIV-1 strains in villagers in 14 remote locations in Cameroon and in hospitalized and STI patients. DNA extracted from PBMC was PCR amplified from HIV(+) subjects. Partial pol amplicons (N = 164) and nearly full virus genomes (N = 78) were sequenced. Among the 3956 rural villagers studied, the prevalence of HIV infection was 4.9%; among the hospitalized and clinic patients, it was 8.6%.

Results: Virus genotypes fell into two distinctive groups. A majority of the genotyped strains (109/164) were the circulating recombinant form (CRF) known to be endemic in West Africa and Central West Africa, CRF02_AG. The second most common genetic form (9/164) was the recently described CRF22_01A1, and the rest were a collection of 4 different subtypes (A2, D, F2, G) and 6 different CRFs (-01, -11, -13, -18, -25, -37). Remarkably, 10.4% of HIV-1 genomes detected (17/164) were heretofore undescribed unique recombinant forms (URF) present in only a single person. Nearly full genome sequencing was completed for 78 of the viruses of interest. HIV genetic diversity was commonplace in rural villages: 12 villages each had at least one newly detected URF, and 9 villages had two or more.

Conclusions: These results show that while CRF02_AG dominated the HIV strains in the rural villages, the remainder of the viruses had tremendous genetic diversity. Between the trans-species transmission of SIVcpz and the dispersal of pandemic HIV-1, there was a time when we hypothesize that nascent HIV-1 was spreading, but only to a limited extent, recombining with other local HIV-1, creating a large variety of recombinants. When one of those recombinants began to spread widely (i.e. became epidemic), it was recognized as a subtype. We hypothesize that the viruses in these remote Cameroon villages may represent that pre-epidemic stage of viral evolution.

Figure 1

Satellite Map of Cameroon with study sites. Study sites are indicated by the two letter code identifying them.

Figure 2

Panel A: Phylogenetic analysis of 164 partial pol sequences from Cameroon. A neighbor-joining analysis of partial pol sequences (protease and the amino terminus of RT) using the Kimura 2-parameter method of distance calculation was performed with representative strains of varying subtypes and CRF (identified by name). The scale bar indicates genetic distance of 1%. Nodes with significant bootstrap support (>70%) and containing Cameroon sequences are indicated with color. Panel B: Relative proportions of different subtypes or CRF. RF = recombinant form.

Figure 3

Schematic showing the genetic types of viruses, based on partial pol sequences, by geographic site. Each virus type is represented as a box, with the abbreviated name of the genetic form in the box. The two letter code for the site and the prevalence at the site are on the left. Letters = subtypes; numbers = CRFs.

Figure 4

Genetic structure of nearly full length unique recombinant genomes by site.

Figure 5

Diagram of a hypothesized scenario of HIV emergence. Different colors represent different strains of the virus. Distance from the center of the circle represents time since the initial emergence. Adapted from Kalish et al., 2004 [18].