Open Access Research

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

Jean K Carr1*, Nathan D Wolfe2, Judith N Torimiro34, Ubald Tamoufe5, E Mpoudi-Ngole5, Lindsay Eyzaguirre1, Deborah L Birx6, Francine E McCutchan7 and Donald S Burke8

Author Affiliations

1 Institute of Human Virology, Univ. of Maryland School of Medicine, Baltimore, MD, USA

2 Global Viral Forecasting Initiative, San Francisco, and Stanford University, Program in Human Biology, Stanford, CA, USA

3 Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon

4 Chantal Biya International Reference Centre, Yaounde, Cameroon

5 Hopital Militaire de Yaoundé, Yaounde, Cameroon

6 Global AIDS Program, CDC, Atlanta, GA, USA

7 Bill and Melinda Gates Foundation, Seattle, WA, USA

8 University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA

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Retrovirology 2010, 7:39  doi:10.1186/1742-4690-7-39

Published: 28 April 2010

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.