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Open Access Short report

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

Marcel Tongo12, Darren P Martin3*, Lycias Zembe1, Eitel Mpoudi-Ngole2, Carolyn Williamson14 and Wendy A Burgers1*

Author Affiliations

1 Division of Medical Virology, University of Cape Town, Cape Town, South Africa

2 Institute of Medical Research and Study of Medicinal Plants, Yaoundé, Cameroon

3 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa

4 National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa

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Virology Journal 2013, 10:29  doi:10.1186/1743-422X-10-29

Published: 22 January 2013

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.

Keywords:
HIV-1 diversity; West central Africa; RDP3; Maximum likelihood; PHYML