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Issecting the earliest evolutionary steps in the emergence of HIV-1M. Keywords: HIV-1 diversity, West central Africa, RDP3, Maximum likelihood, PHYMLFindings The Congo basin in west central Africa is thought to be the origin of HIV, where several cross-species transmission events from chimpanzees to humans occurred [1,2]. Cameroon, located in this region, has one of the most genetically diverse HI
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Cias Zembe1, Eitel Mpoudi-Ngole2, Carolyn Williamson1,4 and Wendy A Burgers1*AbstractBackground: 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 s
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Orrespondence: Darrin.Martin@uct.ac.za; Wendy.Burgers@uct.ac.za 3 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa 1 Division of Medical Virology, University of Cape Town, Cape Town, South Africain west central Africa, at 5.3 [8]. This, together with the co-circulation of divergent variants of multiple clades, h
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One of the newly sequenced gag genes (BS72) was apparently derived through recombination between F2 and CRF36_cpx parental viruses, one of the nef genes was apparently derived through recombination between F and CRF22_01A1 parental viruses. The phylogenetic analysis of gag sequences derived from the Cameroonian samples further revealed four sequences (BS09, BS25, BS16 and BS42) situated on diverge
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Ologyj.com/content/10/1/Page 2 ofparticularly relevant because they encode highly immunogenic proteins that are frequently included in candidate vaccines [9-11]. We sequenced 50 full length HIV-1 gag and 55 nef genes from 59 HIV-infected blood donors in Cameroon. To obtain a phylogenetic view of Cameroonian HIV diversity that explicitly accounted for the confounding effects of recombination, we pe
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Mpled sequences are likely CRF02_AG (accounting for 50 of HIV-1M infections), with the other "pure" subtypes (G, D, A, and F) and CRFs (CRF11_cpx, 36_cpx, 37_cpx, and CRF01_AE) accounting for the remainder of infections. CRF02_AG and clade G viruses are broadly distributed across west central Africa and have apparently been circulating stably there for many years [3,17-19], consistent with the pr
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F known clades. Although the majority of the outlier viruses found in our study were also URFs, they remained outliers after the removal of recombinant segments. It thus appears that these sequences represent viruses that are genuinely highly divergent and are possibly extant descendants of previously unknown early divergingTable 3 Inter and intraclade recombinantsSample ID BS02 BS09 BS11 BS13 BS2
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Issecting the earliest evolutionary steps in the emergence of HIV-1M. Keywords: HIV-1 diversity, West central Africa, RDP3, Maximum likelihood, PHYMLFindings The Congo basin in west central Africa is thought to be the origin of HIV, where several cross-species transmission events from chimpanzees to humans occurred [1,2]. Cameroon, located in this region, has one of the most genetically diverse HI