A putative HIV-1 subtype C/CRF11_cpx unique recombinant from South Africa.

Pascal Obong Bessong,Benson Iweriebor

doi:10.1186/s40064-016-1924-z

Pascal Obong Bessong, Benson Iweriebor

Open Access

https://doi.org/10.1186/s40064-016-1924-z

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Journal: SpringerPlus	Publication Date: Mar 5, 2016
Citations: 4	License type: CC BY 4.0

Affiliation: University of Venda, University of Fort Hare

Abstract

The HIV epidemic in South Africa is overwhelmingly driven by HIV-1 subtype C viruses. The HIV gag, pol, env (C2-V5) and nef sequences of virus 08MB26ZA, obtained from a 47 year old woman, were studied by phylogenetic analysis, REGA and the jumping Profile Hidden Markov Model (jPHMM) tools. The pol gene was further analyzed for recombination by Simplot. The pol and env sequences were examined for genetic drug resistance mutations and predicted co-receptor usage respectively. There was agreement in the assignment of the gag sequence as pure HIV-1 subtype C by phylogenetic, REGA and jPHMM analyses. The pol sequence clustered with CRF11_cpx and in the J-clade by phylogenetic analysis; and to a CRF11_cpx/subtype C recombinant by REGA. The assignment of pol to CRF11_cpx and subtype C was confirmed by Simplot. The recombinant was of the R5 biotype, with no important drug resistance mutations in the pol region. The epidemiologic and biologic significance of the virus are unknown. The finding suggests that complex viruses are being introduced into South Africa with potential implications for diagnosis. This is apparently the first report from South Africa of a putative unique recombinant involving CRF11_cpx and subtype C genomes.

Highlights

Genetic variants of HIV contribute to the pandemic worldwide and have potential consequences for diagnostics, treatment and treatment monitoring, and the development of an effective vaccine (Hemelaar 2013)
Several factors account for the high genetic diversity of HIV: rapid replication turnover, in vivo host selective immune and treatment pressure, and recombination events during replication (Liitsola et al 1998; Corbet et al 2000; Ramirez et al 2008; Taylor et al 2008)
Fragments of subtype J are present in many mosaic recombinant forms originating from West Africa (CRF06_cpx) and Central West Africa (CRF11_cpx, CRF13_cpx, and CRF49_cpx), suggesting that this subtype, either in a pure or in a recombinant form, is probably prevalent across Central and West Africa (Laukkanen et al 1999)

Summary

Introduction

Genetic variants of HIV contribute to the pandemic worldwide and have potential consequences for diagnostics, treatment and treatment monitoring, and the development of an effective vaccine (Hemelaar 2013). Several factors account for the high genetic diversity of HIV: rapid replication turnover, in vivo host selective immune and treatment pressure, and recombination events during replication (Liitsola et al 1998; Corbet et al 2000; Ramirez et al 2008; Taylor et al 2008). Due to this variability, HIV is classified into types 1 and 2; with type 1 further classified into groups M, O, N and P. Few subtype J sequences are available, and these are mostly from the Democratic Republic of Congo, Cameroon, and Senegal (Los Alamos Database 2014).

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