Dearth of full-length HIV-1 sequences obscures the true HIV-1 genetic subtypes distribution in sub-Saharan Africa

Abstract

HIV infection is still a public health problem in sub-Saharan Africa. The broad diversity exhibited by HIV-1 may impact on transmission, disease progression, drug resistance and vaccine development. Most analyses of HIV-1 subtype distribution have been on partial HIV-1 gene sequences, which may not adequately reflect the circulating subtypes. The objective of this study was to estimate the HIV-1 subtype distribution in sub-Saharan Africa using only full-length genome sequences. Using available HIV-1 full-length genome sequences from sub-Saharan Africa, the HIV-1 distribution in the region was analysed and compared with a previous global analysis which was not based entirely on full-length sequences. A total of 934 HIV-1 full-length genome sequences were available from 27 sub-Saharan countries. There was a disproportionate distribution of HIV-1 subtypes among countries with Cameroon having all the four HIV-1 groups. The subtype C was the most available in addition to a large proportion of circulating and unique recombinant forms (CRFs/URFs) especially in Central and West African countries, with frequencies of 32.6 to 90%. There was decreased representation of subtypes A and G in regions where CRFs/URFs were common compared with previous analysis using partial sequences. There is a need for more HIV-1 full-length genome sequences from sub-Saharan Africa for the true distribution of HIV-1 subtypes to be known, as analysis of partial sequences is not truly representative of the circulating subtypes.