Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa

The purpose of this study was to document the genetic diversity of human im munodeficiency virus type 1 (HIV-1) in the Democratic Republic of Congo (DR C; formerly Zaire). A total of 247 HIV-l-positive samples, collected during an epidemiologic survey conducted in 1997 in three regions (Kinshasa [the capital], Bwa-manda [in the north], and Mbuyi-Maya [in the south]), were ge netically characterized in the env V3-V5 region. All known subtypes were fo und to cocirculate, and for 6% of the samples the subtype could not be iden tified. Subtype A is predominant, with prevalences decreasing from north to south (69% in the north, 53% in the capital city, and 46% in the south). S ubtype C, D, G, and H prevalences range from 7 to 9%, whereas subtype F, J, K, and CRF01-AE strains represent 2 to 4% of the samples; only one subtype B strain was identified. The highest prevalence (25%) of subtype C was in the south, and CRF01-AE was seen mainly in the north. The high intersubtype variability among the V3-V5 sequences is the most probable reason for the low (45%) efficiency of subtype A-specific PCR and HMA (heteroduplex mobili ty assay). Eighteen (29%) of 62 samples had discordant subtype designations between env and gag. Sequence analysis of the entire envelope from 13 samp les confirmed the high degree of diversity and complexity of HIV-1 strains in the DRC; 9 had a complex recombinant structure in gp160, involving fragm ents of known and unknown subtypes. Interestingly, the unknown fragments fr om the different strains did not cluster together. Overall, the high number of HIV-1 subtypes cocirculating, the high intrasubtype diversity, and the high numbers of possible recombinant viruses as well as different unclassif ied strains are all in agreement with an old and mature epidemic in the DRC , suggesting that this region is the epicenter of HIV-1 group M.