HIV Type 1 Strains from East and West Africa Are Intermixed in Sudan

Abstract

The genetic subtypes of HIV-1 in the Sudan epidemic have not been characterized. Here we report the partial sequencing and analysis of 30 strains collected from HIV-1-positive patients and blood donors in Khartoum in 1998 and 1999. From analysis of partial pol and env sequences, it was determined that 50% were subtype D and 30% were subtype C. Of interest, some subtype D clustered with those from East Africa whereas others joined subtype D from West Africa. Subtype A, subtype B, and three unique recombinants were also found, some partially unclassifiable. One unclassified strain matched another reported previously from the Democratic Republic of Congo. Sudan borders nine other African countries, and has suffered more than 20 years of civil strife with large population displacements. The intermixing of HIV-1 subtypes previously separated in Africa may be occurring there, with the potential to generate novel new strains by recombination.

Development of a Nucleic Acid Sequence-Based Amplification Assay That Uses gag -Based Molecular Beacons To Distinguish between Human Immunodeficiency Virus Type 1 Subtype C and C′ Infections in Ethiopia

“…In Ethiopia, except for two reported cases of subtype D viruses (3,15), no other subtypes have been documented. These data fit well with observations from neighboring countries and others in the region, in which along with HIV-1 subtype C, other subtypes, mainly subtypes A and D, also cocirculate (12,13,17,19). These subtypes are the ones which are most likely to appear in Ethiopia, given the proximity of the areas in which they predominate.…”

Impact of HIV Subtype on Performance of the Limiting Antigen-Avidity Enzyme Immunoassay, the Bio-Rad Avidity Assay, and the BED Capture Immunoassay in Rakai, Uganda

“…18 Misclassification of HIV subtype D infection has marginal significance on a global level, but is extremely significant in Uganda where subtypes A and D predominate and in Sudan where subtype D is the most common. 17,19 The performance of serologic HIV incidence assays has been shown to vary by HIV subtype. [20][21][22][23] For example, among individuals infected for 2 or more years, being misclassified as assay positive is more likely in subtype D infection than subtype A infection.…”

Worldwide molecular epidemiology of HIV

“…12,83,98 HIV subtype B has been the main epidemic component in the Western Europe (60%), together with subtype A (11%), C (5%) and other subtypes (11%). 32,50,51,130,134 Subtype B is also predominant in Americas, 78,79,144 and in the Australian continent, 48 and also in some Asian countries as Korea, 102 India and Singapure. 122 In Japan, 66,146 where the subtype B has been predominant (74%), other subtypes such as C (3.5%), A (2.0%), F (1.0%) are also circulating together with subtype E (20%).…”

“…18,54 In Argentina, Uruguay, and Brazil the CRF12_BF became prevalent in heterosexual population, and in vertically infected children. 17,36,51,114,116,120,121 In Brazil, the distribution of HIV-1 subtypes assumes diversified patterns according to the geographic regions. In the Brazilian Southern and Southeastern States the rate of subtype B arise to 50%, and subtypes C and F represent 28% and 7%, respectively, 127 while in Northeastern region occurs a high prevalence of B (>80%) followed by a low frequency (<3%) of subtype F and BC recombinant.…”