HIV-1 subtypes and the HIV epidemics in four cities in sub-Saharan Africa

Objective: To describe the distribution of HIV-1 subtypes in two cities wit h high HIV prevalence (Kisumu, Kenya and Ndola, Zambia) and two with relati vely low prevalence (Cotonou, Benin and Yaounde, Cameroon), and to examine whether the differences in prevalence of HIV infection could be due to the predominance within the infected populations of subtypes with differing eff iciency of heterosexual transmission. Methods: For around 100 randomly selected HIV-positive sera from the genera l population and 60 from sex workers in each city, the HIV-1 subtype was de termined in the env fragment. For between 19 and 52 of the sera from the ge neral population and 20-32 sera from sex workers, the subtype was also dete rmined in the gag fragment. Results: Over 70% of infections in Cotonou, Yaounde and Kisumu were with su btype A (by env). However, around one-half of subtype A infections in Coton ou and Yaounde were found to be the circulating recombinant form CRF02(-)AG when the gag fragment was also examined. A large number of different HIV s trains were found in Yaounde, including some belonging to group O. Over 20% of infections in Kisumu and around 10% in Yaounde were with isolated inter subtype recombinant forms. All but a few infections in Ndola were with subt ype C and no recombinants were found. Conclusions: The pattern of distribution of subtypes that we found does not suggest that differences in circulating subtypes play a major role in expl aining the differences in prevalence of HIV-1 infection between the four ci ties. The emergence and spread of recombinants requires close surveillance to adapt testing strategies if needed, to inform vaccine development and to ascertain their role in the future spread of HIV. (C) 2001 Lippincott Will iams & Wilkins.