title: HIV-1 subtypes and the HIV epidemics in four cities in sub-Saharan Africa.
abstract: OBJECTIVE
  To describe the distribution of HIV-1 subtypes in two cities with high HIV prevalence (Kisumu, Kenya and Ndola, Zambia) and two with relatively low prevalence (Cotonou, Benin and Yaoundé, 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 efficiency of heterosexual transmission.
  
  
  METHODS
  For around 100 randomly selected HIV-positive sera from the general population and 60 from sex workers in each city, the HIV-1 subtype was determined in the envfragment. For between 19 and 52 of the sera from the general population and 20-32 sera from sex workers, the subtype was also determined in the gag fragment.
  
  
  RESULTS
  Over 70% of infections in Cotonou, Yaoundé and Kisumu were with subtype A (by env). However, around one-half of subtype A infections in Cotonou and Yaoundé were found to be the circulating recombinant form CRF02_AG when the gag fragment was also examined. A large number of different HIV strains were found in Yaoundé, including some belonging to group O. Over 20% of infections in Kisumu and around 10% in Yaoundé were with isolated intersubtype recombinant forms. All but a few infections in Ndola were with subtype 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 explaining the differences in prevalence of HIV-1 infection between the four cities. 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.
authors.affiliation: Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, UK. Linda.Morrison@lshtm.ac.uk
authors.forename: L
authors.initials: L
authors.lastname: Morison
authors.forename: A
authors.initials: A
authors.lastname: Buvé
authors.forename: L
authors.initials: L
authors.lastname: Zekeng
authors.forename: L
authors.initials: L
authors.lastname: Heyndrickx
authors.forename: S
authors.initials: S
authors.lastname: Anagonou
authors.forename: R
authors.initials: R
authors.lastname: Musonda
authors.forename: M
authors.initials: M
authors.lastname: Kahindo
authors.forename: H A
authors.initials: HA
authors.lastname: Weiss
authors.forename: R J
authors.initials: RJ
authors.lastname: Hayes
authors.forename: M
authors.initials: M
authors.lastname: Laga
authors.forename: W
authors.initials: W
authors.lastname: Janssens
authors.forename: G
authors.initials: G
authors.lastname: van der Groen
mesh_terms: D000293:Adolescent; D000328:Adult; D017954:Africa South of the Sahara / Q000453:epidemiology; D004196:Disease Outbreaks; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015683:Gene Products, gag / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D020180:Heteroduplex Analysis; D020010:Heterosexuality; D006801:Humans; D008297:Male; D015995:Prevalence; D011477:Sex Work; D014505:Urban Population
chemical_list: D015686:Gene Products, env; D015683:Gene Products, gag