title: Update on HIV-1 diversity in Africa: a decade in review.
abstract: BACKGROUND
  HIV-1 strains have diversified extensively through mutation and recombination since their initial transmission to human beings many decades ago in Central Africa in the first part of the 20th Century (between 1915 and 1941). The upward trend in global HIV-1 diversity has continued unabated, with newer groups, subtypes, and unique and circulating recombinants increasingly being reported, especially in Africa.
  
  
  OBJECTIVE
  In this review, we focus on the extensive diversity of HIV-1 over a decade (2000-2011), in 51 countries of the three African geographic regions (eastern and southern, western and central, and northern Africa) as per the WHO/UNAIDS 2010 classification.
  
  
  METHODS
  References for this review were identified through searches of PubMed, conference abstracts, Google Scholar, and Springer Online Archives Collection. We retrieved 273 citations, of which 200 reported HIV-1 diversity from Africa from January, 2000 to August, 2011. Articles resulting from these searches and relevant references cited in those articles were reviewed. Articles published in English and French were included.
  
  
  RESULTS
  There has been a high diversity of HIV-1 in its epicenter, west-central Africa. A few subtypes, namely, A (A1, A2, A3, A4, A5), C, CRF02_AG, and D accounted for about 85% of new infections. Subtype A and D have been stable in East Africa; C in southern Africa; A, G, CRF02_AG, and CRF06_cpx in western Africa; and subtype B and CRF02_AG in northern Africa. Recently a new putative group, designated P, was reported to be found in two Cameroonians.
  
  
  CONCLUSIONS
  The regional distributions of individual subtypes and recombinants are broadly stable, although unique/circulating recombinant forms may play an increasing role in the HIV pandemic. Understanding the kinetics and directions of this continuing adaptation and its impact on viral fitness, immunogenicity, and pathogenicity are crucial to the successful design of effective HIV vaccines. There is need for regular monitoring and review updates, such as the one presented here, to assist countries to plan and anticipate complex forms that may be introduced with time.
authors.affiliation: Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
authors.forename: Raphael W
authors.initials: RW
authors.lastname: Lihana
authors.forename: Deogratius
authors.initials: D
authors.lastname: Ssemwanga
authors.forename: Alash'le
authors.initials: A
authors.lastname: Abimiku
authors.forename: Nicaise
authors.initials: N
authors.lastname: Ndembi
mesh_terms: D016915:AIDS Vaccines / Q000276:immunology; D000349:Africa / Q000453:epidemiology; D005260:Female; D015658:HIV Infections / Q000453:epidemiology / Q000276:immunology / Q000517:prevention & control / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000472:pathogenicity; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D011159:Population Surveillance; D011995:Recombination, Genetic
chemical_list: D016915:AIDS Vaccines