title: Population dynamics of HIV-2 in rural West Africa:  comparison with HIV-1 and ongoing transmission at the heart of the epidemic.
abstract: OBJECTIVE
  To compare the population dynamics of HIV-2 and HIV-1, and to characterize ongoing HIV-2 transmission in rural Guinea-Bissau.
  
  
  METHODS
  Phylogenetic and phylodynamic analyses using HIV-2 gag and env, and HIV-1 env sequences, combined with epidemiological data from a community cohort.
  
  
  METHODS
  Samples were obtained from surveys in 1989-1991, 1996-1997, 2003 and 2006-2007. Phylogenies were reconstructed using sequences from 103 HIV-2-infected and 56 HIV-1-infected patients using Bayesian Evolutionary Analysis by Sampling Trees (BEAST), a relaxed molecular clock and a Bayesian skyline coalescent model.
  
  
  RESULTS
  Bayesian skyline plots showed a strong increase in the 1990s of the HIV-1 effective population size (Ne) in the same period that the Ne of HIV-2 came into a plateau phase. The population dynamics of both viruses were remarkably similar following initial introduction. Incident infections were found more often in HIV-2 transmission clusters, with 55-58% of all individuals contributing to ongoing transmission. Some phylogenetically linked sexual partners had discordant viral loads (undetectable vs. detectable), suggesting host factors dictate the risk of disease progression in HIV-2. Multiple HIV-2 introductions into the cohort are evident, but ongoing transmission has occurred predominantly within the community.
  
  
  CONCLUSIONS
  Comparison of HIV-1 and HIV-2 phylodynamics in the same community suggests both viruses followed similar growth patterns following introduction, and is consistent with the hypothesis that HIV-1 may have played a role in the decline of HIV-2 via competitive exclusion. The source of ongoing HIV-2 transmission in the cohort appears to be new HIV-2 cases, rather than the pool of older infections established during the early growth of HIV-2.
authors.affiliation: Medical Research Council (UK) Laboratories, Fajara, The Gambia. thushandesilva@hotmail.com
authors.forename: Thushan I
authors.initials: TI
authors.lastname: de Silva
authors.forename: Carla
authors.initials: C
authors.lastname: van Tienen
authors.forename: Clayton
authors.initials: C
authors.lastname: Onyango
authors.forename: Abdoulie
authors.initials: A
authors.lastname: Jabang
authors.forename: Tim
authors.initials: T
authors.lastname: Vincent
authors.forename: Maarten F Schim van der
authors.initials: MF
authors.lastname: Loeff
authors.forename: Roel A
authors.initials: RA
authors.lastname: Coutinho
authors.forename: Assan
authors.initials: A
authors.lastname: Jaye
authors.forename: Sarah
authors.initials: S
authors.lastname: Rowland-Jones
authors.forename: Hilton
authors.initials: H
authors.lastname: Whittle
authors.forename: Matthew
authors.initials: M
authors.lastname: Cotten
authors.forename: Stéphane
authors.initials: S
authors.lastname: Hué
mesh_terms: D001499:Bayes Theorem; D016000:Cluster Analysis; D005260:Female; D006169:Guinea-Bissau / Q000453:epidemiology; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000235:genetics; D015498:HIV-2 / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D012424:Rural Population / Q000706:statistics & numerical data*; D012747:Sexual Partners; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus