title: HIV-1 epidemic in the Caribbean is dominated by subtype B.
abstract: BACKGROUND
  The molecular epidemiology of HIV-1 in the Caribbean has been described using partial genome sequencing; subtype B is the most common subtype in multiple countries. To expand our knowledge of this, nearly full genome amplification, sequencing and analysis was conducted.
  
  
  RESULTS
  Virion RNA from sera collected in Haiti, Dominican Republic, Jamaica and Trinidad and Tobago were reverse transcribed, PCR amplified, sequenced and phylogenetically analyzed. Nearly full genomes were completed for 15 strains; partial pol was done for 67 strains. All but one of the 67 strains analyzed in pol were subtype B; the exception was a unique recombinant of subtypes B and C collected in the Dominican Republic. Of the nearly full genomes of 14 strains that were subtype B in pol, all were subtype B from one end of the genome to the other and not inter-subtype recombinants. Surprisingly, the Caribbean subtype B strains clustered significantly with each other and separate from subtype B from other parts of the pandemic.
  
  
  CONCLUSIONS
  The more complete analysis of HIV-1 from 4 Caribbean countries confirms previous research using partial genome analysis that the predominant subtype in circulation was subtype B. The Caribbean strains are phylogenetically distinct from other subtype B strains although the biological meaning of this finding is unclear.
authors.affiliation: Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Nadai
authors.forename: Lindsay M
authors.initials: LM
authors.lastname: Eyzaguirre
authors.forename: Anne
authors.initials: A
authors.lastname: Sill
authors.forename: Farley
authors.initials: F
authors.lastname: Cleghorn
authors.forename: Claudine
authors.initials: C
authors.lastname: Nolte
authors.forename: Manhattan
authors.initials: M
authors.lastname: Charurat
authors.forename: Santiago
authors.initials: S
authors.lastname: Collado-Chastel
authors.forename: Noreen
authors.initials: N
authors.lastname: Jack
authors.forename: Courtenay
authors.initials: C
authors.lastname: Bartholomew
authors.forename: Jean W
authors.initials: JW
authors.lastname: Pape
authors.forename: Peter
authors.initials: P
authors.lastname: Figueroa
authors.forename: William A
authors.initials: WA
authors.lastname: Blattner
authors.forename: Jean K
authors.initials: JK
authors.lastname: Carr
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000302:isolation & purification; D014900:West Indies / Q000453:epidemiology
chemical_list: D017931:DNA Primers; D012367:RNA, Viral