HIV-1 Epidemic in the Caribbean Is Dominated by Subtype B Yuka Nadai1, Lindsay M. Eyzaguirre1, Anne Sill1, Farley Cleghorn1, Claudine Nolte2, Manhattan Charurat1, Santiago Collado-Chastel3, Noreen Jack4, Courtenay Bartholomew4, Jean W. Pape2, Peter Figueroa5, William A. Blattner1, Jean K. Carr1* 1 Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America, 2 GHESKIO, Port-au-Prince, Haiti and Weill Medical College of Cornell University, New York, New York, United States of America, 3 Institute of Biomedical Studies, Santo Domingo, Dominican Republic, 4 Medical Research Foundation, Port of Spain, Trinidad and Tobago, 5 Ministry of Health, Kingston, Jamaica 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. Methodology/Principal Findings: 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. Citation: Nadai Y, Eyzaguirre LM, Sill A, Cleghorn F, Nolte C, et al. (2009) HIV-1 Epidemic in the Caribbean Is Dominated by Subtype B. PLoS ONE 4(3): e4814. doi:10.1371/journal.pone.0004814 Editor: Landon Myer, University of Cape Town, South Africa Received June 24, 2008; Accepted February 4, 2009; Published March 12, 2009 Copyright: 2009 Nadai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by 1R21 A1057084-02 from the National Institute of Allergy and Infectious Disease (PI: F Cleghorn, then WA Blattner) and also by the ‘‘Institute of Human Virology, University of Maryland, Baltimore, AITRP in Brazil, Caribbean and Nigeria’’, NIH grant # 5K43TW001041. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: jecarr@ihv.umaryland.edu Introduction The Caribbean has the second highest HIV-1 prevalence in the world today, approximately 1% in adult men and women, exceeded only by sub-Saharan Africa [1]. There is quite a bit of variability between the different countries in the Caribbean, however. The national adult HIV prevalence rate exceeds 1% in Barbados, Dominican Republic, Jamaica and Suriname, 2% in the Bahamas, Guyana and Trinidad and Tobago, and is greater than 3% in Haiti. The various epidemics in the Caribbean are driven predomi- nantly by heterosexual intercourse, fuelled by commercial sex work in societies with widespread poverty. A background of stagnant tourism-dependent economies, early coitarche, high numbers of sexual partners for both sexes, high rates of sexually transmitted diseases, stigmatization and discrimination against sexual minorities are some of the many factors driving the Caribbean HIV-1 epidemic [2,3,4]. Homosexual intercourse is a minor factor in most of the epidemics, though the extent of its contribution is probably underestimated due to stigma. Injecting drug use drives the epidemics in only two locations: Bermuda and Puerto Rico [4]. Although international efforts to systematically collect, charac- terize, and classify HIV isolates from around the world have increased considerably, data on HIV-1 genetic variations in the Caribbean remains limited. Globally, nine subtypes and 34 circulating recombinant forms have been defined in HIV-1 Group M, which accounts for most of the HIV-1 pandemic. One of the earliest HIV-1 strains characterized by full-genome sequencing (RF) was from a Haitian woman living in the United States but since that time no full genomes have been sequenced to represent the epidemic(s) in the Caribbean [5]. Partial genome sequencing of viruses from multiple Caribbean islands have reported subtype B as virtually the only subtype present (with the exception of Cuba) [6–8]. Because subtype B is the most common subtype in the United States, its presence in the Caribbean would seem unremarkable, but in fact subtype B has never been the most common subtype in a heterosexual epidemic anywhere in the world [9]. As such, the epidemics in the Caribbean are unique. PLoS ONE | www.plosone.org 1 March 2009 | Volume 4 | Issue 3 | e4814