AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 19, Number 10, 2003, pp. 929–932 © Mary Ann Liebert, Inc. Sequence Note Characterization of HIV Type 1 Clades in the Caribbean Using pol Gene Sequences H. E. VAUGHAN, 1 P. CANE, 2 D. PILLAY, 2,4 and R. S. TEDDER 3 ABSTRACT To date, 11 HIV-1 M group clades, A to K, have been characterized, displaying different distributions, preva- lences, and biological properties. Approximately 90% of new HIV-1 infections occur in developing countries, including the Caribbean. However, information on HIV-1 subtypes from this region is limited. We report sub- type characterization of viruses from 71 individuals, obtained during the period 2000–2002. RNA from the pol region was sequenced, generating data on subtype and drug resistance associated mutations for 71 spec- imens from 9 countries. Sixty-seven (94.4%) sequences were classified as clade B, three (4.2%) as D/B, and one (1.4%) as clade C. Numerous polymorphisms were observed, including some associated with drug resis- tance, but not signifying exposure to chemotherapy. This study adds to our knowledge of HIV-1 clades in the Caribbean, and indicates possibilities for monitoring HIV-1 chemotherapy. 929 E LEVEN SUBTYPES OF M-GROUP HIV-1, A to K, have been described to date, and there is no apparent linear descent relationship between clades. 1 They may have varying biologi- cal properties and display different geographical distributions and prevalences, necessitating a need for regional characteri- zation and surveillance. In the absence of surveillance, the emergence of new clades in a region may result in an underes- timate of the impact of the epidemic. Approximately 90% of new HIV-1 infections occur in de- veloping countries, including the Caribbean. 2 However, infor- mation regarding circulating HIV-1 clades from this region is limited. Early studies reveal that in the Americas, including the United States, Brazil, Haiti, and Trinidad, clade B has pre- dominated. 3–5 Studies in several countries, including Cuba, Brazil, Venezuela, and Thailand, 3,6–8 have found sudden shifts in subtype frequenciesover just a few years, underlying the im- portance of assessing trends. Early molecular studies used variability in env to determine HIV-1 clade, either by sequencing or heteroduplexmobility as- say. 6,7,9–12 More recently, pol has also shown sufficient varia- tion to allow classification. 13,14 For this study, pol was selected to allow both cladistic analysis and identification of drug re- sistance. Antiretroviral therapy comprises two main classes of drug: targetting viral protease (PR) and viral reverse transcriptase (RT), often used in combination. Most resistance-conferring mutations occur in the pol gene, which constitutes the coding region for protease, reverse transcriptase, and integrase. Some commercial systems (e.g., ABI and Visible Genetics) have been developed to detect important mutations, and some reference laboratories, for example, in France and the United Kingdom, have developed in-house methodologies. 13,15 The Caribbean Epidemiology Centre (CAREC) is a public health organization administered by the Pan American Health Organization (PAHO), WHO’s regional office for the Ameri- cas. CAREC provides reference laboratory services to 21 coun- tries in the region. 16 Consequently, CAREC has a role both in the surveillance of HIV and as a serum bank. The purpose of this study was primarily to identify which clades are currently circulating in the region and to allow evaluation of the tech- 1 Caribbean Epidemiology Centre (CAREC), Federation Park, Trinidad and Tobago. 2 PHLS, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK. 3 UCL Department of Virology, Windeyer Institute, University College London, London W1T 4JF, UK. 4 Current address: UCL Department of Virology, Windeyer Institute, University College London, London W1T 4JF, UK.