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Gayatri C Jayaraman PhD MPH, Chris P Archibald MDCM FRCPC, Lee Lior MD MSc, Donald Sutherland MD MCommH MSc(Epi) HIV is among the most genetically variable of human pathogens. Two major factors contribute to this genetic diversity: the error-prone activity of reverse transcriptase, which is estimated to introduce an average of one error/genome/replication cycle (1), and recombination, which occurs at a rate of about 2%/kilobase/replication cycle (2). With the advent of international collaborations using powerful new tools that allow for the analyses of nucleotide sequence information, it became apparent that the initial classification of HIV into HIV-1 and HIV-2 based on geographic distribution was inadequate. We now recognize that HIV-1 can be divided into three major phylogenetic groups: ‘M’ (major), ‘O’ (outlier) and more recently, ‘N’ (new). The vast majority of isolates cluster in the M group. Based on sequencing the envelope gene, env, 10 phylogenetic subtypes (A to J) have been identified within this group, with subtypes A to E (also referred to as the circulating recombinant A/E) being the most common (3). The general pattern of subtype distribution by geographic location is shown in Table 1. The second major group of HIV-1, group O, is found mainly in Cameroon and Gabon, and differs from the M group by as many as 50% of residues (4). The N group of HIV-1 was isolated in Cameroon, with genetic characteristics of both the simian immunodeficiency virus and HIV-1 (M group) (5). Although there has been no systematic surveillance for genetic diversity of HIV strains in Canada, existing studies on high risk populations suggest that HIV-1 subtype B is the most common subtype found in this country. Bernier et al (6) have conducted analyses on HIV-1 sequence diversity among 17 infected injection drug users (IDUs) and among five men who have sex with men (MSM) residing in Montreal, and all sequences were of HIV-1 subtype B. As a part of an outbreak study in Newfoundland, Montpetit et al (7) analyzed serological samples from 31 HIV-positive persons of both sexes, comprising approximately 25% of known HIV-positive persons in the province, to determine the extent of HIV-1 subtype variation (7). All samples tested were of HIV-1 subtype B. Strain analysis has been carried out on samples from 13 MSM, two IDUs and two heterosexuals, recruited through POLARIS in Ontario (8). All have been found to be subtype B. The British Columbia Centre for Excellence in HIV/AIDS in Vancouver, British Columbia, has conducted genetic analysis of HIV linked to VIDUS (9). All 64 IDUs tested were infected with subtype B. Despite the predominance of HIV-1 subtype B, non-B subtypes have also been reported in Canada. As early as 1995, HIV-1 subtype A was identified in an African-born male, who moved to Canada in 1983 (10). Studies by the British Columbia Centre for Excellence in HIV/AIDS suggest that non-B subtypes represent at least 4% of HIV infections among

Integrating Laboratory and Epidemiological Techniques for Population-Based Surveillance of HIV Strains and Drug Resistance in Canada