Background:  Approximately 2000 new HIV diagnoses are reported annually in Canada. The Canadian HIV Strain and Drug Resistance Surveillance Program monitors HIV drug resistance in these newly diagnosed, ART-naïve individuals. Here, we present data on the regional distribution of HIV subtypes and drug resistance, as well as results of molecular analyses giving an indication of transmission patterns within and between provinces.

Methods:  Diagnostic sera from newly diagnosed HIV-positive individuals from provincial partners were analyzed for HIV subtype and genotypic drug resistance. Population-based sequencing was performed on polymerase chain reaction (PCR) products and drug resistance interpreted using the Stanford HIV Database and IAS guidelines. Phylogenetic analysis was performed by neighbor-joining analysis (K-2-P) as implemented in MEGA 3.1.

Results:  Sequence data were available from 423 specimens collected between January and December 2004, representing approximately 20% of newly diagnosed HIV infections. Within the cohort, 8.9% had at least 1 primary drug resistance mutation. The prevalence of drug resistance varied from 7.1% to 13.2% among provinces, and 1.9% of the samples contained HIV resistant to drugs from 2 or more classes. The distribution of non-B strains also varied widely among provinces with prevalence as low as 6% and as high as 37%. The overall rate of non-B infection was 18% with the following breakdown:  11% C, 3.6% A, 2.0% A recombinant (AE, AD, AG), and 0.3% each of D, G, and H. Of first-time positive individuals, 41% were located in 34 provincial infection clusters consisting of as many as 7 individuals. An additional 7 clusters spanned 2 provinces, and 1 cluster involved individuals from 3 provinces. Also found within 1 province were 2 subtype A clusters.

Conclusions:  The prevalence of drug resistance in Canada has remained between 6.5% and 11.5% since 2000. Drug resistance prevalence was highest (13.2%) in the province that has historically had the highest drug-resistance rates. Overall, non-B strains represented 18% of newly diagnosed HIV infections. However, 40% of new infections in 1 province were non-B strains. This province concomitantly had the highest rates of drug resistance. The identification of numerous transmission clusters may indicate that individuals who are unaware of their HIV status are the source of new infections. Tracking changes in the pattern of the Canadian HIV epidemic, through the use of integrated surveillance, can lead to improved patient care and the ability to target prevention strategies.