HIV-1 Strain and Primary Drug Resistance in Canada

Surveillance Report to June 30, 2001

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HIV-1 Subtypes in Canada

Data Sources

This section highlights the main findings related to HIV-1 subtype from the CHSDRSP up to June 30, 2001. It is important to note that the results presented here represent individuals who sought testing, were properly diagnosed, and were reported as being HIV positive. Furthermore, they represent only those individuals for whom sufficient serum specimen, taken for the purposes of diagnostic testing was available to send to the National HIV Laboratories and, of these, the subset for whom RT-PCR amplification and sequencing to obtain subtype results were successful.

As of June 30, 2001, British Columbia, Alberta, Manitoba, Saskatchewan and Newfoundland have submitted 1,604 serum specimen from individuals newly diagnosed between 1996 and 2000 and corresponding non-nominal epidemiologic data for subtype analysis. These data are collected through convenience sampling methods and may not be representative. However, it is anticipated that serum specimen and corresponding enhanced epidemiologic data of ALL persons newly diagnosed with HIV will be collected prospectively from provinces currently participating in CHSDRSP and analyzed for both subtype and primary mutations associated with drug resistance. Discussions are also under way to expand the CHSDRSP to the remaining provinces and territories. Additional samples have been received through reference services (the sentinel arm of the CHSDRSP), and the results from the analysis of these samples are described in the next section.

At the time of writing this report (December 31, 2001), a total of 1,048 samples have been analyzed for subtype by the National Laboratory for HIV Genetics. Viral RNA has been successfully amplified from 87.7% of the serum specimen. This high level of success in amplifying virus from serum specimen will likely improve further as sample quality is enhanced and various primer combinations for RT-PCR amplification are identified and used.

The distribution of HIV-1 subtypes based on the sequence analysis of the HIV envelope gene is shown in Table 6. Although the majority (91.6%) of samples are of subtype B, other subtypes have been identified. In decreasing order of prevalence they include subtype C (4.8%), A (2.5%), E (0.5%), D (0.4%), and the recombinant A/B (0.1%). Of note is that the recombinant subtype A/G, from three individuals, has been identified in Ontario from samples sent through reference services and subtyped by the National Laboratory for HIV Genetics (Table 9).

Preliminary evidence shown in Table 7 indicates that there is geographic variation in the distribution of non-B HIV-1 subtypes. Whereas all 40 samples from Newfoundland were identified as subtype B, 13.2%, 7.9%, 8.6% and 8% of the analyzed samples from Manitoba, Saskatchewan, Alberta and BC respectively belonged to non-B HIV-1 subtypes. B.C. had the greatest genetic variation among the non-B HIV-1 subtypes. It should be noted however, that sample sizes are not representative of the total diagnosed population in each of the indicated provinces. Furthermore, the provinces of Quebec and Ontario, which report the highest prevalence of HIV infections, are not represented.

Results from other Canadian epidemiologic studies have also identified non-B subtypes across Canada:

• As of November 2000, all samples of 31 recent seroconverters from the POLARIS cohort in Ontario are of subtype B (Major C for POLARIS Study Group. BHST Annual Meeting, Halifax, NS, Nov 16-18, 2000)
• The B.C. Centre for Excellence in HIV/AIDS has identified subtypes A, C, and D in at least 4% of individuals linked to cohort studies and to the B.C. HIV drug treatment program (Alexander C et al. 7^th Conference on Retroviruses and Opportunistic Infections. San Francisco, CA, Jan 31-Feb 2, 2000, Abst# 174)
• All HIV-1 sequences analyzed among injection drug users (n = 17) and men who have sex with men (n = 5) residing in Montreal were of subtype B (Bernier L et al. CJID 1999; 10 (suppl B): 104).

Gender, ethnicity, year of first diagnosis with HIV, and risk factors were significantly associated with HIV-1 non-B subtype infection (Table 8). Specifically, significantly higher proportions of non-B infections were observed among (1) females (13.6% versus 6.3% of males), (2) individuals of African or Asian origin (62.5% and 19% respectively versus 0%-6.8% for other reported ethnic groups), (3) individuals newly diagnosed in 1996 (23.1% versus 4.9%-9.1% for other years), and (4) individuals who reported heterosexual contact as the primary exposure factor (18.4% versus 3.4%-6.1% for the other risk groups). The probability of infection with a non-B HIV-1 subtype was 2.3-fold higher among females than among males; 17.2-fold and 2.6-fold higher among people of African and Asian origin respectively as compared with all other reported ethnic groups; 5.7-fold higher if the individual was newly diagnosed in 1996 as compared with all other years of diagnoses; and 5.7-fold higher if heterosexual contact was the primary reason for exposure as compared with all other risk factors. Of note is that out of the five pediatric cases, three were infected with non-B subtypes. All three individuals were of African origin.

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