HIV-1 Strain and Primary Drug Resistance in Canada

Surveillance Report to June 30, 2001

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Background

HIV can develop resistance to various anti-retroviral drugs as a result of mutations in the genes coding for protease and reverse transcriptase (RT), two viral proteins that are required for HIV to replicate. Current anti- retroviral drugs impede viral replication by binding to these proteins and inhibiting their ability to function. However, largely because of its rapid and relatively inaccurate replication, HIV is able to mutate and diminish the ability of the drugs to interact with these viral proteins.

For some drugs (e.g. non-nucleoside reverse transcriptase inhibitors), a single mutation is sufficient to confer drug resistance. Such a mutation is called a "primary" mutation. For other drugs (e.g. protease inhibitors), a combination of mutations is required to confer resistance. Such mutations are known as "secondary" mutations. Most mutations are lethal or neutral, and the wild type strain usually dominates because it replicates more efficiently.

Laboratory Tests to Detect Drug Resistance

Two types of tests are used to detect drug resistance, genotypic and phenotypic. Genotypic tests provide information about the genetic makeup of the virus by identifying the mutations that are strongly associated with resistance. Phenotypic testing measures the ability of a virus to replicate in the presence of varying drug concentrations. Although the methodologies for both tests are well established, each has its limitations, as described in the section Data Limitations.

Primary and Secondary Drug Resistance

In general, two types of drug resistance have been described. "Primary drug resistance" is used to describe reduced susceptibility to drugs seen among patients who have never received treatment for HIV. So presumably these patients have been infected with drug-resistant HIV. "Secondary drug resistance" is the term used to describe drug resistance among patients already receiving treatment, and this phenomenon has been widely described in the context of treatment failures. (Note, these terms should not be confused with "primary" and "secondary" mutations.)

Primary drug resistance is becoming more widespread in most countries where highly active anti-retroviral therapy is used. People infected with drug-resistant variants of HIV may be at increased risk of drug failure, despite never having received treatment. However, the prevalence of primary drug resistance and the variation of this prevalence over time, geographic area, and population risk group are not well understood.

Data Sources

This section highlights the main findings 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 HIV positive. Furthermore, the findings include only those on 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 identify primary mutations were carried out successfully.

As of June 30, 2001, B.C., Alberta, Manitoba, and Saskatchewan have submitted 1,354 serum specimen from individuals newly diagnosed between 1997 and 2000 and corresponding non-nominal epidemiologic data for primary mutational 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 on ALL people newly diagnosed with HIV will be collected prospectively from the provinces currently participating in CHSDRSP and analyzed for both subtype and primary mutations. Discussions are also under way to expand CHSDRSP to the remaining provinces and territories.

At the time of writing this report (December 31, 2001) a total of 563 samples have been analyzed for primary mutations by the National Laboratory for HIV Genetics. Viral RNA had been successfully amplified from 85.4% of the serum specimen. This high level of success in amplifying virus from serum specimen specimens will likely improve further as sample quality is enhanced and various primer combinations for RT-PCR amplification are identified and used.

Primary mutations identified in the protease and RT enzymes of HIV are defined by the consensus of listings reported by Stanford University (http://hivdb.stanford.edu/hiv/) and the Los Alamos HIV Sequence Database (http://resdb.lanl.gov/Resist_DB/). Please refer to Appendix 2 for a list of primary mutations used in this report.

The distribution of primary mutations based on sequence analysis of protease and the first 253 amino acids of RT are shown in Table 1. The results indicate that primary mutations were present in at least 5.9% of the sample population of 481 newly diagnosed, treatment naïve individuals. Note that none of these individuals had previously received treatment, and so had presumably been infected with a drug-resistant strain of HIV-1. The prevalence of primary mutations to reverse transcriptase inhibitors (RTIs) and protease inhibitors (PIs) was 4.2% and 1.5% respectively. One individual in the sample population (0.2%) was infected with virus harbouring mutations to both RTIs and PIs. Of note is that multi-drug resistant HIV was also identified in a sample from Ontario that was sent to the National Laboratory for HIV Reference Services, but since this individual had been receiving anti-retroviral treatment previously primary drug resistance could not be ascertained.

Of the individuals harbouring HIV-1 resistant to RTIs, the majority (19, or 4%) were infected with virus containing mutations associated with resistance to the nucleoside RTIs (NRTIs) AZT, ddC, 3TC, abacavir and adefovir. The remaining individual (0.2%) was infected with HIV containing mutations associated with resistance to the non-nucleoside RTI (NNRTI) foscarnet. The most common mutation that was identified in RT was the replacement of the amino acid methionine (M) with leucine (L) at position 41. This mutation, associated with a high level of resistance to AZT, was identified in 11 individuals (2.3%). Primary mutations associated with resistance to the PIs ritonavir, amprenavir, and indinavir were identified in seven individuals (1.5%). The most common primary mutation identified in protease was the replacement of methionine with isoleucine (I) at position 46, associated with a high level of resistance to ritonavir. Four individuals (0.8%) in the sample population of 481 were infected with HIV containing this mutation. Of note is that one individual (0.2%) harbouring mutations associated with multi-drug resistance was identified. The replacement of methionine (M) with valine (V) at position 184 of the RT enzyme (associated with resistance to the NRTIs 3TC, abacavir, and adefovir) and of leucine (L).with methionine (M) at position 90 of the protease enzyme (associated with resistance to nelfinavir) were identified. Other primary mutations and the anti-retroviral drug to which they confer resistance are shown in Table 2.

Table 3 shows the epidemiologic characteristics of individuals harbouring primary mutations associated with a high level of resistance to RTIs and to PIs. Univariate analysis to test for significant associations with primary drug resistance were not conducted because of small sample sizes in the cells. However the prevalence of primary drug resistance may be increasing over time.

The following additional observations can be cautiously made. Primary drug resistance has been identified

• among adults of both sexes aged 16-69 years at first diagnosis with HIV;
• among individuals identifying male-to-male sex (MSM), injection drug use (IDU) and/or heterosexual contact as the primary risk factors;
• across most ethnic backgrounds, including people of Caucasian, Aboriginal, African and Asian origin;
• in people with HIV-1 subtypes A, B, or C.

Results from the CHSDRSP and other cohort and cross-sectional studies suggest that, in Canada, the overall prevalence of primary drug resistance to at least RTIs is between 4.2% and 20% (Table 4). Primary drug resistance to PIs is between 1.5% and 6.5%. Primary drug resistance to more than one class of anti-retroviral drug (multi-drug resistance) has been observed in Canada, and preliminary studies suggest an overall prevalence of between 0.2% and 6%.

The studies also suggest that, in total, drug resistance (both primary and secondary drug resistance) is between 5.9% and 26% in Canada.

Studies from the United States and other countries in Western Europe also give similar results (Table 5). A column summarizing the total number of primary mutations could not be constructed because this information was not available for most of the studies cited.

Note: Table 4 is NOT meant for inter-study comparisons. It is difficult to make such comparisons and arrive at firm conclusions because of differences in study design. For example, prevalence rates depend on the population being studied (high risk versus general population), the types of laboratory tests used (genotypic and/or phenotypic testing) and differences in the mutations studied and reported.

Note: Interpretation and inter-study comparisons are difficult because of differences in study design as noted previously.

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