HIV-1 Strain and Primary Drug Resistance in Canada

Surveillance Report to June 30, 2001

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An Overview of the Canadian HIV Strain and Drug Resistance Surveillance Program

The CHSDRSP is a collaborative effort between the provinces and territories and the Centre for Infectious Disease Prevention and Control, Public Health Agency of Canada, Health Canada. It forms a key component in a national system for the enhanced and integrated surveillance of HIV/AIDS, STD, emerging retroviruses, and other sexually transmitted blood-borne pathogens. The program was initiated to characterize and monitor the genetic diversity of the HIV epidemic in Canada, addressing the concerns of public health authorities, primary care physicians, and researchers.

The program consists of two key components: (1) serum specimen from individuals newly diagnosed with HIV for subtype and primary drug resistance testing, and, (2) non-nominal epidemiologic data, which include information collected through the national or provincial HIV reporting form and additional data to interpret the laboratory results. Data collection, analysis and transfer are shown in Figure 1.

Figure 1. Data Collection, transfer and analysis

The provincial and territorial (P/T) partners in the CHSDRSP send serum specimen taken for diagnostic testing from treatment naïve individuals and corresponding epidemiologic data to the Centre for Infectious Disease Prevention and Control (CIDPC). Note that only samples from individuals newly diagnosed with HIV in Canada are included under the CHSDRSP. Subtype analysis and primary drug resistance genotyping are conducted in the National Laboratory for HIV Genetics at the National HIV and Retrovirology Laboratories. Samples with unusual laboratory results are sent through the sentinel arm of the CHSDRSP and are analyzed for subtype by the National Laboratory for HIV Genetics. This information is linked using unique specimen identifiers to the epidemiologic data, and the Division of HIV Epidemiology and Surveillance conducts further analyses at the national level. Laboratory results are sent to the P/T partners for local analysis.

As of June 30, 2001, British Columbia, Alberta, Manitoba, Saskatchewan, Ontario, and Newfoundland are participating in CHSDRSP. The results presented in this report represent samples on which HIV subtype analysis and primary drug resistance genotyping were completed successfully as of June 30, 2001. Samples and epidemiologic data continue to flow to Health Canada from participating provinces, and results from these analyses will be presented in future reports. Discussions are currently under way to expand the collection of samples and epidemiologic data to the remaining provinces and territories.

Goals of CHSDRSP

A 1998 consensus workshop in Vancouver established the following goals for CHSDRSP:

1) To enhance the safety of the blood supply

In order to ensure the safety of the blood supply, all HIV tests need to reliably detect the strains circulating in the country. The precedent for this goal was the discovery of HIV-2 and highly divergent group O strains of HIV-1, which required modification of some serologic screening tests by the addition of new antigens to ensure detection. The sentinel arm of CHSDRSP, through the reference services of the National HIV Laboratories, addresses this goal by testing samples with unusual serologic, PCR (polymerase chain reaction), or other virologic test results that are provided by the provincial health laboratories. This relationship between provincial and national laboratories also serves other external programs, including quality assurance and the monitoring of diagnostic kits.

2) To inform vaccine development

It is important to know the distribution of the viral subtypes and intrasubtype variations to target vaccine development and testing, since the efficacy and effectiveness of vaccines may be subtype-specific.

3) To assess genetic markers of HIV drug resistance

Although anti-retroviral therapies have led to a reduction in HIV-related morbidity and mortality in Canada, there is concern that their widespread use, the increased number of treatment failures, and high HIV infection rates may result in increased transmission of drug-resistant virus. In fact, studies have shown that transmission of drug-resistant virus is increasing. The CHSDRSP aims to assess the prevalence of primary drug resistance and the variation of this prevalence over time, geographic area, and population risk group. The resulting information can be used to develop treatment guidelines at the population level for initial therapeutic regimens and to develop more effective HIV prevention strategies, including the prevention of mother-to-child transmission.

4) To determine HIV transmission, pathogenesis and progression to HIV-related diseases

Although genetic analyses have been used to assess the spread of HIV globally, there is little consensus on whether differences in HIV subtype and mutations conferring drug resistance affect the rate of transmission, pathogenesis or HIV-related disease progression. Knowing the distribution of HIV variants in Canada, along with corresponding epidemiologic information, will help to address these questions. The public health implications of such findings, including prevention and treatment strategies, are of special interest.

Methodology

The provincial laboratories send archived serum specimen collected from newly diagnosed, treatment naïve people to the Centre for Infectious Disease Prevention and Control at Health Canada for HIV subtype analysis and primary drug resistance genotyping. The genetic testing algorithm used during PCR amplification is shown in Figure 2. Primary mutations identified in the protease and reverse transcriptase genes 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/), and the results are sent back to the provinces. Although the majority of these mutations are consistent with the list of mutations identified by the International AIDS Society-USA¹, some differences exist. Appendix 2 provides the list of primary mutations used for this report.

Non-nominal epidemiologic information is also collected and sent to the Centre for Infectious Disease Prevention and Control at Health Canada. The data include information routinely collected on the national or provincial HIV case reporting forms and, where available, additional information that will help interpret the laboratory results, including treatment history, viral load at diagnosis, and previous HIV negative testing history. Laboratory and epidemiologic data are linked using unique specimen identifiers, and further analysis is conducted using the statistical package SPSS^c (SPSS Inc. Chicago).

The algorithm used by the National Laboratory for HIV Genetics to identify subtypes and primary mutations associated with drug resistance is shown in Figure 2. After extraction of the RNA and an initial one-step RT-PCR reaction, nested PCR amplification of the pol gene (protease/reverse transcriptase) is performed using a combination of published and in-house Group M consensus primers. The PCR product is directly sequenced with internal PCR primers on a Li-Cor 4200L automated sequencer. In this way, a complete double stranded sequence for the entire protease gene and the first 253 amino acids of reverse transcriptase are used to assess subtype and primary mutations associated with drug resistance. Previously, the C2-V5 region (233 amino acids) of the envelope protein was used to assess HIV subtype. When PCR products sequence poorly, they are resolved by cloning the PCR product, sequencing about 10-12 clones/person.

Figure 2. Genetic testing algorithm used by the National Laboratory

¹ Resistance Mutations Project Panel. Update on drug resistance mutations in HIV-1. Topics in HIV Medicine 2001; 9(6):21-23.

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