Interim Guidance for Laboratory Testing for Detection and Characterization of Pandemic H1N1 (2009) Virus

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Executive Summary

Detection of, and discrimination between, seasonal and pandemic influenza virus strains is critical to surveillance, diagnosis, treatment and infection control. Further, the pandemic H1N1 (2009) virus (pH1N1) should be monitored for anti-viral resistance and antigenic variations. It is also important to note the need to track other common viral agents that co-circulate during the influenza season.

The Pandemic Influenza Laboratory Preparedness Network (PILPN) of the Canadian Public Health Laboratory Network (CPHLN) has developed this document as a comprehensive Interim Best Practice Guidelines for detection and characterization of pH1N1. To ensure a consistent approach across the country, this document highlights Best Practices for specimen collection, transportation, testing and biosafety from the perspective of Canadian public health laboratories.

The following summarizes Best Practices recommendations.

1. Population-based testing for influenza viruses should be carried out for surveillance (e.g. sentinel physician networks). Once the pH1N1 becomes widespread, diagnostic testing should focus on hospitalized patients with severe respiratory illness (SRI) or influenza-like illness (ILI), and patients for whom testing will assist decisions regarding care, infection control, or management of close contacts. Testing is also recommended for those who died of an acute illness, in which influenza is suspected, those with potential antiviral (zanamivir or oseltamivir) resistance and for adverse events (e.g. patients who are clinically ill and hospitalized; those who are deteriorating clinically).
2. Nasopharyngeal swab (NPS) is the specimen of choice for routine testing. Flocked swab should be used for collection, with either viral transport medium (VTM) or universal transport medium (UTM) for specimen submission. In SRI, endotracheal aspirate (ET) or bronchoalveolar lavage (BAL) should also be collected in addition to a NPS (specimen type depends on assay validation and this varies from location to location. A bronchial wash, if validated may be acceptable as BAL if the data can show equivalence. However, yield for BAL is more significant then bronchial wash, which has yields equivalent to ET). Autopsy specimens may include respiratory swab specimens and tissues.
3. Nucleic acid-based testing (NAT) such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is the method of choice for routine testing of pH1N1. Viral culture using Madin-Darby canine kidney (MDCK) or primary rhesus monkey kidney cell lines is required for monitoring anti-viral resistance and antigenic variation.
4. Rapid point of care (POC) tests may be considered in remote areas. Due to limited sensitivity of POC tests, a negative result does not rule out influenza, especially pH1N1. Further, POC tests cannot differentiate between pH1N1 and seasonal influenza strains. Therefore, the use of POC tests is not recommended for informing clinical decisions about diagnosis and treatment in individual patients.
5. Each province should ideally have at least one laboratory capable of genotypic testing for anti-viral resistance. Where this is not feasible, there should be arrangements to obtain this service.
6. Provincial public health laboratories (PHL) should submit a proportion (up to 10%) of community and hospital-based influenza isolates, especially pH1N1 to the National Microbiology Laboratory (NML) on an ongoing basis to monitor anti-viral resistance and antigenic variations.
7. NML should continue to provide reference testing and routinely perform phenotypic and genotypic testing to monitor anti-viral resistance and antigenic variations. NML should advise PILPN of any mutations associated with anti-viral resistance other than the H275Y mutation. NML should standardize single nucleotide polymorphism (SNP) assays for H275Y mutation for both pandemic and seasonal H1N1 viruses.
   
8. Co-circulation of other viral agents associated with ILI should be monitored during the influenza season as part of ongoing surveillance.
9. The decentralization of NAT testing for influenza virus to hospital laboratories should be promoted to increase the diagnostic capacity required to meet increased demands.