These guidelines were developed by the Pandemic Influenza Laboratory Preparedness Network of the Canadian Public Health Laboratory Network.
Although the protocol for Severe Acute Respiratory Infections (SARI) was initially developed as a response to the 2003 SARS outbreak, its intended use is to facilitate the diagnosis of severe respiratory infections due to both unknown and known respiratory pathogens that have the potential for large scale epidemics. With both MERS-CoV and the emerging H7N9 virus, a key factor is the determination of risk based on epidemiologic factors, which is in turn related to exposure in an “area of concern”. The initial risk assessment must be done in concert with your local Ministry of Health (MOH). SARI alerts should trigger clinicians to “Think, Tell and Test"
Although the risk assessments will be modified as new information becomes available, at this time the probability that a severe acute respiratory illness is due to MERS-CoV or H7N9 is extremely low. Therefore, in patients with no epidemiological risk factors the most common pathogens should be ruled out before considering an unusual or more highly virulent pathogen. This may be done at the local laboratory or the Provincial Public Health Laboratory (PPHL) depending on local capacity and expertise.
Specimens to be considered for collection include sputum, nasopharyngeal swab (NPS), bronchoalveolar lavage (BAL), endotracheal secretions, and throat swab. For pediatric patients, a nasopharyngeal aspirate is a suitable replacement to a NPS.
Pathogens that should be excluded on preliminary testing include:
Limited data suggests that MERS-CoV can present as a co-infection with other viral pathogens. As such, in addition to specimens that are negative for conventional pathogens, those that do have other identified pathogens but are consistent with suspect cases of MERS-CoV based on the PHAC case definition should be tested for the MERS-CoV. The details regarding testing and some control materials for method development are available from the National Microbiology Laboratory (NML). To date only a few PPHLs have developed the capacity to test for this pathogen in-house. All other PPHLs will forward the suspect specimens to the NML for further testing.
Influenza viruses that are positive on the initial influenza identification test but cannot be subtyped using RT-PCR should be further characterized. Laboratories that have the capacity to further characterize the specimens by sequencing methods (e.g. sequence the M gene) to determine the subtype of the virus will do so. Those that lack this capacity will rely on the NML for further characterization. However, given that subtyping assays are usually less sensitive than the identification assays, weak positives may not be able to be typed. Based on local experience, each laboratory should evaluate these on a case by case basis in concert with their local clinicians and Public Health colleagues.
Influenza positive specimens outside the influenza season or obtained from patients with a history of exposure animals (e.g. pigs or chickens), should be routinely submitted to the NML for characterization.
NOTE: While initial analysis of in house assays used by many labs suggest they should be effective in identifying H7N9, it is difficult to determine the effect on the sensitivity of testing. This is particularly true of the performance of commercial assays whose primer sequences are not known.
The initial tests (as outlined above) would be similar but supplemental testing will be required at the PPHL. The Laboratory should communicate with the clinician to ensure that the following specimens are collected:
If the case has been linked to another proven case of a novel respiratory virus, or has strong epidemiological evidence to link it with avian influenza, then please handle the specimen in the manner prescribed below; otherwise treat specimens as routine clinical specimens:
Transport by Land:
If the suspected agent is classified as Risk Group 3,use a Type 1A package.
(There is a modification possible for transport by air,see below.)
Other requirements of the TDG regulations such as training, labeling, marking and documentation apply.
Transport by Aircraft:
The International Civil Aviation Organization (ICAO) Technical Instructions (TI) with some additional provisions of the TDG Regulations, may be used for the transportation of diagnostic specimens by aircraft. Consignments prepared this way may be transported by road to and from the airport as well.
Under the ICAO TI, the shipping name DIAGNOSTIC SPECIMEN, UN3373 must be used for all diagnostic specimens if they may contain influenza Risk Group 3 agent. Diagnostic specimens are exempted from other requirements in the ICAO technical instructions if they are packaged in packaging of good quality, capable of passing a 1.2m drop test. A Type 1A package meets these requirements. A Type 1B package may only be used if it meets the additional ICAO requirements regarding cushioning of the secondary receptacle, drop test and pressure retention capability.