SARS-Coronaviruses and Highly Pathogenic Influenza Viruses
Section 5: Initiation of laboratory testing
Laboratory testing will be performed at the Wadsworth Center when the Risk Assessment Group indicates that it is warranted. For these assays, there will be no cost to the employee or their health insurance. If the employee requests testing, but the Risk Assessment Group does not feel it is warranted, a decision will be made by the Wadsworth Center senior administration as to whether or not to proceed. Annual serological screening of staff will be performed for evidence of previous or current infection, even in the absence of reported exposure events or compatible illness.
Samples required for laboratory testing will be taken by designated staff at the designated Healthcare Facility and tested at the Wadsworth Center. Recommended samples for influenza testing are nasal pharyngeal/oropharyngeal (NP/OP) swabs (collected in viral transport medium), bronchial lavage or sputum. Serum should also be submitted for serologic testing.
The appropriate samples to eliminate a diagnosis of SARS by both RT-PCR and serology are dependent on the time after onset of illness and are shown in the table below.
| Specimen | <1 week Post-onset | 1-3 weeks post-onset | >3 weeks post-onset |
|---|---|---|---|
| Serum for serology | ++ | ++ | ++* |
| Blood (EDTA/purple top tube) | ++ | + | _ |
| Respiratory samples including NP/OP swabs, sputum and bronchial lavage. Sputum preferred. | ++ | ++ | + |
| Stool | - | ++ | ++ |
*Serum must be collected >28 days post-onset to rule out SARS serologically.
++ Indicates a priority specimen
- Indicates not recommended
The priority of the tests performed will depend on which pathogen the employee has worked with, e.g., SARS-CoV or HPIV. The primary samples will not be inoculated into cell culture in a BSL-2 laboratory until SARS or HPI has been ruled out.
5.1: For SARS-CoV the Wadsworth Center's real-time RT-PCR assay will be performed first. In addition, acute sera will be tested for the presence of SARS IgM in the Diagnostic Immunology Laboratory using the CDC/LRN ELISA assay.
5.2: For influenza, the first test performed will be a Directigen Rapid Antigen Detection assay. The antigen detection assay is not particularly sensitive on primary diagnostic samples but it will be performed because, when positive, it provides a rapid result. Irrespective of the result, the Wadsworth Center's real-time RT-PCR assays for influenza A and B will be performed. If a positive result is found for influenza A, a conventional RT-PCR-based typing assay will be performed. It should be noted that the limit of detection of this conventional RT-PCR assay may not allow typing without prior amplification in cell culture.
5.3: Test interpretation and testing for alternative agents
5.3.1 A positive PCR result for SARS-CoV or HPI virus should be confirmed by a qualified second laboratory to ensure that this result is not an artifact of laboratory contamination. Positive results will be confirmed by repeat testing of the same aliquot and separate aliquots of the original specimen and by testing the specimen in an independent laboratory. The Wadsworth Center will also send the specimen to the CDC for repeat testing.
5.3.2 A negative PCR result in a given patient sample does not rule out SARS-CoV infection in the patient due to the low viral load that is present in some clinical specimens. SARS-CoV infection can only be ruled out by a negative antibody result on a serum specimen collected >28 days post-onset of illness.
5.3.3 The significance of negative PCR results for SARS-CoV and HPIV will be reinforced by confirming the presence of another agent. Once the absence of SARS-CoV and HPI virus in a particular sample has been confirmed by RT-PCR, the Wadsworth Center Virus Reference and Surveillance Laboratory and the Bacteriology Laboratory will perform further testing using a combination of real-time PCR and culture. Priority will be given to molecular assays because of speed, and to avoid amplifying a potentially harmful pathogen. Detection assays will be performed for pertussis, mycoplasma, chlamydia, respiratory syncytial virus, parainfluenza virus, enterovirus, adenovirus and human metapneumovirus.