Posted March 30, 2021. Past health advisories and alerts are archived for historical purposes and are not maintained or updated.
The Washington State Department of Health (DOH) has increased whole genome sequencing capacity at the WA Public Health Laboratory (PHL) to track SARS-CoV-2 variants of concern and other emerging variants. DOH is working toward sequencing a geographically representative sample of at least 5% of positive SARS-CoV-2 RT-PCR tests in Washington State. DOH has additional capacity to sequence individual specimens to investigate other situations as outlined below.
Whole genome sequencing can also be used to identify possible transmission patterns via phylogenetic analysis for complex outbreaks. Clinicians, clinical laboratory staff, and other healthcare staff can assist public health authorities by identifying cases for sequencing. It is often astute clinicians who connect the dots and identify the first cases of new infectious and noninfectious conditions. We appreciate your partnership as we learn more about genetic variants of SARS-CoV-2. We also encourage clinicians and laboratorians to review recently updated CDC guidance on SARS-CoV-2 variants.
Information on cases prioritized for sequencing
Currently, DOH is prioritizing the following case categories for sequencing:
Reporting of sequencing results
At this time, sequencing at PHL is conducted for public health surveillance using laboratory methods that are not CLIA-approved. Individual sequencing results will be available to public health authorities in the state reportable disease database (WDRS) but will not be reported to patients or clinicians. Aggregate results for the entire state are described weekly in a publicly accessible report.
If providers specifically want the results from their patient’s sequence, the University of Washington lab does have a CLIA approved test. Information about this test, specimen submission guidelines and reporting can be found here.
How to submit a specimen to PHL for sequencing
Clinicians and healthcare facilities should contact SRHD Epidemiology to coordinate submission of a specimen for sequencing. Please note that all cycle threshold (Ct) values must be <30 in order to submit a specimen for sequencing (unless the test platform does not provide Ct values; in this situation any sample can be submitted). The following specimen types can be submitted for sequencing:
All specimen types should be frozen at <-70 °C and shipped on dry ice.
Please contact Spokane Regional Health District Epidemiology at 509-324-1442 to coordinate specimen submission to PHL.