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Posted on: March 24, 2021

Clinician Advisory: Identifying Cases for SARS-CoV-2 Sequencing to Detect Variants

Requested Actions:

Case TypeDefinition*
Vaccine breakthroughFully vaccinated cases (i.e., ≥14 days have elapsed between the final vaccine dose and the specimen collection date)
Suspected reinfectionRepeat PCR-positive test ≥90 days after the initial PCR positive test
Unusual clinical presentationsCritical illness or death in a previously healthy child or young adult, unusual symptoms or laboratory findings, or other unusual cases
International travelCompleted travel ≤14 days prior to symptom onset (or specimen collection date if the individual is asymptomatic)
Zoonotic transmissionSuspected animal-to-human transmission
Outbreaks with a suspected variant of concernInvolve features noted above and/or high attack rate, unexpected proportion of cases with severe illness, or suspected unusual mechanism of transmission (e.g., longer-range airborne transmission, brief exposure, outdoor transmission, fomite, foodborne)
*Also requires a Ct < 30 on RT-PCR results to be eligible for WGS.


  • The Washington State Department of Health (DOH) has increased whole genome sequencing capacity to track SARS-CoV-2 variants of concern and other emerging variants, aiming for a geographically representative sample representing at least 5% of positive SARS-CoV-2 RT-PCR tests in Washington State. 
  • DOH has additional capacity to sequence individual specimens to investigate situations suspicious for variant involvement (see table above).
  • 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.
  • At this time, sequencing 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 cannot be reported to patients or clinicians. Aggregate results for the entire state are described weekly in a publicly accessible report

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