COVID-19 Advisory for Healthcare Providers

SARS-CoV-2 Sequencing Information for Clinicians and Healthcare Facilities

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:

  • Vaccine breakthrough cases in which the individual is fully vaccinated (≥14 days have elapsed between the final vaccine dose and the specimen collection date).
  • Any suspected reinfection case, regardless of whether the prior sample is available. A suspected reinfection case is defined as a repeat PCR positive test ≥90 days after the initial PCR positive test.
  • Unusual clinical presentations of COVID-19, such as critical illness or death in a previously healthy child or young adult, unusual symptoms or laboratory findings, or other unusual cases identified by clinicians.
  • Any individual reporting international travel in the 14 days prior to symptom onset (or specimen collection date if the individual is asymptomatic).
  • Suspected cases of zoonotic transmission.
  • Outbreaks with a suspected variant of concern based on features, such as a linked case with a known variant of concern, recent travel, high attack rate, unexpected proportion of cases with severe illness, cases with reinfection or vaccine breakthrough, suspected unusual mechanism of transmission (e.g., longer-range airborne transmission, brief exposure to an infected individual, suspected outdoor transmission, suspected fomite or foodborne transmission, etc.), or other unusual features identified by clinicians, laboratorians, or other healthcare staff.

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:

  • RNA extract (preferred)
  • Nasal swab, nasopharyngeal swab, or mid-turbinate swab in VTM/UTM or transport medium
  • Lower respiratory tract fluid (BAL, tracheal aspirate, or sputum) if the patient is intubated

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.