Molecular Epidemiology Program

The Washington State Department of Health (DOH) Molecular Epidemiology Program collaborates with public health partners to build capacity for national genomic epidemiology. We integrate genomic and epidemiologic data, develop and share best practices in genomic data analysis and visualizations, and prepare communication for public audiences.

What we do


Published Studies by the Washington State Molecular Sequencing Team

Nextstrain builds

Nextstrain builds are updated twice a week on Mondays and Wednesdays. The analysis focuses on SARS-CoV-2 sequences for Washington State.

Submitting COVID-19 specimens For Whole Genome Sequencing

All specimen submitted for sequencing to the Public Health Laboratory must be either submitted through the RedCap process or the QRP process for COVID-19 Whole Genome Sequencing.

Protocol Documents

How to submit specimens


Epidemiologic Criteria Specimen Criteria How to Submit

Outbreaks: Only submit 3-5 specimens per outbreak, because the rationale for testing specimens from suspected outbreaks is to determine whether they were caused by a concerning variant or sublineage.





All CT values<30,


CT values unavailable from the test platform



Complete the RedCap submission process:
and ship the specimen(s) following the guidance above.

Only use the REDCap link provided above for forwarding previously positive specimens.

Newly collected specimens must be submitted through the PHL’s QRP process:


Any case reporting international travel in the 14 days prior to symptom onset (or specimen collection date if asymptomatic).

Suspected zoonotic transmission. Approval is not required, but please notify

Unusual clinical presentations that may be associated with more severe or different clinical syndromes such as critical illness or death in a previously healthy child or young adult (age <40) or any other unusual clinical presentations identified by clinicians, LHJs or Tribes.


Contact Us

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