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
- Provide expert support for Local Health Jurisdictions (LHJs) and Tribal Partners
- Produce the weekly SARS-CoV-2 Sequencing Report
- Maintain Nextstrain Builds for SARS-CoV-2
- Facilitate collection of specimens for Whole Genome Sequencing (WGS)
- Monitor SARS-CoV-2 variant emergence and spread through the WA DOH sequencing sentinel surveillance program
Resources
- Published Studies by the Washington State Molecular Sequencing Team
Nextstrain builds
Nextstrain builds are updated every other week. The analysis focuses on SARS-CoV-2 sequences for Washington State.
- 2 month build
Washington State SARS-CoV-2 genomic analysis for past two months
https://nextstrain.org/groups/waphl/ncov/wa/2m
- 4 month build
Washington State SARS-CoV-2 genomic analysis for past four months
https://nextstrain.org/groups/waphl/ncov/wa/4m
- 6 month build
Washington State SARS-CoV-2 genomic analysis of the Omicron Variant
https://nextstrain.org/groups/waphl/ncov/wa/6m
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
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Epidemiologic criteria Specimen criteria How to submit Outbreaks:
Submit up to 25 specimens per outbreak. If interested in submitting >25 specimens, please request approval via email wgs-epi@doh.wa.gov
Travel:
Any case reporting international travel in the 14 days prior to symptom onset (or specimen collection date if asymptomatic).
Suspected zoonotic transmission:
Please notify the Zoonotic team zd@doh.wa.gov upon REDCap submission
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.
RNA specimens with a Ct value <30 may be submitted.
RNA specimens with Ct >30 will not be accepted for sequencing.
RNA specimens with Ct values unavailable from the test platform will be accepted.
Original specimens will be PCR tested at PHL. If positive and Ct value <30, it will be accepted for sequencing.
Complete: https://redcap.link/sequencesubmission
Confirm with Molecular Epi that REDCap form is completed by emailing wgs-epi@doh.wa.gov Label specimens with Specimen ID indicated on REDCap form. Include paper with specimen shipment indicating: REDCap specimens Specimen IDs Facility name Ship the specimen(s) following the collection, shipping and handling instructions from WA DOH.Note: REDCap specimens do not need any addition requisition form or QRP form completed with the shipment.
Contact us
Email the Molecular Epidemiology program for more information (wgs-epi@doh.wa.gov).
Washington residents or healthcare providers should contact their local health jurisdictions for assistance.