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Military Labs Use Whole Genome Sequencing of COVID-19 Variants

Image of Lab technician at work. A lab technician at the Naval Health Research Center prepares samples for whole genome sequencing. The DOD SARS-CoV-2 Whole Genome Sequencing Action Plan brings together laboratories to conduct whole genome sequencing across the Military Health System in response to the COVID-19 pandemic.

Editor's note: This is the first article in a 7-part series that highlights the work of technicians and scientists working in service laboratories that support the Military Health System, and who worked to identify COVID-19 variants using special sequencing technology.

A Department of Defense SARS-CoV-2 Whole Genome Sequencing Action Plan for the Military Health System was developed in response to the COVID-19 pandemic and signed on June 25. The plan brings together the service laboratories to conduct whole genome sequencing across the MHS.

Under this plan, the Under Secretary of Defense for Personnel and Readiness endorsed the efforts of five stateside laboratories and five overseas laboratories who sequenced a large volume of SARS-CoV-2 samples since June 2021. These laboratories also contributed to the rapid detection and reporting of SARS-CoV-2 variant emergence and distribution among MHS beneficiaries. Since the beginning of the pandemic in March 2020, the laboratories have received 39,640 samples for sequencing, with 93% of sequenced samples among active duty service members.

"The Armed Forces Health Surveillance Division, and particularly the Global Emerging Infections Surveillance Branch, have provided critical support to near-real time surveillance at the point of impact in various global communities. GEIS was critical in leading the expansion of this capability to mitigate any new biology health threats that may impact our service members," said AFHSD's chief and U.S. Air Force Col. Patrick W. Kennedy.

The results of this sequencing will benefit individual service members and local communities.

"WGS is a valuable research tool that has many applications. During this critical time, the most important role it plays is in the detection of clinical pathogen mutations. If a virus is detected, the WGS process will allow the clinical community to mitigate the more virulent or transmissible virus with additional protective measures," said Kennedy.

The laboratories will continue to work together to collect and sequence samples to monitor variant emergence, identify and respond to outbreaks, and describe the frequency of COVID-19 infections in DOD-relevant populations into the future.

"Information sharing is a critical force multiplier that will allow us to produce better outcomes as we face potential pandemics. The coordination and rapid identification used in the WGS plan will help to determine spread and protect potentially vulnerable populations for the safety of our operational forces," said Kennedy.

To learn more about these efforts, the Defense Health Agency will post a series of short stories to highlight the joint effort of our service laboratories. Labs highlighted will include:

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