U.S. Army Spc. Lawrence Martinez performs a quality check on samples before preparing them for genetic sequencing at USAMRIID. The effort is part of the DOD SARS-CoV-2 Whole Genome Sequencing Action Plan, which brings together laboratories to conduct whole genome sequencing across the Military Health System in response to the COVID-19 pandemic. Photo by Timothy R. Butcher, USAMRIID VIO

“We typically perform several site visits to assist in training personnel, provide custom software for analysis, and perform confirmatory sequencing on several samples to demonstrate that the laboratory is capable of performing whole genome sequencing to standard,” said Kugelman. “The two major complications we encountered during the pandemic were the difficulties of moving large data sets up to the gigabyte range, and the limitations of virtual training tools for a hands-on activity such as sequencing.”

In the past, the CGS team would travel to the outbreak. However, due to the pandemic, their support was complicated by travel restrictions. It was important to belong to a connected family of laboratories across the MHS.

“GEIS published the ‘SARS-CoV-2 Whole Genome Action Plan for the DOD Military Health System,’ which delineated the process for GEIS sequencing support of the COVID-19 response. Thanks to this coordinating document, USAMRIID could accept samples and provide support across the DOD for COVID-19 variant characterization without the delays often seen with standard material transfer agreements,” said Kugelman.

As a part of the GEIS Network, “This collaborative framework transformed a loose and disparate collection of cross-service labs into a unified sequencing response, which collectively sequenced tens of thousands of patient samples throughout the outbreak,” he added.

This work is important to military and local civilian populations.

“Simply put, sequencing can provide commanders with information on what, when, and how a pathogen is circulating in their area of operation and community. This information is critical as a planning factor to maintain readiness through force health protection measures and to develop the necessary medical countermeasures,” Kugelman said. “Over 20 technicians and scientists, both soldiers and civilians, supported this effort over a two-and-a-half-year period. They worked long hours under considerable stress to provide support to the DOD, and I am honored by their efforts and excellence.”