A team of researchers and clinicians at Dartmouth’s Geisel School of Medicine and Dartmouth-Hitchcock Medical Center has begun working together on a National Institutes of Health grant to track the development and spread of COVID-19 variants that are detected in the Upper Valley. From left to right, Michael L. Whitfield, PhD, a professor of biomedical data science and of molecular and systems biology and chair of the Department of Biomedical Data Science at Geisel, and Joel A. Lefferts, PhD, primary investigator on the study and assistant director of Clinical Genomics and Advanced Technology lab at DHMC, work in the lab. (Courtesy photo)

LEBANON – A team of researchers and clinicians at Dartmouth’s Geisel School of Medicine and Dartmouth-Hitchcock Medical Center (DHMC) has begun working together on a National Institutes of Health (NIH) grant to track the development and spread of COVID-19 variants that are detected in the Upper Valley.

The one-year project is part of an initiative by the NIH’s National Institute of General Medical Sciences (NIGMS) to support surveillance studies of SARS-CoV-2 viral strains in rural, underserved communities. The Institute has awarded a total of $15 million to 21 centers in the effort to advance research on the emergence, evolution, and infectivity of variants circulating in the U.S.

“It’s extremely important for us to be able to identify and monitor variants of concern, such as the recent Delta variant, in our local population to inform public health efforts and to aid in the development of any future vaccines that may be needed,” says Michael L. Whitfield, PhD, a professor of biomedical data science and of molecular and systems biology and chair of the Department of Biomedical Data Science at Geisel, who secured the grant funding and is helping to lead the effort.

DHMC’s Clinical Genomics and Advanced Technology (CGAT) laboratory has begun to perform sequencing on some retrospective and all prospective positive patient samples.

“Our lab was among the first in the Northeast to begin sequencing the novel coronavirus back in August of 2020,” says Gregory J. Tsongalis, PhD, who directs the CGAT lab at DHMC. “Since then, we’ve sequenced over 120 samples. Continued sequencing of our stored samples, made possible by this grant, should yield very interesting results and will allow us to see when some of these variants first appeared in our region. We’re learning about this virus in real time, and sequencing is a valuable tool in helping to understand its complexities and developing treatments and, hopefully someday, a cure.”

The medical center will handle retrieval and preparation of about 4,000 archived COVID-19 specimens from the CGAT lab’s freezers that have been collected since the start of the pandemic.

The project team will also be working with the University of New Hampshire’s genomic laboratory, which has collaborated with Dartmouth in the past, and will be assisting on the front end of the project.

“We’ll be sequencing a large set of the historical samples,” says Kelly Thomas, PhD, professor of molecular, cellular, and biomedical sciences and director of the Hubbard Center for Genomic Studies at UNH. “Then, their researchers will take the raw data and do the back-end analyses, which Dartmouth is one of the best in the country at.”

These analyses, which will include epidemiological and bioinformatics studies of the variants, will leverage resources from a 5-year, $12.5 million Center for Biomedical Research Excellence grant from the NIGMS that Whitfield received in 2019, that helped him establish the Center for Quantitative Biology at Dartmouth.

New positive COVID-19 specimens collected at DHMC going forward will be sequenced at the CGAT lab, says Joel A. Lefferts, PhD, primary investigator on the study and assistant director of CGAT.

“We will also be able to link available demographic and clinical information to the samples to explore possible correlations,” Lefferts explains. “All sequence data will be uploaded into public repositories to increase representation of rural New England cases in SARS-CoV-2 sequence databases.”

Newsletter