Scientists are tracking the SARS-CoV-2 virus that causes COVID-19 by sequencing the genome of virus samples collected from diagnostic testing. Using next generation sequencing on SARS-CoV-2 will help accurately diagnose the novel coronavirus, identify mutations and track its history.

A study by scientists at the UNC School of Medicine (Chapel Hill, NC, USA) has shown how next generation genetic sequencing can track mutations in the SARS-CoV-2 virus, which can in effect help with transmission tracing, diagnostic testing accuracy and vaccine effectiveness. This type of virus monitoring is also important in diagnostic testing. Much of the testing developed to diagnose COVID-19 looks for one portion of the gene sequence that causes the novel coronavirus. If that sequence mutates, the test is no longer accurate and results will be affected.

Their recent study is the largest to focus on suburban and rural communities in which the researchers were able to reconstruct the mutational landscape of cases seen at the UNC Medical Center. Within their study, the team of scientists did find variations in the virus’ genetic sequence, but fortunately none of the variations were located in the portion of the virus targeted in common diagnostic testing. 175 samples from confirmed COVID-19-positive patients were analyzed, out of which 57% carried the spike D614G variant noted in similar studies. The presence of this variant is associated with a higher genome copy number and its prevalence has expanded throughout the pandemic.

The researchers will continue using NGS to track the SARS-CoV-2 virus through the remainder of 2020. The goal is to enroll every patient at UNC Hospitals with flu or respiratory symptoms for COVID-19 diagnostic testing. These samples will be sequenced and compiled to form a comprehensive profile of any virus that these patients carry, information that will continue to help a community of researchers in their fight against SARS-CoV-2 and potentially novel coronaviruses.

“We are concerned about future mutations though,” said Dirk Dittmer, PhD, professor of microbiology and immunology at the UNC School of Medicine, and senior author of the study. “It is inherent in a virus’ nature to mutate. Changes in other areas of the genetic sequence can not only disrupt testing, but hinder the effectiveness of vaccines.”

“Because we are only looking at one gene sequence for the virus, we have told the FDA that we will continually monitor for changes in this gene sequence so that we can be assured that our test is still reliable,” said Melissa Miller, PhD, director of UNC Medical Center Microbiology and Molecular Microbiology Laboratories, and a co-author of the study. “NGS will help us do that.”

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