Nevada Researchers Conduct Genomic Sequencing on COVID-19 Samples
A team from the University of Nevada is completing genomic sequencing on COVID-19 samples to better understand the virus.
Source: Thinkstock
By Jessica Kent
- The Nevada Genomics Center at the University of Nevada, Reno (UNR) is conducting genomic sequencing on samples from northern and southern Nevada that initially tested positive for COVID-19.
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The project is a joint effort with the Nevada State Public Health Lab (NSPHL), as well as researchers in the department of microbiology and immunology, both part of the University of Nevada, Reno School of Medicine.
Researchers around the world are sharing genomes of the virus to establish its phylogenetic tree, which will help advance scientific understanding of COVID-19. Genomic analysis may also improve researchers’ understanding of factors related to severity of the disease.
While underlying conditions and genetics can help explain why the virus leaves some more sick than others, there is still a question of whether the viral strain could be a contributor as well.
“There are so many questions that can be asked and answered,” said UNR Med associate professor Subhash Verma, PhD.
Researchers have sequenced more than two dozen samples, with the goal of sequencing nearly 200 total samples from Nevada. Before the samples leave the NSPHL, an RNA extraction process inactivates the virus and eliminates any chance of infection as they are further tested. The samples are assigned an identification number to maintain patient anonymity.
Researchers will deposit sequenced results into an international database, and the UNR Med team will complete further study and analysis.
“We have quite a long history of sequencing viruses here at UNR, and additional equipment and expertise have allowed more capability,” said assistant professor Cyprian Rossetto, PhD.
The UNR team has developed a more direct method of next-generation sequencing directly from the extracted patient sample. In some laboratories, the sample must be cultured first.
With this innovative method, researchers use a kit to amplify very low amounts of RNA, followed by enrichment of coronavirus-specific sequence to allow individuals to study the genome in greater detail. This is a strong approach for a range of nasal or oral swabs taken from patients.
NSPHL is the first public health lab in the nation to construct its own COVID-19 sample collection kits. The manufacturing process involves creating 3D printed testing swabs and producing viral transport media (VTM) to complete the testing kit. The process has helped Nevada achieve above the national average of tests per 100,000 residents.
"Our job is to provide COVID-19 testing and to help the state remain vigilant and prepared to respond to infectious diseases, including COVID-19. We're not just standing around waiting for equipment to show up. Instead, we're being proactive and innovative about creating our own manufactured supplies, now,” said Mark Pandori, PhD, director of NSPHL.
In addition to the sample collection kits, NSPHL is preparing to start limited antibody testing in the coming weeks.
By conducting genomic sequencing on COVID-19 samples, UNR Med researchers will help deepen scientific knowledge of the virus and its impact on patient populations.
“Probably the largest benefit will be to learn what strains of the virus are in northern and southern Nevada,” said Paul Hartley, PhD, director of the Nevada Genomics Center, one of several core laboratory facilities at the University.
“The coronavirus genome can acquire mutations, and with the right amount of data, one can do epidemiological studies to understand how the virus may have spread.”
