Stepping up

Genomics sequencing of coronavirus samples at the University of Nevada, Reno

COURTESY/UNR: Paul Hartley, director of the Nevada Geonomics Center at the University of Nevada, Reno, projects DNA sequencing will be completed on nearly 200 total samples from Nevada.

Genomics sequencing of coronavirus samples is taking place at the University of Nevada, Reno
Genomics sequencing of Nevada COVID-19 samples is under way at the University of Nevada Reno. According to a press release, the Nevada Genomics Center has joined with the State Health Lab and School of Medicine researchers in this effort to advance scientific knowledge of novel coronavirus through DNA sequencing.

The Nevada Genomics Center is completing sequencing on samples from northern and southern Nevada that initially tested positive for the virus through the Nevada State Public Health Lab [NSPHL]. It’s happening in collaboration with the NSPHL and researchers in the department of Microbiology and Immunology.

In the press release, Paul Hartley, Ph.D., director of the Nevada Genomics Center, said, “Probably the largest benefit will be to learn what strains of the virus are in northern and southern Nevada. … 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.”

Researchers across the globe are sharing genomes of the virus. Their work may help determine things like if certain strains of the virus spread faster and perhaps if some strains respond better to antiviral treatments currently being tested. They’re also seeking to learn if certain strains of the virus cause more severe illness. Of course, many have heard that underlying conditions and genetics help explain why the virus leaves some people more severely sick than others, but the viral strain might also be a contributor. According to the press release, the researchers are working to map out the virus’s “phylogenetic tree or, as UNR Med Associate Professor Subhash Verma, Ph.D., describes it, a complete view of the virus.”

Genomic analysis has already indicated the virus in New York is a variant from Europe, while in western states it tends to be a variant of the virus in Asia.

“There are so many questions that can be asked and answered,” said Verma.

Hartley has sequenced more than two dozen samples, and his goal is to sequence nearly 200 total samples from Nevada.

According the press release, “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.”

It takes about a week to complete the sequencing because there’s a process Hartley must undertake to prepare the samples, convert them into what are called “libraries,” enrich said libraries for viral sequencing and sequence the libraries.

The sequenced results will be deposited into an international database, and further study and data analysis will be completed by UNR Med researchers, including Verma and Assistant Professor Cyprian Rossetto, Ph.D., and director of the NSPHL, Mark Pandori, Ph.D.

Under Pandori’s leadership, the NSPHL became the first public health lab in the nation to construct its own COVID-19 sample-collection kits and is preparing to start limited antibody testing in the coming weeks.

This genomics analysis project is supported through the university’s department of Research & Innovation and the UNR Med Department of Microbiology and Immunology. The knowledge it produces will be contributed to the Centers for Disease Control’s new SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium, which was launched late last week. The consortium is comprised of some 40 state and local public health departments, several large clinical laboratories and over two dozen collaborating institutions across the federal government, academia and the private sector.

According to a CDC press release, “This national network of sequencing laboratories will speed the release of SARS-CoV-2 sequence data into the public domain … and provide consistent, real-time sequence data to the public health response teams investigating cases and clusters of COVID-19 across the country.”

The idea is that better data will help public health officials interrupt chains of transmission, prevent new cases of the illness and protect and save lives.

“The U.S. is the world’s leader in advanced rapid genome sequencing,” said CDC Director Robert Redfield, M.D., in the press release. “This coordinated effort across our public, private, clinical, and academic public health laboratories will play a vital role in understanding the transmission, evolution, and treatment of SARS-CoV-2. I am confident that our finest, most skilled minds are working together to help us save lives today and tomorrow.”

Learn more about the Nevada Genomics Center here.

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