Picture viral RNA as a single component you can break into one million pieces.
Now imagine reassembling those pieces, literally like a jigsaw puzzle.
If there’s a chipped corner or if a piece won’t fit as it should, consider that a virus mutation or variant.
That’s genomic sequencing, in a nutshell, when it comes to identifying variants of COVID-19, according to Peter Stoilov, associate professor of biochemistry at the West Virginia University School of Medicine.
Stoilov helps lead the laboratory efforts of a statewide partnership between WVU Medicine, Marshall University and the state Department of Health and Human Resources to identify SARS-CoV-2 variants.
Despite the ongoing COVID vaccine rollout and relaxing of public health and safety guidelines, concerns have arisen in recent weeks over the various strains — B.1.1.7 (United Kingdom), B.1.351 (South Africa), P.1 (Brazil) — that have evolved from the original virus.
Stoilov and fellow scientists were prepared. From the onset of the pandemic, a statewide collaborative scientific task force took up the needs of the health crisis, including establishing the WVU Rapid Development Laboratory. Recognizing this solid framework already intact, Dr. Clay Marsh, vice president and executive dean at WVU Health Sciences and West Virginia’s coronavirus czar, requested Laura Gibson, senior associate vice president of Research and Graduate Education, form a team to sequence positive samples from across West Virginia.
In February, Stoilov detected West Virginia’s first three cases of the UK Variant.
“It was a little awkward because I was training a student how to perform data analysis,” he said. “I wasn’t expecting to see that.”
Stoilov sent the findings to Jim Denvir, associate professor of biomedical sciences at Marshall University’s Joan C. Edwards School of Medicine and collaborator on the sequencing project.
“I had developed an automated data analysis pipeline, which starts from the individual genomic sequence fragments, runs through the process of assembling them into whole-genome sequences, and then identifies variants and flags variants of concern,” Denvir said. “I was quickly able to run this pipeline on the data and confirm Peter’s suspicions.”
In just a few hours, multiple entities stretched across West Virginia, identified and confirmed the new variant and relayed the information to the masses.
Covering the bases
The first three cases of the UK Variant came from positive COVID-19 samples collected through the WVU and Monongalia County Health Department testing programs.
Scientists are now processing nearly 200 samples a week, with the aid of a robot, for variant sequencing.
Stoilov said the ultimate goal is to scale it up to 700 samples a week.
“Those first batches were WVU samples, but we’re working on a pipeline to get samples from the rest of the state. That’s very important because we want to have a good look at all of West Virginia, not just one corner. That can be misleading.”
The machine takes two or three days to churn out the sequencing data.
Sequence to sequence
When biologist Ryan Percifield first arrived at WVU in 2010, his first job was managing Stoilov’s lab in the biochemistry department.
The Genomics Core Facility offers next-generation sequencing, technology capable of deciphering the entire human genome within a single day and a vital key to the statewide variant detection efforts.
The facility serves as one of the first links in the chain of sequencing.
Percifield has worked closely with the Bioinformatics Core facility at Marshall, under Denvir’s leadership, and the Genomics Core facility there, under the leadership of another sequencing collaborator, Don Primerano, since 2011.
Evolving along with the virus
Much like the virus itself, the statewide partnership and its work continually evolves — as this may be a project that sticks around for quite a while.
In addition to the original main three variants (UK, South Africa, Brazil), other dominant mutations have emerged, including strains from California and New York. The Centers for Disease Control and Prevention has even classified new variants into three categories, ranked from least to most severe: variants of interest, concern and high consequence.
There are currently no SARS-CoV-2 variants that rise to the level of high consequence, though the UK, Brazil, South Africa and two California strains identified fall into the variant of concern category.
Because of the unpredictable nature of the virus mutating, it remains ever important to continue to get tested and to properly wash hands, mask up and social distance, according to health experts.