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University at Buffalo scientists used genetic sequencing to identify variants of concern in specimens from Erie County residents
The Erie County Department of Health on Friday announced five specimens collected from Erie County residents in January have been identified as containing COVID-19 “California variants.” This comes from the genetic sequencing of nearly 1,000 specimens by the interdisciplinary team at the University at Buffalo’s New York State Center of Excellence in Bioinformatics and Life Sciences.
As viruses mutate, they can exhibit changes in certain characteristics, like transmissibility, disease severity, resistance to known treatments, and vaccine effectiveness in preventing severe illness. The “California variant” was named for where it was first identified in July 2020. The Centers for Disease Control and Prevention stated the B.1.427 and B.1.429 “California variants” are 20% more transmissible than the novel coronavirus SARS-CoV-2 strain. The treatments developed for COVID-19 have a reduced effectiveness against this branch of variants.
“With vaccination rates rising and public health measures still largely in place, we would expect to see case numbers and hospitalizations decline since January,” Commissioner of Health Dr. Gale Burstein said. “Instead, we now see the number of new cases and hospitalizations increasing. We need to continue this sequencing work before drawing any firm conclusions, but it is very possible that more transmissible SARS-CoV-2 variants are preventing further decreases in our case numbers.”
UB scientists found three samples with the B.1.427 variant, collected on Jan. 15, and two with the B.1.429 variant, collected on Jan. 20. These samples were from Erie County residents.
“Genetic sequencing can be like putting together a puzzle when you do not know the final picture, and can’t be sure you have all the right pieces. Though this field has been around for decades, it remains at the leading edge of scientific discoveries,” Burstein said. “We are incredibly fortunate to have the UB Center of Excellence in Bioinformatics and Life Sciences with its highly specialized equipment and accomplished research team, here in Erie County. Their enthusiasm and commitment to this disease surveillance project was evident right away.”
When COVID-19 variants became a concern at state and federal levels earlier this year, ECDOH began working with Jennifer A. Surtees, Ph.D., co-director of the Genome, Environment and Microbiome Center of Excellence and associate professor of biochemistry in the Jacobs School of Medicine and Biomedical Sciences at UB. Her lab and the Genomics and Bioinformatics Core in UB’s Center of Excellence in Bioinformatics and Life Sciences have the capability to analyze and sequence COVID-19 samples to detect mutations in the novel coronavirus SARS-CoV-2 genetic sequence, first identified in Wuhan Province, China, in 2019.
“Since last spring, our team with UB's Genomics and Bioinformatics Core has been focused on monitoring how this virus is evolving in Western New York through genome sequencing, part of the worldwide research network that is building a map of SARS-CoV-2 mutations in real-time,” Surtees said. “When combined with public health surveillance and contact tracing, the mapping that we do provides context for public health officials as they work to control this virus, for clinicians treating patients, and for our understanding of the virus.”
Data for these samples has been uploaded to GISAID, a global science initiative that provides open-access to genomic data of viruses. The New York State Department of Health and its Wadsworth Center are aware of this development. During the week of March 28, UB will begin sequencing additional specimens collected by ECDOH and Kaleida Health during February and March 2021.