Researchers Detect California COVID-19 Variants in WNY

The Centers for Disease Control and Prevention (CDC) says these California variants are 20 percent more transmissible than the SARS-CoV-2 strain. The treatments developed for COVID-19 are reported to have a reduced effectiveness against this branch of variants.

While the arrival of more transmissible variants of the virus in Western New York raises public health concerns, it isn’t surprising, according to Jennifer A. Surtees, PhD, associate professor of biochemistry and co-director of UB’s Genome, Environment and Microbiome Center of Excellence (GEM), who leads the team doing the sequencing.

“When organisms replicate or copy themselves, there is always the probability that mistakes will be made,” Surtees says. “So as we have infections happening around the world, we are going to get more and more variations of the virus. That’s what we’re seeing.”

She noted that the emergence of new and potentially more contagious variants reinforces the need for the U.S. to increase its genomic sequencing capacity and work closely with global partners such as GISAID (Global Influenza Surveillance & Response System), a Germany-based initiative that promotes the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19.

“We need to do more widespread genomic sequencing of the entire SARS-CoV-2 genome across the country in a coordinated way with open data sharing via the CDC and globally via GISAID,” Surtees says. “With this critical data sharing, it will become possible to pick up lineages that are spreading in different places at different rates.”

Surtees cautions that the presence of variants in general doesn’t necessarily translate into more transmissibility or more severe patient outcomes. She noted that most variations in the genome of the virus won’t affect how the virus works, but the persistent level of infections is a key factor in increasing the rate at which mutations occur.

“By continuing to transmit the virus so widely, we are accelerating its evolution; in effect, we are carrying out a massive, global molecular evolution experiment with this virus,” she says.

The vaccines are still expected to produce immunity — even against new variants — and Surtees notes that the presence of variants makes increasing the rate of vaccinations locally and nationally even more critical.

“It’s important to vaccinate as many people as possible because not everyone responds equally to the vaccine,” she explains. “Herd immunity protects people who cannot get vaccinated, as well as those people who got the shot but who may not be able to mount as robust an immune response.”

Ultimately, the only way to slow down the evolution of potentially more transmissible or more lethal variants is to slow the circulation of the virus, she adds.

“From a public health perspective, we should all be behaving as though these and many other, as yet undetected, variants are among us because they probably are. So we need to keep using masks or double masks, staying physically distant and working on getting more vaccines into people. We don’t know what is out there so we should behave as though variants of concern are out there. We need to really still be vigilant,” Surtees says.

In their most recent batch of SARS-CoV-2 sequencing, researchers found 42 variants of concern out of 138 samples, including B.1.427/429 (California variants) and B.1.1.7 (United Kingdom variant). 

“This is likely the cause for the recent spike in cases. This information has been shared with the Erie County Department of Health and New York State Department of Health; Erie County is working to identify the patients and proceed accordingly,” Surtees says.

They continue to receive samples from Kaleida Health and Erie County and continue to sequence.

Surtees stresses some important points:

“These samples were all from February until March 20, with 30 percent variants of concern, as compared to January, with 3 percent variants of concern. More recent samples may show a further increase in proportion,” she says. “In addition, the variant profile is quite distinct from New York City, which has a significant amount of the so-called New York variant (50 percent), with 25 percent B.1.1.7 and virtually no California variants. This highlights the importance of doing this work regionally, so that we can monitor what is happening in our community and respond accordingly.

The multidisciplinary team that is sequencing SARS-CoV-2 virus samples includes researchers in the Department of Biochemistry and scientists in the Genomics and Bioinformatics Core in UB’s New York State Center of Excellence in Bioinformatics and Life Sciences (CBLS).

“Our ability to sequence and interpret SARS-CoV-2 genomes for genomic surveillance of variants is a result of our investment in technology and experts at the Genomics and Bioinformatics Core with data analytics powered by the computational resources at the Center for Computational Research, all housed within the Center of Excellence in Bioinformatics and Life Sciences,” says Norma J. Nowak, PhD, professor of biochemistry, executive director of the CBLS and co-director of GEM.