Stanford Medicine launches large-scale surveillance of coronavirus variants in Bay Area

Stanford Medicine researchers are screening diagnostic samples to identify known coronavirus variants circulating in the Bay Area, including those from the United Kingdom, South Africa and Brazil.

- By Krista Conger

Benjamin Pinsky is the medical director of the Stanford Clinical Virology Laboratory, where researchers are screening samples for known coronavirus variants circulating in the Bay Area.
Steve Fisch

In March, Stanford Medicine was one of the first academic medical centers in the country to develop a diagnostic test for the novel coronavirus that causes COVID-19. Now, researchers in Stanford’s Clinical Virology Laboratory have developed additional tests to detect the presence of coronavirus variants, or strains, already spreading in the United Kingdom, South Africa, Brazil and some parts of the United States. 

One strain, known as L452R, has been identified as the cause of an outbreak of COVID-19 in late December and early January in San Jose. 

Tracking viral variants and quickly identifying new mutations is critical to understanding whether they will spread more easily, cause more-severe disease or render vaccines less effective — all vital questions in the worldwide fight against the virus. 

The Stanford researchers have started screening hundreds of viral samples collected from people across the Bay Area, with plans to ramp up significantly in the coming days. They also began sequencing whole viral genomes to identify new mutations as they arise in key viral proteins. 

“In most cases it is too early to say whether or how these variants will influence the course of the pandemic, but it is important to monitor their evolution and spread,” said Benjamin Pinsky, MD, PhD, associate professor of pathology and of infectious diseases at the School of Medicine. “Our surveillance testing is specifically designed to allow large-scale screening of viral samples to identify specific strains circulating in the Bay Area and throughout California.”

Pinsky is the medical director of the Stanford Clinical Virology Laboratory. 

Virus mutates regularly

Like many viruses, the coronavirus that causes COVID-19 mutates regularly inside infected cells. Most of these mutations are inconsequential, but some occur in genes encoding key viral proteins, including the spike protein that the virus uses to attach to and infect host cells. Changes in the spike protein are particularly concerning to virologists and clinicians because they may help the virus spread more easily from person to person — something that appears to be happening in the U.K. variant known as B.1.1.7. It’s also possible that spike protein mutations could reduce the effectiveness of available vaccines.

Stanford’s new test uses a technology called reverse transcription polymerase chain reaction, or RT-PCR, to identify the presence of viral genetic material in samples collected from nasal passages. Using different panels of DNA tags, or probes, allows the researchers to discern not only whether a person is infected, but also whether they are carrying the original strain of the coronavirus, or one of the new variants. Currently, the test is designed to detect the U.K. variant, which has now been found in dozens of countries, including the United States, as well as the variants from South Africa and Brazil.

When one of the known variants is suspected, the researchers sequence all of that virus’s genetic material to confirm its identity. This whole-genome sequencing is also necessary to identify other single mutations, including the L452R variant now circulating in the Bay Area. 

“Our hope is that Stanford’s increased surveillance, combining RT-PCR and whole-genome sequencing, will provide critical information to help public health efforts during the coming months,” Pinsky said. 

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit

2024 ISSUE 1

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