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  • Pam King Sams

Bushman Lab at Perelman School of Medicine working to find SARS-CoV-2 Variants.

New variants of the SARS-CoV-2 coronavirus are being investigated in the lab of Frederic Bushman, PhD, chair of Microbiology at the Perelman School of Medicine and co-director of the Penn Center for Research on Coronaviruses and Other Emerging Pathogens, through a partnership with the Philadelphia and Pennsylvania Departments of Health to identify them in the region. Bushman's team identified the United Kingdom virus variant recently in a sample from a southeast Pennsylvania resident. They have been leading efforts to study the virus genome as it evolves since April 2020.


Evidence of infection by the highly transmissible B.1.1.7 variant of the COVID-19 coronavirus first identified in the United Kingdom has been found in a southeast Pennsylvania resident.


Following an investigation by the Philadelphia Department of Public Health and the Bucks County Health Department, a sample was sent to the lab of Frederic Bushman, PhD, chair of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, for genetic sequencing. The health departments announced that the variant was found in a woman in her 50s who began experiencing symptoms the last week of December and was briefly hospitalized. She is currently recovering. She is a resident of Philadelphia and Bucks County. This is the second case of B.1.1.7 variant COVID-19 in Pennsylvania.


Philadelphia Health Commissioner Dr. Thomas Farley said, “While it is still not proven that the B.1.1.7 variant is more transmissible than other variants of the COVID-19 coronavirus, we are concerned that it is present in Philadelphia. Everyone in the area should take this information as a reminder to be even more consistent in wearing masks and keeping distance from others.”


Bucks County Health Department Director Dr. David Damsker said it is not unusual for a virus to change and mutate. “We are not overly concerned about this development because all available evidence shows that the existing vaccines are effective against this variant,” Damsker said. “So long as that continues to be the case, we will treat this variant the same as our other cases.”


Bushman’s research team began working with the Philadelphia Department of Health at the start of the pandemic last spring. As they began sequencing SARS-CoV-2 whole genomes from hospitalized patients at Penn Medicine in an effort to understand the virus and its spread in the community, they maintained contact with the department.


“Collaboration between our researchers and public health officials is more important than ever so that we can use science to drive decision-making to protect our communities, and move as quickly as possible to meet new challenges like this one,” Bushman said. “I don’t think it’s surprising to have found the variant here, as it has already been detected elsewhere in Pennsylvania and in many locations across the U.S. All these detections support the idea that the virus is more infectious, and reinforces that we need to take the precautions we know work — wear masks, social distance, don’t go to crowded places, and get a COVID-19 vaccine when it is available to you.”


Bushman noted that sequencing the whole viral genome is a technologically complicated thing to do, from complex processes like purifying the RNA to DNA, to the need for sophisticated equipment that can perform next generation sequencing. His lab decided early on in the pandemic they wanted to set this up and to help by providing this kind of data.


As the U.K. strain began to be identified in the United States, the Philadelphia Department of Health identified a high priority sample—the Bucks County COVID-19 patient with ties to the U.K. Based on their already established collaboration, the city health department asked Bushman’s lab to sequence the viral genome from the sample to determine whether it was the UK strain. Bushman’s team found that the sequence contained 22/23 of the diagnostic substitutions characteristic of the UK strain, including all the substitutions in the Spike protein hypothesized to make the variant more infectious.


The team also shared results from a paper on viral genome sequences and analysis from the first wave, Later the question arose of whether the UK strain, proposed to be more infectious, was in our area. The DOH folks identified a high priority sample—an individual who became positive after contact with someone who had become positive after recent travel to England. We offered to sequence the viral genome from the sample to determine whether it was the UK strain. The sequence contained 22/23 of the diagnostic substitutions characteristic of the UK strain, including all the substitutions in the Spike protein hypothesized to make the variant more infectious.


Bushman’s lab will continue sequencing new samples from COVID-19 patients at Penn Medicine, the health department, and other groups, and be on the lookout for new variants and mutations.


The U.S. Centers for Disease Control and Protection reports that more research about this new variant is ongoing, but current data seems to show that it is more easily transmitted between people than the current, dominant strain of COVID-19 in the United States. Cases have been reported in several states. It is believed that this strain of the virus is susceptible to the COVID-19 vaccine. It is difficult to identify this strain of the virus because it requires genetic sequencing testing.





Members of the Bushman lab, led by Frederic Bushman, PhD, chair of Microbiology, are working with the Philadelphia Department of Health to sequence samples from COVID-19 patients in an effort to uncover SARS-CoV-2 variants in the community.

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