Philadelphia working with Penn microbiologists to check for coronavirus variant

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Pennsylvania confirmed its first case of COVID-19 from the B.1.1.7 variant of the virus on Jan. 7.

That’s a version that emerged in the U.K. and seems to spread more quickly, according to preliminary data. The person infected with the variant was exposed while traveling outside the United States.

One of the ways to check whether someone has been infected with the B.1.1.7. variant, or other variants, is called viral whole genome sequencing. That means looking at all the genetic material of a virus to see how it compares to another one. The Centers for Disease Control and Prevention notes that right now there is no evidence that the variants lead to more severe illness or a high risk of death from COVID-19.

But it’s hard to tell if there are more of these cases in this country because the U.S. is not doing enough of the sequencing to check for the variant. A July report from the National Academies of Sciences, Engineering, and Medicine said current sources of coronavirus genome sequence data in the U.S. and efforts to integrate that with clinical and epidemiological data are “patchy, typically passive, reactive, uncoordinated, and underfunded.” The Washington Post looked at several databases along with their reporting and in December ranked the U.S. 43rd in the world when it comes to the percentage of coronavirus cases that were sequenced.

Scientists in Philadelphia have started doing lab work to see whether people are getting infected by this variant. Microbiologists at the University of Pennsylvania have already started sequencing samples from patients at Penn Medicine hospitals.

The city has also sent a sample to the university for sequencing, and they are working out the details of a partnership going forward, according to James Garrow, director of communications for Philadelphia’s Department of Public Health. He added that the city is working with the Association of Public Health Laboratories and the CDC on either doing more sequencing in the city, or sending samples to the CDC.

The CDC has been sequencing samples from state health departments and public health agencies since November, and the system is being scaled to process 750 samples nationally per week, according to a Jan. 3 update from the agency.

Children’s Hospital of Philadelphia is the other organization that can do this kind of sequencing, city Health Commissioner Thomas Farley said at a press conference on Jan. 5. A hospital spokesperson said all they can say right now is that they are “ramping up efforts to test for the new strain.”

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