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Philly health department's new lab a key resource for tracking COVID

Jason Laughlin, The Philadelphia Inquirer on

Published in News & Features

PHILADELPHIA — A newly opened lab gives the Philadelphia Department of Public Health the technology to identify COVID-19 variants, a long-awaited resource with the potential to also track other health hazards, from E. coli to syphilis.

The genetic sequencing lab went live at the end of July, making Philadelphia one of only four big American cities with their own such facility, said Bernadette Matthis, the health department’s public health lab director. At full capacity, the lab could process more than 300 samples a week.

“We just wanted to have in-house testing, so we could turn it around quickly,” Matthis said.

In its first week of operation, the lab sequenced about 50 samples. While the sequencer is up and running, staff are still working out the data streaming between the technology and a processing and storage system. Resolving that should allow the lab to process far more samples.

Genetic sequencing provides information on the building blocks that make up a virus’ RNA, which shape how effectively a virus like COVID-19 can spread and cause symptoms.

As seen with COVID-19, mutations of the same kind of virus can mean significant differences in how the virus spreads and evades immunity. Sequencing allows scientists to spot new variants more quickly, and give the public information about how to respond.

Even after identifying a new variant’s presence in Philadelphia, such ongoing sequencing will allow public health experts to conduct surveillance to determine how widely it is circulating.

COVID-19 revealed a lack of sequencing resources in the United States. In Pennsylvania, just 2.5% of all positive test results are sequenced, and New Jersey sequences just 3%, according to the Centers for Disease Control and Prevention. Health experts have said between 5% and 10% of positive samples need to be routinely sequenced to quickly identify new variants.


Before the city lab opened, the health department relied on Children’s Hospital of Philadelphia and Drexel University for sequencing. University of Pennsylvania also has a sequencing lab. By conducting sequencing in-house, Matthis said, the city can reduce by half the wait time for sample results, to about two weeks.

Sequencing itself takes five to six days, said Vincent Tu, a bioinformatician working in the lab, and the analysis that follows takes about another week.

The city approved opening the lab in December, and since then has built the facility with $4 million in federal grant money and $1 million in city funds. It also added staff, including Tu and a molecular biologist, Mazen Sidahmed.

Prisons, ambulatory health centers, and primary care and long-term care settings will likely provide many of the COVID-19 test results for sequencing. The lab also expects to sequence the samples taken through the city’s wastewater testing program.

The equipment can be adapted for use with other viruses and bacteria, said Sidahmed. City officials anticipate being able to identify sexually transmitted diseases, types of E. coli and other bacteria involved in food poisoning.

“Right now, COVID is the priority,” Matthis said. “I think it’s going to expand to other things as well.”

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