Chicago and Rush Partner to Detect New Strains of COVID-19

Molecular lab will run genome sequencing of SARS-CoV-2 samples from across Chicago
Stefan Green, PhD, and Mary Hayden, MD, in Rush's new lab site

Rush University Medical Center is opening an advanced molecular laboratory that will examine COVID-19 samples from across Chicago to detect new strains of the COVID-19 virus for the Chicago Department of Public Health.

CDPH awarded Rush a $3.5 million contract to create the Regional Innovative Public Health Laboratory, which will work in partnership with CDPH and other local academic medical centers to detect new strains and determine which strains of the virus are spreading the fastest and where they are spreading. Building coordinated, regional capacity for this type of advanced molecular laboratory has been a top priority for CDPH.  

Rush will collect COVID-19 positive specimens from hospitals across the city and use molecular biology tools such as whole genome sequencing to answer questions that CDPH wants addressed, according to Mary Hayden, MD, chief of the Division of Infectious Diseases and director of the Clinical Microbiology Laboratory at Rush University Medical Center. Hayden is co-principal investigator on the CDPH contract with Stefan Green, PhD, director of the Genomics and Microbiome Core Facility at Rush. 

“For example, if the city wants to understand some COVID-19 hot spots, the genomic information can help to identify chains of transmission so that public health resources can be used most effectively to break the chain,” Hayden said.

National effort to surveil COVID-19

With the laboratory, Rush and CDPH join a national effort to step up surveillance of SARS-CoV-2, the virus that causes COVID-19, detect any variants of the virus and identify genetic changes in these variants. New strains, such as those first found in the United Kingdom, South Africa and Brazil, now are spreading to other places, including the United States. The UK strain was first reported in Chicago in mid-January.

“These few new strains are not going to be the end of it, so we need to know more than just whether people have the virus. We also need to know which strain they are carrying,” said Green, who recently joined Rush to establish and oversee the laboratory.

Like other viruses, the COVID-19 virus constantly changes through mutation, and new variants emerge over time. “SARS-CoV-2 is mutating, though not at an especially rapid rate compared to other viruses, such as influenza,” Green added.

Genomic sequencing can answer a number of questions. It can detect which strains of COVID-19 are circulating in Chicago, and it can monitor the spread in certain neighborhoods or within certain populations. 

“There’s also interest in whether people who become ill with COVID for a second time are infected with a new strain of the virus or the same strain as the first infection, and whether it is a relapse and the infection never really went away,” Green said. 

Another question of interest is whether variants will “escape” the immunity provided by the COVID-19 vaccines.

“While the SARS-CoV-2 vaccines have been shown to be very effective, one focus of RIPHL will be to sequence viruses from vaccinated persons who develop COVID, to monitor whether certain variants are more likely to cause infection after vaccination,” Hayden said.

The contract was awarded in December, and the lab is expected to be fully operational by March. CDPH, which is working with the federal Centers for Disease Control and Prevention and State of Illinois to contribute to national surveillance of SARS-CoV-2 strains, says the lab partnership will increase public health surveillance of possible COVID-19 variants.

Rush and CDPH have partnered on other public health initiatives, including a comprehensive data resource hub that centralizes hospital information. Launched in December, the big data analytics tool is designed to aid in the fight against COVID-19 and other public health issues. 

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