City forges $3.5M partnership with Rush to help track coronavirus variants in Chicago

The Chicago Department of Public Health got the go-ahead on Wednesday to forge a ground-breaking partnership with Rush University Medical Center to undertake “genomic sequencing” to track the spread of coronavirus variants in Chicago.

The City Council’s Committee on Budget and Government Operations signed off on the $3.5 million partnership that will cover sequencing of up to 6,000 sample specimens from Chicagoans who test positive for COVID-19.

It will be bankrolled by a $3 million “epidemiology and capacity grant” received during the first few months of the pandemic from the Centers for Disease Control and a $500,000 grant for the same purpose awarded to the city in December.

Tina Anderson, deputy commissioner of the Health Department’s COVID Response Bureau, said genomic testing capacity is “vital” to help the city determine whether any of the COVID-19 variants detected around the world — in the UK, South Africa, Brazil, Japan or elsewhere — are spreading in Chicago.

“These variants are here in Illinois and they are spreading. Some of these variants have been documented to spread more quickly. More people can kind of catch them from one sick person and they will impact a third wave of increased cases in Chicago,” Anderson told aldermen.

“CDPH needs to be able to monitor the spread of these to be able to inform policy decisions around the city’s response. We need to know and understand how more transmissible these variants are or if they are causing more severe disease in those who are infected. Additionally, we need to understand if there are possible cases of re-infection. People who have ... gotten it a second time with variants or become sick after receiving the vaccine.”

To monitor the spread of coronavirus variants, you either need a “highly-specialized test, which is not readily available” or the ability to “run genomic sequencing on a test sample after the patient has been diagnosed as positive,” Anderson said.

“This requires a diagnosing lab to give the test sample to a lab which can run sequencing and identify the viral strain which has infected the patient,” Anderson said.

“The city does not have the ability to monitor this because we do not have a public health laboratory, nor a partnership with a lab that has this capability. To build our own public health lab would cost millions of dollars in start-up costs and several years to construct and fully certify. It would also require much cost to maintain thereafter.”

When the city received the first round of CDC funding last year, a request for proposals to forge a public-private partnership to build that “critical capacity” was issued. It was distributed to a handful of academic centers and professional laboratories that “even have this advanced genomic sequencing capacity.”

Rush University Medical Center submitted the only response.

Rush will be “staffing and hiring for the contract,” with support staff provided by City Hall —both existing staff and newly-hired employees.

Ald. Carrie Austin (34^th) asked Anderson whether results of Rush’s genomic sequencing would be provided to a City Council riding herd over the city’s pandemic response.

“If we have any cases that … have policy implications — if we have detected that there’s a more severe outcome with one of these variants — that will absolutely inform our public health response,” Anderson said.

Ald. James Cappleman (46^th) asked whether that same information would also be shared with the Illinois Department of Public Health. Anderson assured him that it would be shared “to help them understand how that was potentially affecting other jurisdictions around us and be able to coordinate the public health response.”

“Thank you. I mean — this seems just perfect. This is what the Chicago Department of Public Health [should be doing]. This is their main mission,” Cappleman said.