How the highly contagious COVID strain is detected
A highly contagious strain of COVID-19 that has caused a widespread lockdown in England where it was first detected has been confirmed in two Connecticut cases.
The cases involve two people living in New Haven County who are between the ages of 15 and 25, according to the governor’s office. Both recently traveled — one to New York, the other to Ireland.
Researchers at Yale found the two cases after samples from their positive tests were genetically sequenced.
So what does that mean? For researchers at the Yale School of Public Health, the process starts with a used COVID-19 test kit.
“Think the tube with the swab and media,” said Joseph Fauver, an associate research scientist in epidemiology.
From there, the team extracts the RNA and performs a test to see how much of the virus is contained in the sample. Other steps “amplify” the virus’ genome, and add “bits and pieces” to the ends of the nucleic acid so it can be read by a device, Fauver said.
The sample then goes into a small sequencing device “about the size of a thumb drive,” which is read by a laptop set up for the role, Fauver said.
“Once the sample is on the sequencer, we can actually see the data being generated in real time to determine how much of the virus genome we generated,” Fauver said.
After an hour or two, “we can typically pull out the complete viral genome from these samples,” which lets them study its evolutionary history, he said.
It’s unclear exactly how much lab capacity exists in Connecticut to conduct that work. In practice, the test works a little more like a barometer for the number
of cases involving the strain than an exact number.
“We’ll continue to do this sequencing to see how frequently we find it, but we had over 3,000 cases that we reported (Thursday), for example,” said Deidre Gifford, acting commissioner of the state Department of Public Health. “We won’t be doing genomic sequencing on every single case.”
So if you test positive for the disease “you should assume that there’s a good possibility that you have this variant,” she added.
The state lab does not perform genetic sequencing, but it is coordinating with Jackson Labs and the Yale School of Public Health to provide samples, Gifford said. Sema4, in Stamford, also performs genetic sequencing, according to Josh Geballe, Gov. Ned Lamont’s chief operating officer.
The Centers for Disease Control and Prevention is also ramping up its sequencing efforts to handle 750 samples a week, according to its website. The agency also has partnerships with national reference labs to sequence 1,750 samples per week, along with other sites.
Fauver said the time it takes to sequence a sample varies, but for urgent cases, the lab can complete the
process in 24 to 36 hours.
“Typically, we can get through about 50 samples a week with our current workflows,” he said.
But Fauver said a grant is being used to establish the Yale Genomics Surveillance Initiative to increase the number of samples they can examine.
Besides confirming the variant was present in Connecticut, researchers also use sequencing to trace the origin of the virus. Fauver was part of a team of researchers who published an article in May that relied on sequencing and air travel data to explain how the virus spread.
For the governor and Gifford, the two confirmed cases of the new strain are a sign to reinforce COVID safety measures.
“What that just means is, take your isolation and isolation recommendations very seriously,” Gifford said. “And for all the rest of us, it means double down on the mask and the physical distancing and the ventilation.”
Lamont echoed similar thoughts.
“It just means be even more careful,” he said. “If you’re standing less than 6 feet from someone for more than 15 minutes and you’re not wearing the mask, the chance of you getting infected ... has just gone up.”