This week public health officials confirmed Connecticut’s first case of a coronavirus variant originally detected in South Africa. But the extent to which Connecticut is screening for COVID variants remains unknown. The state public health lab lacks the capacity to test for COVID variants, and while the state is working with two outside labs to conduct variant surveillance, it has formalized no contracts to outline the parameters of that work.
The state is working with The Jackson Laboratory and Yale to monitor the presence in Connecticut of a pool of COVID-19 variants that are emerging globally.
So far, both the United Kingdom (B.1.1.7) variant, which the Centers for Disease Control and Prevention said is more contagious, and the South African (B.1.351) variant have been detected in Connecticut residents.
But state officials said Tuesday there are no contracts governing the extent of the state’s variant surveillance and no immediate plans to draw up arrangements that would formalize how variant sequencing is done or how often the work will take place.
“I really did not think of that at this moment,” said Jafar Razeq, director of the State Public Health Laboratory.
“Moving forward, would the time come that we may need to have a formal agreement and a contract? Maybe. And maybe not,” Razeq said. “From my perspective, if it’s working the way it is right now, I’m not sure. Why do we need to have a formal agreement?”
Both The Jackson Laboratory (JAX) and Yale said they are not charging the state for variant surveillance. But it’s unclear whether that will remain the case.
How Much Sequencing Is Enough?
So far, the DPH has reported 42 cases of the B.1.1.7 variant that emerged in the U.K. in addition to the one reported case of the South African variant.
Maura Fitzgerald, a spokesperson for the state Department of Public Health, said Tuesday that a hospital in New York identified the South African variant in a Connecticut resident, not JAX or Yale.
As the CDC report of the number of variant cases nationwide grows daily, scientists across the country find themselves facing a question: After you test a population for COVID generally, how many of those COVID-positive tests warrant a closer look via genetic sequencing to see if a COVID variant is the root cause?
“That’s really a tough question,” Razeq said. “Sequencing, obviously, it’s more expensive and it’s time consuming … there [are] limitations in manpower and other things.”
As of Wednesday, JAX reported sequencing a total of 41 COVID samples for variants. Within those samples, it found 14 belonged to the U.K. variant. But that sample selection is biased, because JAX limited its pool to COVID-positive samples containing a specific mutation that makes them much more likely to be the B.1.1.7 variant. Right now, that variant is the only one the lab is screening for.
“We’re working toward being able to screen all positives to determine if they are the U.K. strain, and to add other variants of concern,” Mark Adams, deputy director of JAX Genomic Medicine, said in an email.
Nathan Grubaugh, an assistant professor at the Yale School of Public Health, wrote in an email that getting a handle on the frequency of COVID variants in the state “isn’t straightforward.”
To target their sequencing work, his lab, like JAX, also first creates a subset of COVID samples that are more likely to contain a mutated virus.
At both JAX and Yale, thousands of samples have been pre-screened in this way to assess whether they warrant further study.
“We have a PCR assay that screens samples ahead of time, so we can selectively sequence B.1.1.7. Right now, the sample selection is biased and the % will be misleading,” Grubaugh wrote. “We are working on analyzing the data to determine this, and will release those results when we are confident in them.”
Grubaugh said his lab also sequences samples that have not been screened up front, “some, but very few of these turn out to be B.1.1.7,” he wrote.
“We haven’t sequenced enough from this group to estimate a true population frequency,” he wrote. “This is one of our top priorities, and we’ll provide this information as soon as we have enough data to analyze this in a meaningful way.”
JAX’s Adams cited the work of the COVID-19 Genomics UK Consortium, which has sequenced more than 200,000 SARS-CoV-2 genomes, and said it recommends “that at least 5% of positive samples be sequenced.”
But with no formal agreements in place, it’s difficult to assess how many positive samples Connecticut will work with partners to sequence going forward.
As variants continue to spread across Connecticut, Razeq, of the state public health lab, said he is optimistic the CDC will soon publish guidance on how many positive COVID tests a state should set aside to be sequenced for variant surveillance.
He said he’s also hopeful the state lab will “in a few weeks” be able to augment the work of JAX and Yale by doing some COVID sequencing in-house.
“Is the time going to come … [when] the sequencing happening in the state is not enough and we may need to do beyond that? Probably,” Razeq said. “That may happen in the near future. And we may end up having a formal contract.”
“We’re really going to be looking at this week to week,” Razeq said. “Whatever we do collaboratively is better than nothing.”