Yale: Omicron subvariant may be spreading in Conn.
An omicron subvariant called BA.2 may be spreading in Connecticut, a month later than was initially expected.
BA.2 is a direct descendant of the omicron variant, also referred to as “BA.1,” which caused a spike in infections and hospitalizations across and beyond Connecticut.
When BA.2 emerged in Europe, public health experts feared it would quickly surpass its ancestor.
“We’ve all been thinking this was going to happen for a long time, waiting for it to happen,” said Nathan Grubaugh, whose laboratory at Yale conducts the lion’s share of genetic sequencing of coronaviruses in the state. “Our first detection of it in Connecticut was on Jan. 8 and I think we were thinking it was more transmissible than BA.1 than it actually is.”
Grubaugh said omicron, BA.1, is about 100 percent more transmissible than the delta variant. He was concerned when BA.2 first emerged that it was that much more infectious than BA.1.
“A lot of those early warnings, at that point we don’t really know its properties,” he said.
More recent data suggests that BA.2 is about 30 percent more transmissible than omicron, which Grubaugh said is “still a lot.”
“I still think it’s going to arise and become dominant, it's just off by a month or two,” he said. “There are a lot of interesting parallels between the emergence of BA.2 and alpha a year ago. That, we first detected in Connecticut very early January and it didn't become dominant until March or April.”
The Centers for Disease Control and Prevention released Friday the results of a study showing an “omicron infection resulted in high transmission among household contacts.”
The study, which covered patients in four United States jurisdictions, including Connecticut, showed family transmission was particularly high among patients “who were not vaccinated or who did not take measures to reduce the risk of transmission to household contacts.”
While they are relatives, the subvariant differs from omicron in some significant ways.
One feature of omicron is an “S-gene dropout.” BA.2, similar to delta, does not have that feature. Samples must be genetically sequenced to confirm which variant caused an infection.
Testing for the S-gene dropout is a faster and simpler process, but it’s not conclusive. If a sample presents with that feature, it’s probably omicron, Grubaugh explained.
Last week, 98 percent of samples were most likely omicron, Grubaugh said. This week, there was about a 10 percent drop to 88 percent, he said.
“I have a hard time putting a value on the percent rise in BA.2 from last week,” Grubaugh said. “Ten percent is in the range of possibility, but it could be 3 percent. A 10 percent rise is higher than I would have expected.”
Several factors may have contributed to BA.2’s slower-thanexpected rise, including the spike in cases caused by omicron.
Because BA.1 and BA.2 are so closely related, “there’s evidence that infection with BA.1 is effective, at least in the short term, against infection from BA.2,” Grubaugh said.
He said “you really need three” vaccine doses to be protected from severe infection from both omicron and BA.2. However, he said, “based on preliminary studies, it doesn't seem to impact vaccines any more than BA.1.”
Because of the high rate of infection caused by omicron and the vaccination rate in Connecticut, Grubaugh said he does not expect the subvariant to cause a significant spike in cases, at least in the near future.
“The most likely scenario is that it extends our decline, but it doesn't create a big wave in cases,” he said.