BA.2 May Not Disrupt U.S. COVID Case Declines

The Omicron sublineage BA.2, which raised alarms because of its transmission advantage, accounts for just 4% of cases in the U.S., and experts suggested it’s not likely to reverse the current downward trend of cases overall.

BA.2 has certainly increased in prevalence, but its been a slow trajectory, according to CDC data. BA.1.1, another Omicron sublineage, actually became the dominant strain in the U.S. in mid-January, the agency reported, with the original lineage, B.1.1.529, currently accounting for about 23% of U.S. cases.

“The BA.2 Omicron variant is increasing in prevalence slowly in both CDC and private data,” tweeted Scott Gottlieb, MD, former FDA commissioner and current Pfizer board member. “While it may become a dominant strain in time, it appears increasingly unlikely that it will cause a significant change in the downward trajectory of the current epidemic wave.”

That has certainly been the case for South Africa, where BA.2 accounts for nearly 100% of cases, according to Tulio de Oliveira, PhD, of the Centre for Epidemic Response & Innovation in Stellenbosch.

“This comes on a background of decreasing infections,” de Oliveira tweeted. The country now has a 7-day average of about 2,500 daily infections, down from a peak of about 23,000 in mid-December.

“At present, the Omicron BA.2 is not of great concern in South Africa,” he tweeted. “But our network is following very close and is alerted to its emergence.”

In the U.K., BA.2 accounted for about 4% of cases as of the end of January, according to a February 11 Health Security Agency technical briefing. That report noted that the variant was on the rise as measured by increases in S-gene target positivity (SGTP) on PCR testing. The variant lacks the S-gene deletion at position 69-70 of the original Omicron lineage, so it doesn’t cause S-gene target failure. SGTP rose to 18.7% of tests as of February 6, up from 5.1% on January 24, according to the report.

While cases are down from a peak of about 180,000 per day in early January in the U.K., their rapid descent stalled around the end of the month and has been coming down more slowly, to a 7-day average of about 70,000 cases. It’s not clear whether that’s due entirely to BA.2.

As of February 8, there were about 49,000 sequences of BA.2 from 67 countries documented in the global tracking initiative GISAID, with an increasing number in recent weeks, the report stated. Denmark and the U.K. contribute the highest proportions of BA.2 sequences on GISAID, with Denmark leading the way.

BA.2 is the dominant strain in Denmark, where it makes up about two-thirds of cases. It got an early lead, accounting for nearly half of cases by mid-January. After lifting all of its restrictions in recent weeks, cases have stalled at an all-time high of 45,000 daily cases, but that’s in a country where 80% of people are fully vaccinated and 60% are boosted.

Gottlieb doesn’t seem to suspect that U.S. case loads will stall out as they did in the U.K. and Denmark. He cited the South Africa data, which suggest that “even as a new variant overtakes original strain of Omicron, in places where Omicron has already spread widely, BA.2 is unlikely to cause a new wave of infection.”