Concern is rapidly growing over emerging omicron coronavirus variant BQ.1 and its sibling BQ.1.1, which experts say appear to be strong candidates for a winter surge in the U.S. and could knock the BA.5 variant out of its dominant spot.
The BQ.1 and BQ.1.1 variants, descendants of BA.5, were first identified in mid-July, according to UC Berkeley infectious disease expert John Swartzberg. They were first detected in the U.S. just a month ago and each rose quickly to account for 5.7% of cases sequenced nationwide for the week ending Oct. 15, according to updated estimates from the
Centers for Disease Control and Prevention’s variant tracker.
Meanwhile, BA.5, which has dominated the U.S. coronavirus picture since the summer, has been on the decline, dropping from its Aug. 20 height of 86.5% of sequenced cases to 67.9% on Oct. 15
BQ.1 and BQ.1.1 are worrisome because they both appear to be more transmissible, and could possibly be more immune evasive than earlier variants.
Dr. Anthony Fauci, President Biden’s chief medical adviser, expressed concern over the two new variants last week. “When you get variants like that, you look at what their rate of increase is as a relative proportion of the variants, and this has a pretty troublesome doubling time,” he said in
an interview Friday with CBS News.
Infections from BQ.1.1 have been doubling weekly since mid-September in the United Kingdom, leading to a significant increase in hospitalizations.
BQ.1.1 has an estimated growth advantage of 15% compared to BA.5, according to UCSF infectious disease expert Peter Chin-Hong. In a
recent Chronicle story
about emerging variants that could cause a winter surge, Stacia Wyman, senior genomics scientist at the Innovative Genomics Institute at UC Berkeley, noted that BQ.1.1 has a growth advantage of 14% over BA.5.
The BQ.1.1 variant, which is increasing in New York and Germany as well as other European countries, “is perhaps the most immune evasive subvariant circulating,” Swartzberg said. “This makes it the leading contender to overtake BA.5 in the next few weeks.”
Chin-Hong said some BQ.1 and BQ.1.1 mutations in the receptor binding domain (where the spike protein attaches to the body) “may be associated with antibody evasion,” and some lab studies support that finding. In addition, BQ.1 is the first variant to prove resistant to the two available antibody therapies Evusheld and bebtelovimab, he said.
“However, I must emphasize that (the therapies) will still be protective and that we don’t know if it is truly immune evasive until we see what happens in real life, not just the laboratory,” he added. “We also need more studies about BQ.1 specifically.”
That BQ.1 is a “grandchild” of omicron and a “child” of BA.5 bodes well for the effectiveness of vaccines, especially the new bivalent booster shots, both Chin-Hong and Swartzberg said.
“It is highly likely that an omicron-updated booster which target BA.5 will provide excellent protection against infection, and continue to provide spectacular protection against serious disease and death,” Chin-Hong said.
Against infection from these new variants, the boosters will possibly provide protection for only two to three months, “but protection against serious disease will continue for many, many months if not years,” Chin-Hong said.
He added that antivirals such as Paxlovid and remdesivir “work without regard to the spike protein appearance so they will continue to work very well.”
The BQ.1 sublineage was first reported in Nigeria in July, and has since been found in a number of European countries and Japan, but is not yet dominant anywhere, Chin-Hong said.
He explained that some variants stay off the global radar until multiple countries report them, they get mentioned on social media, or they show up on global COVID variant tracking site GISAID.
That’s why BQ.1 seemed to suddenly burst on the scene, to the surprise of many virus watchers, he said.
“It likely came out of nowhere because they were all classified as BA.5 previously, because that is the parent sub-lineage,” he said. “With these sub-sub-variants (or grandchildren) you can’t often find them until you actually sequence for, and look for them.”
Dr. Eric Feigl-Ding, head of the COVID Risk Task Force at the New England Complex Systems Institute,
tweeted Thursday about the BQ.1 and BQ.1.1 variants
and suggested the CDC might have been holding onto the BQ variant data, as they only just showed up on the agency’s tracker.
Chin-Hong said that while the CDC gets data only once a week and says it doesn’t include any variants with a proportion under 1%, “it appears that (BQ.1 and BQ.1.1) were surprisingly retroactively added,” and he personally was “shocked” when CDC site was updated.
“I kept reading and re-reading the figures, adding up the percentages, and pinching myself to make sure I wasn’t dreaming,” he said.
Omicron subvariants with similar mutations to the spike protein are proliferating because of “convergent evolution,” Swartzberg said.
“It’s like all these different Omicron viruses are settling on the same strategy,” he said. “They have found something they like.”
The high transmissibility and growth advantage of the BQ.1 and BQ.1.1 variants make it seem increasingly likely that they will eventually become dominant in the U.S., and lead to a surge in cases and hospitalizations later this fall and winter, Chin-Hong said.
Swartzberg said BQ.1.1 was likely to come out on top. “It is perhaps the most immune evasive subvariant circulating,” he said. “This makes it the leading contender to overtake BA.5 in the next few weeks.”
Unvaccinated, elderly and immunocompromised individuals would likely have the worst outcome of the surge, Chin-Hong said.
“I don’t think hospitalizations and deaths will approach what we have seen in the last two winters, because the overall population is very immunologically experienced at this time,” he said. However, “Many people may become infected, or re-infected, and this could be disruptive to the community even though many of these will be mild clinically.”
Kellie Hwang is a San Francisco Chronicle staff writer. Email: kellie.hwang@sfchronicle.com Twitter: @KellieHwang