COVID-19 Data Dispatch

Tag: BQ.1 and BQ.1.1

  • National numbers, October 23

    National numbers, October 23

    New Omicron subvariants are spreading across the U.S. BQ.1 (medium green) and BQ.1.1 (dark green) are particularly prevalent in the Northeast. Chart via the CDC.

    In the past week (October 13 through 19), the U.S. reported about 260,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 37,000 new cases each day
    • 79 total new cases for every 100,000 Americans
    • 2% fewer new cases than last week (October 6-12)

    In the past week, the U.S. also reported about 22,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,200 new admissions each day
    • 6.7 total admissions for every 100,000 Americans
    • 4% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,600 new COVID-19 deaths (390 per day)
    • 11% of new cases are caused by Omicron BA.4.6; 17% by BQ.1 and BQ.1.1; 7% by BF.7;  3% by BA.2.75 and BA.2.75.2 (as of October 22)
    • An average of 400,000 vaccinations per day (CDC link)

    Official COVID-19 case numbers continue to drop nationwide, according to the CDC, but I remain concerned that a fall surge is coming soon—if it isn’t already here.

    As the CDC transitioned this week from daily to weekly case reporting (more on that later in the issue), the agency’s “COVID Data Tracker Weekly Review” report, which I use to write these posts, is now using three-week rolling averages for its trends instead of one-week averages. The three-week average suggests reported cases are down 30% in the last month. But the actual case numbers report a dip of just 1% from last week to this week, suggesting a plateau in cases.

    Data from Biobot’s dashboard similarly suggest a plateau in nationwide transmission trends, with the Northeast reporting more viral transmission than other regions. The wastewater data suggest that, nationwide, coronavirus transmission is on a similar level to what it was in early fall last year, before Omicron arrived. But the case numbers are now much lower thanks to limited testing access.

    Consider this: recent estimates from the Institute for Health Metrics and Evaluation suggest only 4% to 5% of actual coronavirus infections make it into the public health system now. If this is correct, actual infection numbers in the U.S. are 20 times higher than our actual count, amounting to 740,000 true cases a day.

    The Northeast remains a hotspot, as the first region to note signs of a new surge. Some New England cities and counties—including Boston—are seeing spikes or high plateaus in their coronavirus levels in wastewater, Biobot reports. States in this region, especially New York and New Jersey, report more BQ.1 and BQ.1.1 than other parts of the country; if new variants aren’t contributing yet to a surge, they will be soon.

    Overall, BQ.1 and BQ.1.1 are now causing about one in six new cases in the U.S. and are anticipated to become dominant subvariants within a few weeks. This could have implications for treatments such as Evusheld, a monoclonal antibody drug for immunocompromised people. While the bivalent/Omicron-specific booster shots should still work against BQ.1 and BQ.1.1, uptake of these vaccines remains very low. (See last week’s post for more subvariant details.)

    more national numbers

  • COVID source callout: Do not follow this Twitter sensationalist

    As discussed earlier in this issue, the CDC’s variant prevalence estimates now include BQ.1 and BQ1.1—two newer sublineages that have evolved from BA.5. The agency started breaking out these subvariants in Friday’s variant data update; their presence was previously included in the overall BA.5 category.

    Throughout 2022, as Omicron has continually mutated and produced further lineages, the CDC’s policy has generally been to break out subvariants when they cause at least 1% of all cases in the U.S. Sometimes, though, it can be tricky to distinguish between subvariants, leading to bigger updates like the one we saw this Friday (with BQ.1 and BQ.1.1 both causing more than 5% of cases nationwide).

    Again, the CDC’s behavior here is pretty reasonable, in my opinion—especially when one considers that more limited PCR testing these days is making it harder to track new variants. But you might have gotten a different impression if you follow a certain sensationalist personality on Twitter, Eric Feigl-Ding.

    I’m not linking to Feigl-Ding’s Tweet, because I don’t want to give him attention. His tweet, which started with “Scoop—MOTHER OF GOD,” painted the CDC’s fairly normal data update as some kind of conspiracy by the agency to prevent Americans from learning the truth about circulating variants.

    For more details on why Feigl-Ding’s Tweet here was dangerous, please see this helpful thread by actual genomics expert Duncan MacCannell:

    It’s also worth noting that Feigl-Ding has done this kind of thing before, to the point where he has a reputation among legitimate experts for sensationalizing COVID-19 news and misleading his audience. (See this profile for more details.) I have personally had him blocked on Twitter for a while. Basically, do not follow this guy, and be skeptical if you see any of his posts on your timeline.

    more source spotlights
  • The Omicron subvariants start coming and they don’t stop coming

    The Omicron subvariants start coming and they don’t stop coming

    A veritable alphabet soup of subvariants. Chart from the CDC, data as of October 15.

    When the CDC updated its variant prevalence estimates this week, the agency added new versions of Omicron to the dashboard. In the U.S., COVID-19 cases are now driven by: BA.5, BA.4.6, BQ.1, BQ.1.1, BF.7, BA.2.75, and BA.2.75.2. And possibly more subvariants that we aren’t tracking yet.

    As evolutionary biology expert T. Ryan Gregory pointed out on Twitter recently, Omicron’s evolution is “off the chart.” 

    Or, to parody Smash Mouth: the Omicron variants start coming and they don’t stop coming and they don’t stop coming and they don’t stop coming…

    Let’s go over the veritable alphabet soup of variants we’re dealing with right now, as well as one newer variant identified in east Asia that experts are closely watching.

    BA.5, BA.4, BA.4.6

    BA.5 is currently the dominant Omicron lineage in the U.S., causing about two-thirds of new COVID-19 cases in the week ending October 15. Along with BA.4, BA.5 split off from the original Omicron lineage and was first identified by South African scientists over the summer.

    As these two subvariants spread around the world, it quickly became clear that they could spread faster than other versions of Omicron and reinfect people who’d previously gotten sick with those prior lineages. For more details, see this post from June. BA.5 later pulled out from BA.4 as the most competitive lineage.

    BA.4.6 evolved out of BA.4. It appears to have a small advantage over BA.5, but can’t really compete with the newer subvariants we’re seeing now; according to the CDC’s estimates, it’s been causing around 10% to 12% of new cases nationwide for the last few weeks (without much growth).

    BQ.1 and BQ.1.1

    BQ.1 and its descendant BQ.1.1 are the two newest subvariants to show up in the CDC’s prevalence estimates, both causing about 5.7% of new cases nationwide in the last week. They actually evolved out of BA.5: BQ.1 is shorthand for a much longer, more unwieldy variant name that nobody wants to type out on Twitter.

    In the U.S., BQ.1 and BQ.1.1 are starting to outcompete their parent lineage, BA.5. They’ve grown from causing less than 1% of new cases to over 10% of new cases in the last month. These subvariants are also now outcompeting other strains in the U.K. and other European countries.

    As CBS News’s Alexander Tin explains, health experts are concerned that COVID-19 treatments like monoclonal antibodies might work less well against BQ.1 and BQ.1.1. We don’t have clear data on this yet, but pharmaceutical companies will test out the newer variants in the weeks to come. The Omicron bivalent boosters, at least, are expected to continue working against this lineage.

    BF.7

    BF.7 is another offshoot of BA.5 (again, this is shorthand for a longer name). I dedicated a post to it in late September, and the subvariant’s position hasn’t changed significantly since then: it seems to be a bit more transmissible than BA.5, but not so much that it is quickly outcompeting the parent lineage. BF.7 caused about 5% of new cases nationwide in the last week.

    Similarly to BQ.1 and BQ.1.1, there are some concerns that COVID-19 treatments will be less effective against BF.7 than other versions of Omicron based on the subvariant’s spike protein mutations, but we do not have clinical data at this point.

    BA.2.75 and BA.2.75.2

    BA.2.75, as you might guess from the notation, evolved out of BA.2—the same original Omicron lineage that produced BA.2.12.1 and drove surges in places like New York City over the summer. It has also remained present at fairly low levels across the U.S. recently, causing just 1.3% of new cases in the last week, according to the CDC’s estimates.

    But BA.2.75 now has its own offshoot, called BA.2.75.2, that appears to be a bit more competitive. The CDC recently started splitting BA.2.75.2 out of its parent lineage in its prevalence estimates, showing that it’s growing a bit faster (from 0.4% to 1.4% in the last month). Of course, this growth rate pales in comparison to what we’re seeing from the BA.5 sublineages described above.

    XBB

    XBB is the latest international subvariant of concern, identified this week in several east Asian countries. It has spread particularly quickly in Singapore, as described in this article by David Axe at the Daily Beast.

    Like BA.2.75, XBB descended from Omicron BA.2—though it’s gone through more rounds of spike protein mutation; this is why experts are calling it XBB, rather than a long string attached to BA.2. Data so far indicate its growth advantage over BA.5 is similar to what we’re seeing from BQ.1.1. XBB has also raised concerns about treatment and vaccine efficacy, since the bivalent boosters were developed from BA.4 and BA.5. 

    The CDC and other health agencies have yet to identify XBB in the U.S.; experts are closely watching how this new subvariant might be able to compete with our current variations on BA.5.

    Overall takeaways

    Overall, both in the U.S. and around the world, we’re seeing a lot of competition between these subvariants. All of them have small growth advantages over BA.5—which is currently dominant in the U.S.—but none are so different that they’re completely pulling ahead.

    As I wrote last weekend, many experts are anticipating a surge this fall and winter, driven by both new subvariants and less-cautious beavior. We likely won’t see a huge spike at the level of last winter’s massive Omicron surge, but this season will still have plenty of infections (and reinfections).

    We will need more data on how all these newer variants respond to vaccines and treatments, especially the antiviral Paxlovid. But it’s at least promising that many of the circulating variants right now evolved from BA.5, against which our bivalent boosters were specifically designed. It’s a great time to get that booster!

    More variant data