COVID-19 Data Dispatch

Tag: Omicron variant

  • National numbers, October 30

    National numbers, October 30

    BA.5 caused just under half of new COVID-19 cases nationwide in the last week, according to CDC estimates. But we have yet to see a new subvariant clearly take over.

    In the past week (October 20 through 26), the U.S. reported about 270,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 38,000 new cases each day
    • 81 total new cases for every 100,000 Americans
    • 2% more new cases than last week (October 13-19)

    In the past week, the U.S. also reported about 23,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,200 new admissions each day
    • 6.9 total admissions for every 100,000 Americans
    • 1% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,600 new COVID-19 deaths (380 per day)
    • 27% of new cases are caused by Omicron BQ.1 and BQ.1.1; 8% by BF.7;  3% by BA.2.75 and BA.2.75.2 (as of October 29)
    • An average of 400,000 vaccinations per day

    The national COVID-19 picture continues to be somewhat murky, thanks in part to poor-quality data. Both nationwide cases and new hospital admissions trended slightly upward in the last week (by 2% and 1%, respectively); this could reflect the beginnings of fall surges in some places, but it’s hard to say for sure.

    Wastewater data from Biobot continue to suggest the Northeast is seeing more COVID-19 transmission than other parts of the country, though this region reported a decrease in viral levels over the last two weeks. Other regions are reporting plateaus in transmission, according to Biobot.

    One reason we’re not seeing a definitive national surge yet could be that the newest iterations of Omicron have yet to fully dominate the country. BA.5 caused just under half of new COVID-19 cases nationwide last week, according to the CDC’s latest estimates, but the remaining half of cases were driven by a variety of new lineages: BQ.1, BQ.1.1, BA.4.6, and BF.7 all contributed over 5%.

    When one of these subvariants (likely BQ.1.1) outcompetes the others, we will likely see a clearer picture of its impact on transmission. Also worth noting: XBB, the subvariant spreading quickly in Singapore and other Asian countries, has been identified in the U.S.—though its prevalence is too minimal to show up in the CDC’s estimates, at this point.

    New York is a hotspot again: the state has a higher prevalence of BQ.1 and BQ.1.1 than other parts of the country, and some experts are concerned about rising COVID-19 hospitalizations here. In New York City, official cases have remained relatively stable for the last few weeks even as hospitalizations are going up, suggesting how continued low testing may make cases even less useful as a metric to watch.

    This isn’t the only region seeing the start of a fall surge, though. The Twin Cities area in Minnesota reported a major spike in wastewater this week, with viral prevalence the highest it’s been since the original Omicron surge. Some counties in the South and West coast are showing similar warnings, according to Biobot’s dashboard.

    And COVID-19 isn’t the only respiratory virus wreaking havoc right now, as we’ll discuss more in this issue. Places like NYC are seeing rising hospitalizations from the flu and RSV, placing additional strain on an already-overburdened healthcare system. Even if the coronavirus doesn’t have a drastic surge this winter, we could still see a lot of respiratory infections.

    more national numbers
  • 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

  • The U.S. needs to step up its booster shot campaign

    The U.S. needs to step up its booster shot campaign

    About half of U.S. adults haven’t heard much about the updated COVID-19 booster shots, according to a recent survey done by the Kaiser Family Foundation.

    New, Omicron-specific booster shots are publicly available for all American adults who’ve been previously vaccinated. This is the first time our shots actually match the dominant coronavirus variant (BA.5), and possibly the last time that the shots will be covered for free by the federal government.

    So… why does it feel like almost nobody knows about them? Since the CDC and FDA authorized these shots, I’ve had multiple conversations with friends and acquaintances who had no idea they were eligible for a new booster. My own booster happened in a small, cramped room of a public hospital—a far cry from the mass vaccination sites that New York City has offered in past campaigns.

    This week, the Kaiser Family Foundation (KFF) provided some data to back up such anecdotal evidence. According to the September iteration of KFF’s Vaccine Monitor survey, about half of U.S. adults have heard only “a little” or “nothing at all” about the new boosters. That includes more than half of adults who have been previously vaccinated.

    Moreover, the KFF survey found that 40% of previously vaccinated adults (who received the full primary series) are “not sure” if the updated booster is recommended for them. Another 11% said the new booster is not recommended for them—which is not true! The CDC has recommended these boosters for everyone who previously got vaccinated.

    Booster eligibility knowledge is even lower in certain demographics, KFF found. That includes: 55% of previously vaccinated Black adults and 57% of Hispanic adults don’t know that they’re eligible for boosters. Same thing for 57% of vaccinated adults with less than a college education and 58% of those living in rural areas.

    As of September 28, only 7.6 million Americans have received an updated booster shot, the CDC reports.

    Overall, the CDC reports that about 7.6 million Americans have received an updated booster shot as of September 28, including 4.9 million who received a Pfizer shot and 2.7 million who received a Moderna shot. This represents less than 4% of all fully vaccinated adults who are eligible for the new boosters. And we don’t have demographic data yet, but I expect the patterns will fall among similar lines to what KFF’s survey found.

    “Clear and consistent messaging accompanied by strategies to deliver boosters is needed to narrow these gaps,” said public health expert Anne Sosin, sharing the KFF findings on Twitter. We need big, public campaigns for the new boosters in line with what we got for the original vaccines in 2021—or else the new shots won’t be very helpful in an inevitable fall/winter surge.

    More vaccine data

  • National numbers, October 2

    National numbers, October 2

    Coronavirus levels in Boston, Mass. wastewater spiked intensely last week. Chart via MWRA/Biobot.

    In the past week (September 24 through 30), the U.S. reported about 330,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 47,000 new cases each day
    • 100 total new cases for every 100,000 Americans
    • 13% fewer new cases than last week (September 17-23)

    In the past week, the U.S. also reported about 26,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,800 new admissions each day
    • 8.0 total admissions for every 100,000 Americans
    • 6% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,400 new COVID-19 deaths (350 per day)
    • 81% of new cases are caused by Omicron BA.5; 13% by BA.4.6; 3% by BF.7;  1% by BA.2.75 (as of October 1)
    • An average of 400,000 vaccinations per day

    Official COVID-19 numbers continue to drop nationwide, with case counts down 13% and new hospital admissions down 6% this week compared to the prior week. Still, signals from wastewater suggest this is no time to let our guard down, especially if you live in the Northeast.

    Biobot’s wastewater surveillance dashboard is back this week (after a one-week hiatus). Nationally, this surveillance suggests coronavirus transmission is at a high plateau close to what we saw during early fall of last year, before Omicron hit. The Northeast is driving that recent trend, with an overall coronavirus concentration twice as high as the concentrations reported in other regions.

    This region remains a hotspot for Omicron BF.7, the subvariant of BA.5 that could be the U.S.’s next dominant lineage. Nationwide, BF.7 is slowly competing with BA.5: it’s grown from causing about 1% of new cases to 3.4% over the last month, according to CDC estimates. BA.4.6 also continues to grow, while BA.2.75 has remained relatively constant.

    Within the Northeast region, Boston stands out: the city’s wastewater surveillance program (run by Biobot) reported a major spike last week. And by major spike, I mean an increase of more than 100% week-over-week, according to the city’s public health department. “This spike in our wastewater concentration is of great concern and another reminder that the pandemic is far from over,” said Dr. Bisola Ojikutu, Boston’s public health commissioner, in a press release.

    Wastewater spikes typically precede case spikes by a couple of weeks, though we’ll have to see whether the significant drop in PCR testing in recent months changes this pattern. Either way, this is a good time to get a booster shot (more on boosters below), stock up on masks and rapid tests, and start planning safety measures for the holidays.

    Boston is running vaccine clinics in response to this potential new surge, and the city public health department “recommends” masking indoors. But any further mitigations are likely out of the question, even though they could have a huge impact.

    more national numbers
  • BF.7, yet another Omicron subvariant of concern

    BF.7, yet another Omicron subvariant of concern

    BF.7 (shown here in light green) is among the Omicron subvariants starting to push out BA.5. Chart via the CDC.

    Omicron BF.7, an offshoot of BA.5, is the latest subvariant to raise red flags among experts tracking COVID-19 in the U.S.

    This week, BF.7 passed BA.2.75, another worrying lineage, in the CDC’s prevalence estimates: the CDC found that it caused about 2.3% of new cases nationwide in the week ending September 24. It’s most prevalent in the Northeast right now: in New England, it caused almost 4% of new cases last week, the CDC estimates.

    BF.7 has an additional spike protein mutation compared to BA.5, CDC spokesperson Jasmine Reed told CBS News last week. The agency is concerned that this “genetic change” could lead to Evusheld, an antibody drug used by immunocompromised people, becoming less effective. It could also contribute to a new wave of reinfections, as we’ve seen with other Omicron subvariants in the last few months.

    Here’s a quote from Dr. Stuart Ray, a data expert at John Hopkins’ Department of Medicine, in a Fortune article about BF.7:

    “The same growth advantage in multiple countries makes it reasonable to think that BF.7 is gaining a foothold,” and that it’s potentially more transmissible than parent BA.5, Ray said. Children of variants “don’t grow relative to their parent unless they have an advantage.”

    We have relatively little data on BF.7 so far, but it’s worth monitoring closely in the coming weeks.

    More on variants

  • National numbers, September 25

    National numbers, September 25

    Reported COVID-19 cases in New York City have started going up slightly in the last few days, according to the city health department.

    In the past week (September 17 through 23), the U.S. reported about 380,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 54,000 new cases each day
    • 116 total new cases for every 100,000 Americans
    • 11% fewer new cases than last week (September 10-16)

    In the past week, the U.S. also reported about 28,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 4,000 new admissions each day
    • 8.5 total admissions for every 100,000 Americans
    • 10% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,400 new COVID-19 deaths (350 per day)
    • 83% of new cases are caused by Omicron BA.5; 12% by BA.4.6; 2% by BF.7;  1% by BA.2.75 (as of September 24)
    • An average of 300,000 vaccinations per day

    Nationally, official COVID-19 case counts continue to decline: reported cases are down about 11% last week compared to the prior week, while new COVID-19 patients in hospitals are down 10%. But signals from wastewater and variants suggest a fall surge may be starting soon. 

    “Currently, most of the country is reporting moderate to high SARS-CoV-2 levels in wastewater,” CDC officials noted in this Friday’s COVID Data Tracker Weekly Review. For almost 20% of sites, these coronavirus levels are the highest seen since December 2021, the CDC reports. About half the wastewater sites in the CDC’s network are reporting an increase in coronavirus levels and half are reporting a decrease.

    Notably, many of the wastewater sites reporting increased coronavirus spread are in the Northeast, a region that’s also a hotspot for Omicron subvariants BA.2.75 and BF.7. BF.7, a new sublineage that evolved from BA.5, is particularly worth watching (more on that below). Overall, the U.S.’s variant composition is slowly shifting from BA.5 to these two subvariants, along with BA.4.6—which caused 12% of new cases nationwide in the week ending September 24.

    According to the latest Community Profile Report, states reporting significant increases in cases from week to week include Nevada, California, New Hampshire, Kentucky, Massachusetts, New Jersey, New York, and Oregon. In New York City—often a bellwether for new surges—cases have started to tick up slightly, according to the city’s health department, after a long (and slow) decline from July’s summer peak.

    Meanwhile, other common respiratory viruses might make a comeback this fall, report Dr. Katelyn Jetelina and Dr. Caitlin Rivers in a joint issue of their newsletters. Data so far on the flu, RSV, rhinovirus, and other viruses we consider part of a normal fall season suggest that children in the U.S. might have a particularly virus-heavy fall and winter—putting more pressure on the healthcare system.

    One of the best ways to protect yourself from COVID-19 this fall is by receiving one of the new, Omicron-specific booster shots. According to the CDC, about 4.4 million Americans have received one so far, as of September 21. The new shots have brought our vaccine administration counts to over 300,000 new doses given a day, but that still pales in comparison to the millions administered daily during the spring 2021 campaign.

    I received my own booster on Friday at a NYC Health + Hospitals site. Unlike my primary series doses, for which my girlfriend and I had to wait in long lines with hundreds of other New Yorkers, we got our new shots in a small, hard-to-find room tucked away in a small corner of a south Brooklyn hospital campus. This vaccination campaign seems to be almost an afterthought when it deserves primetime attention.

    more national numbers
  • National numbers, September 18

    National numbers, September 18

    Wastewater trends in the past couple of weeks are looking a bit messy, with a potential new surge in the Northeast and plateaus in other regions. Chart via Biobot, retrieved on September 18.

    In the past week (September 10 through 16), the U.S. reported about 420,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 60,000 new cases each day
    • 128 total new cases for every 100,000 Americans
    • 16% fewer new cases than last week (September 3-9)

    In the past week, the U.S. also reported about 31,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 4,400 new admissions each day
    • 9.3 total admissions for every 100,000 Americans
    • 6% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,500 new COVID-19 deaths (0.8 for every 100,000 people)
    • 85% of new cases are caused by Omicron BA.5; 10% by BA.4.6; 1% by BA.2.75 (as of September 17)
    • An average of 25,000 vaccinations per day (per Bloomberg)

    Officially-reported COVID-19 cases are still on the decline nationwide this week, as are newly hospitalized patients (a more reliable metric). About 4,400 people with COVID-19 were admitted to hospitals across the country, compared to over 6,000 a day in late July.

    These declines may be short-lived, as reopened schools and increased indoor gatherings contribute to new outbreaks this fall. Last week, I warned that Biobot’s wastewater data showed a slight uptick in coronavirus levels across the country; this week’s update shows a continued increase in the Northeast while other regions are in plateaus.

    Will the Northeast be the first region to experience a new surge again? It seems feasible, based on data from both Biobot and the CDC—though this region also has better wastewater surveillance coverage than other parts of the country, ABC News reporter Arielle Mitropoulos points out. Boston, one long-running wastewater surveillance location, is reporting high coronavirus concentrations at a level not observed since earlier in the summer.

    Nationwide, BA.5 continues to be the dominant variant, causing about 85% of new cases in the week ending September 17 per CDC estimates. But it’s facing competition from newer Omicron subvariants, including BA.4.6 (10% of new cases this week), BA.2.75 (1.3% of cases), and BF.7 (1.7% of cases). As of this week, the CDC is now reporting BA.2.75 and BF.7 separately rather than combining them with other lineages.

    BA.2.75, also called Centaurus, is a subvariant from BA.2 that evolved some additional mutations. BF.7 actually evolved from BA.5; its longer name is BA.5.2.1.X. There hasn’t been much reporting yet on BF.7, but it appears to be present in the Northeast—particularly in New England—at higher levels than in other regions. (Possibly another driver of a new surge in this area.)

    Overall, while COVID-19 spread in the U.S. is occurring less right now than it did earlier in the summer, the risk of encountering this virus is still pretty high across the country. According to the CDC’s “Community Transmission Level” guidance (pre-February), more than 90% of U.S. counties should require masks indoors.

    Instead, we have no masking requirements, increasingly-limited testing, and a booster shot campaign that many Americans do not even know is happening. Between 300 and 400 Americans still die of COVID-19 every day—a number that should be unacceptable—and I fear this number will only go up as we head into winter.

    more national numbers
  • BA.2.75 (Centaurus) is still a subvariant worth watching

    BA.2.75 (Centaurus) is still a subvariant worth watching

    The CDC’s variant prevalence estimates suggest that BA.2.75 has started to spread more in the U.S. in recent weeks.

    BA.2.75, a newer subvariant that evolved from BA.2, has been driving increased coronavirus transmission in some other countries recently. You might also see it referred to as “Centaurus” on social media. This lineage has yet to be identified in large numbers in the U.S., but I was inspired by a recent reader question to share what we’ve learned about it since my previous post in July.

    Scientists are concerned about BA.2.75 because it has several new mutations that are distinct from BA.2, most of those in the spike protein (where the virus binds to human cells). And some preliminary research, including recent studies in the Lancet Infectious Diseases and in the New England Journal of Medicine, have found that BA.2.75 is less susceptible to neutralizing antibodies from prior infections or treatments than past variants.

    This could mean people who previously caught BA.2 or other versions of Omicron could be susceptible to BA.2.75, reports Hannah Flynn in Medical News Today. Of course, more research and data are needed on the new variant. But BA.2.75 has been driving new surges in India, Nepal, and other countries—another signal that it’s worth watching.

    As I noted in today’s National Numbers post, the CDC is not yet reporting BA.2.75 prevalence estimates separately from other versions of BA.2. But it has reported an increase in BA.2 overall in recent weeks, from 0.6% of new cases in the week ending August 27 to 1% in the week ending September 10. This is probably BA.2.75, given that older versions of BA.2 haven’t been competitive in the U.S. for a few months.

    Helix, a COVID-19 testing company that works with the CDC and other agencies on variant surveillance, is tracking BA.2.75 separately from BA.2 on its dashboard. According to Helix’s data, original BA.2 has stayed at very low prevalence in recent weeks while BA.2.75 has risen to 1% of cases sequenced.

    It’s currently unclear—as it was in July—to what extent BA.2.75 might be able to compete with BA.5 or BA.4.6, which are the main subvariants of concern spreading across the U.S. right now. But if BA.2.75 does become dominant, it will be helpful that the newly-authorized booster shots include genetic material from the original, Wuhan variant, not just BA.4 and BA.5.

    More variant reporting