COVID-19 Data Dispatch

Category: Variants

  • 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
  • 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

  • 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 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

  • Sources and updates, September 4

    Sources and updates, September 4

    Omicron BA.4.6, a newer version of BA.4, is currently more prevalent in the Midwest than other regions of the country. Chart via the CDC, retrieved September 4.
    • Slow rise of BA.4.6 is worth watching: As I mentioned in today’s National Numbers post, a newer subvariant labeled BA.4.6 is gaining ground over other versions of Omicron in the U.S. BA.4.6 evolved from BA.4, and has an additional mutation in the virus’ spike protein that enables it to bypass protection from prior infections. It’s unclear whether BA.4.6 will be able to fully outcompete BA.5, which is currently causing the vast majority of U.S. COVID-19 cases—these two strains are similar enough that the competition may go slowly. So far, the subvariant has been more prevalent in the Midwest than other regions of the country, according to CDC data. Also worth watching: BA.2.75, a subvariant that is dominating some European countries but hasn’t shown up significantly in the U.S. yet.
    • Up to 4 million people may be out of work due to Long COVID: Last week, policy research organization the Brookings Institute published a new report discussing the massive impacts Long COVID is having on America’s labor force. The report utilizes recent data from the Household Pulse Survey (released in June) estimating Long COVID prevalence, in conjunction with research on how many long-haulers might be out of work due to their condition. The results: between two and four million Americans potentially lost their jobs (or are working significantly less) due to Long COVID, costing at least $170 billion a year in lost wages. Even the low ends of these estimates are staggering.
    • U.S. life expectancy declined again in 2021: Americans born in 2021 may expect to live for 76 years on average, according to the CDC’s National Vital Statistics System. This is the lowest life expectancy has been since 1996. CDC researchers attribute the sharp decline in the last two years to the pandemic and drug overdose deaths. Disparities in life expectancy have also increased: Native Americans born in 2021 may expect to live only 65 years on average and Black Americans may expect to live 71 years, compared to 76 years for white Americans.
    • Biobot expands wastewater surveillance for opioid tracking: In the last couple of months, we’ve seen wastewater used to track monkeypox and polio, in addition to COVID-19—suggesting the technology’s capacity for broader public health surveillance. This week, leading wastewater company Biobot announced a new initiative to track opioid use and other high-risk substance use through a similar platform to its current COVID-19 efforts. Tracking the opioid crisis was actually the original focus for Biobot’s founders pre-pandemic, so it’s notable to see the company expanding in this direction now.
    • New technical report on monkeypox outbreak: Speaking of monkeypox, the CDC recently released a detailed report on how the disease has spread through the U.S. and other countries. It’s a new reporting format for the CDC, with the agency releasing data more rapidly than it might have in a scientific study—possibly emulating the U.K. Health Security Agency’s Technical Briefings. Notably, the CDC Center for Forecasting and Outbreak Analytics, the agency’s new modeling center, was a key contributor to the report. Former CFA leader Caitlin Rivers shared key findings from the report here. (And for more on CFA, see this story I wrote for FiveThirtyEight in June.)

    All featured sources
  • BA.2.75 is the latest Omicron subvariant of concern

    BA.2.75 is the latest Omicron subvariant of concern

    BA.2.75 has further mutations which could allow the variant to bypass past immunity. Figure via scientist Ulrich Elling on Twitter.

    As if BA.4 and BA.5 aren’t already enough to worry about: some COVID-19 experts are sounding the alarm about BA.2.75, a new version of Omicron that evolved out of BA.2.

    This subvariant was first identified in India in late May, and has now been reported in the U.K., Germany, and several other countries, according to the World Health Organization. Scientists are concerned because it has new spike protein mutations that could heighten its ability to bypass immunity from past infections or vaccinations—including, potentially, from BA.4 or BA.5.

    At least three BA.2.75 cases have been reported in the U.S. so far, according to a Friday press release from the surveillance company Helix. Two of these cases were on the West Coast, in Washington and California. These cases are currently lumped in with other versions of BA.2 on the CDC dashboard.

    The information on BA.2.75 is fairly preliminary at this point; the WHO is monitoring it as an additional lineage of Omicron, not a separate variant of concern, and watching for new data. It’s unclear how competitive it might be with BA.5, now dominant in the U.S., but is worth keeping an eye on. As Dr. Katelyn Jetelina points out in a recent issue of Your Local Epidemiologist, the spread of BA.2.75 could further complicate fall booster shot plans. 

    More variant reporting

  • National numbers, July 3

    National numbers, July 3

    New hospital admissions for COVID-19 increased 12% last week over the week prior, a signal of the continued surge. Chart via the CDC.

    In the past week (June 25 through July 1), the U.S. reported about 800,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 110,000 new cases each day
    • 234 total new cases for every 100,000 Americans
    • 11% more new cases than last week (June 18-24)

    In the past week, the U.S. also reported about 35,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 5,000 new admissions each day
    • 10.6 total admissions for every 100,000 Americans
    • 12% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,200 new COVID-19 deaths (0.7 for every 100,000 people)
    • 48% of new cases are Omicron BA.2.12.1-caused; 52% BA.4/BA.5-caused (as of June 25)
    • An average of 150,000 vaccinations per day (per Bloomberg)

    BA.4 and BA.5 are now the dominant coronavirus lineages in the U.S., and they’re reviving our recent surge: from the plateau of recent weeks, national COVID-19 cases are clearly going up again. Reported cases rose 11% last week from the week prior. And, as always, this number is a significant undercount of true infections.

    New hospital admissions also went up last week: about 5,000 Americans were admitted to hospitals with COVID-19 each day, up 12% from the week prior. While the vast majority of COVID-19 cases may now be mild—thanks to vaccinations, prior infections, and treatments—this is a reminder that severe symptoms are still very possible.

    Wastewater data from Biobot indicate a continued plateau in transmission at the national level. At the regional level, COVID-19 levels are trending down in the West and South, but ticking up again in the Northeast, likely as BA.4 and BA.5 take over from BA.2.12.1 in these areas.

    In my FAQ post last month ago, I wrote that scientists weren’t yet sure whether BA.4 and BA.5 would be able to outcompete BA.2.12.1, the offshoot of BA.2 first identified in New York. Now, it seems clear that BA.4 and BA.5 are capable of dominating: these two subvariants caused over half of new cases nationwide in the week ending June 25, as well as in most regions.

    Even places like New York City, which saw a major BA.2/BA.2.12.1 wave, is now reporting another uptick in cases, according to data from the local health department. The city’s test positivity rate went over 10% on Thursday for the first time since January, a signal of the underreporting in recent weeks as PCR testing becomes less popular. And yet, city leadership is not interested in implementing any new safety precautions.

    Remember, the problem with these subvariants is that they’re built for reinfection. Even if you had Omicron BA.1 in the winter, or even had BA.2 this spring, you could easily get BA.4 or BA.5. These infections are, at best, a week-long inconvenience, and at worst, could turn into Long COVID.

    The holiday tomorrow will interrupt COVID-19 reporting, as holidays always do. Stay safe this weekend, and don’t be fooled if you see a brief downturn in case numbers.

    more national numbers
  • As Omicron keeps mutating, variant surveillance remains important

    As Omicron keeps mutating, variant surveillance remains important

    BA.4 and BA.5 caused more than 20% of new COVID-19 cases nationwide in the week ending June 11, according to CDC estimates.

    This week, I had a new story published at TIME’s online news site, explaining what Omicron BA.4 and BA.5 could mean for COVID-19 trends in the U.S.

    The story makes similar points to my FAQ post on these subvariants from earlier in June: basically, BA.4 and BA.5 have evolved to get around antibodies from a prior coronavirus infection or vaccination, and the U.S. is likely to see a lot of reinfections from these subvariants—even among people who already had BA.1 or BA.2 earlier this year. BA.2.12.1 has mutated in a similar way, leading experts to suspect that one of these subvariants (or all three) will dominate the next phase of the pandemic. 

    When I talked to variant experts for my TIME story, I asked them for their thoughts on surveillance. “Is it getting harder to identify and track new linages like BA.4 and BA.5 as fewer people use PCR tests and more use at-home tests?” I asked. “What improvements or shifts would you like to see in surveillance?”

    All three experts I spoke to had different perspectives, which I found interesting—and worth sharing in the COVID-19 Data Dispatch, since I wasn’t able to include this (somewhat wonkier) information in my TIME story.

    Here’s what they said:

    Marc Johnson, a microbiology and immunology professor at the University of Missouri who leads the state’s wastewater surveillance program, thinks that expanding wastewater monitoring is the way to go (though he admitted his bias, as someone who works in this area). “Sewershed monitoring is a really good way to track variants going forward,” he said. “It gives you a comprehensive view without costing you hundreds of thousands of dollars… or without having to sequence a thousand people.”

    Shishi Luo, associate director of bioinformatics and infectious diseases at Helix (a genomics and viral surveillance company), is thinking about how to ensure her company consistently receives enough PCR test samples to get useful data from sequencing. At the moment, pharmacies and community testing sites are still providing enough samples that Helix has sufficient information to track variants, she said. But, anticipating that those numbers may dwindle, Helix is connecting with urgent care clinics and hospitals that do diagnostic testing. “I think those places will continue to collect samples and perform qPCR tests,” she said.

    Paul Bieniasz, a professor at Rockefeller University who studies viral evolution, thinks that the current levels of surveillance are sufficient—at least, when it comes to policymaking and updating vaccines. “I would like to keep surveillance at a level such that such that we can have a pretty accurate picture about what’s going on,” he said. But he wants to prioritize “the really important things”: namely, understanding changes to vaccine effectiveness, which treatments to use, and identifying a new “major antigenic shift” like the one that produced Omicron as soon as it occurs.

    “But it can always be better,” he said. “The more intense the surveillance, the more sensitive it is, and the earlier you detect things that might be of concern in the future.”

    More variant reporting