COVID-19 Data Dispatch

Tag: SARS-CoV-2 variants

  • HV.1, JN.1: Variants to watch this fall and how we’re tracking them

    HV.1, JN.1: Variants to watch this fall and how we’re tracking them

    HV.1, a relative of the XBB.1.5 variant family, is the most prevalent variant in the U.S. right now, according to CDC estimates.

    As winter approaches, pretty much every public health expert I follow is anticipating a COVID-19 surge. Experts anticipate that indoor gatherings and travel for the holiday season—with fewer COVID-19 precautions than we had earlier in the pandemic—will lead to more disease spread, just as these behaviors have historically contributed to more spread of flu and other common pathogens this time of year.

    While it seems a surge is likely, the size and severity of that surge may depend in part on SARS-CoV-2 variants. Variants can evolve to more efficiently reinfect people who got COVID-19 recently or to evade our vaccines. These explosive variants can add fuel to the fire when people are already spending a lot of time indoors together with relatively few precautions, as we saw with the original Omicron in winter 2021-22. 

    As a result, experts are closely watching a few current variants that might lead to faster COVID-19 spread this winter. Here’s a review of what’s circulating right now, what to watch for in the coming weeks, and how our public health system is tracking the variants.

    XBB.1.5 and relatives

    Omicron XBB emerged in late 2022 when two different versions of BA.2, one of the first Omicron lineages, merged together in an evolutionary process called recombination. While the original XBB didn’t really take off globally, it started to mutate as it spread in the U.S., leading to XBB.1.5 in early 2023. See my FAQ post from January for more details.

    XBB.1.5 has remained a dominant lineage in the U.S. and globally for much of this year. Scientists tracking variants have mostly identified new variants that descend from XBB.1.5, though you might not guess it from the naming schemes which often shorten names for convenience (for example, XBB.1.9.2.5 became EG.5). As a result, the FDA advised vaccine manufacturers to base their COVID-19 shots for this year on XBB.1.5.

    EG.5 and FL.5.1

    EG.5 and FL.5.1 are two of those XBB.1.5 relatives, descended from the XBB recombinant variant with enough evolutionary steps that virologists gave them these shorthand titles. These two variants are notable because they share a specific mutation, dubbed “FLip,” which helped the variants reinfect people more easily after prior infection or vaccination.

    The CDC’s variant surveillance estimates suggest that EG.5 and FL.5.1 have been prominent—but not really dominant—variants in the U.S. this fall. In the CDC’s most recent update, the agency estimates that these variants caused 22% and 12% of cases respectively during the two weeks ending October 28. They don’t appear different enough from other XBB.1.5 relatives to really break through and cause a surge.

    HV.1, descendant of EG.5

    HV.1 evolved from EG.5, making it another XBB.1.5 relative. It’s the most common variant in the U.S. right now, with the CDC’s latest update estimating that it caused about one in four COVID-19 cases during the last two weeks. Like the other variants discussed above, HV.1 has a slight evolutionary advantage over its relatives; but it’s not significantly different enough to cause a huge surge right now.

    BA.2.86

    BA.2.86 got some attention when it emerged in August. This variant, unlike the others that have circulated in 2023, is not related to XBB.1.5. Instead, it takes us back in the coronavirus’ evolution, as it evolved directly from BA.2—a version of Omicron that spread widely back in early 2022. Scientists expressed concern about some worrying mutations in BA.2.86 and wondered if our vaccines, matched to XBB.1.5, might not work well against it.

    Two months later, BA.2.86 hasn’t spread widely around the world as scientists worried that it might. It doesn’t appear to have a huge advantage over the XBB.1.5 descendants. While CDC surveillance has identified BA.2.86 across the U.S., it’s caused less than 1% of cases, according to the agency’s estimates.

    JN.1, descendant of BA.2.86

    But BA.2.86 could still indirectly cause some problems: this variant, like all the others, has been mutating. In the last couple of weeks, scientists have started to closely watch one BA.2.86 descendant called JN.1. JN.1 has picked up mutations that make it better at evading immunity from past infections or vaccinations, leading, of course, to faster spread.

    Eric Topol describes the global rise of JN.1 in a recent Substack post:

    JN.1 has shown up in many countries now, besides France and the UK, including the US, Iceland, Portugal, Belgium, Israel, Spain, Netherlands, Canada Germany, and Singapore. Other derivatives of BA.2.86 such as JN.2 and JN.3 are also being identified in multiple countries.

    We won’t know for a few weeks as to whether JN.1 will be linked with a significant rise in COVID or how well our immune response from prior vaccinations, infection(s) and the XBB.1.5 new booster will keep us protected.

    So, while BA.2.86 itself may be more benign than expected, JN.1 and its relatives are worth watching. Sequence data shared in the global repository GISAID suggest that this variant is spreading quickly globally, and may be contributing to increased spread in France in particular.

    How we’re tracking variants

    As I described in my post about BA.2.86, the U.S. has a few ways of tracking variants. The CDC recently highlighted four key surveillance systems in a report about monitoring BA.2.86, published in the agency’s Morbidity and Mortality Weekly Report:

    • The national SARS-CoV-2 genomic surveillance program, in which the CDC and commercial partners anonymously select and sequence samples from people who had positive COVID-19 PCR tests;
    • The Traveler-based Genomic Surveillance program, in which international travelers returning to U.S. airports can voluntarily get PCR-tested in groups;
    • The National Wastewater Surveillance System, in which some public health labs sequence sewage samples that are part of the CDC’s wastewater surveillance program (with about 400 sewersheds participating in sequencing);
    • Digital public health surveillance, using coronavirus sequences that are shared on public, open-source platforms like GISAID.

    CDC scientists use all four of these systems to keep track of variants circulating in the U.S. Sequencing wastewater samples is particularly important these days with fewer PCR tests available, I argued in a post last month.

    Variants don’t happen in isolation

    Sometimes, news reports about coronavirus variants cover the virus’ evolution as though it happens in isolation. Like the virus is just mutating in a vacuum, and would do so forever regardless of our human behavior.

    But this isn’t accurate. The coronavirus mutates because we keep spreading it, with each infection creating an opportunity for new mutations to arise. If our public institutions really took measures to stop COVID-19 from spreading, it would also be much harder for the virus to keep evolving and evading us.

    As variant expert J.P. Weiland pointed out on Twitter: “Timing is so important for impact.  If it [JN.1] becomes dominant before the holidays, the wave will be quite a lot bigger than dominance in Jan.”

    So, in case you need another motivator to keep up the COVID-19 precautions this holiday season: consider it doing your part to reduce viral evolution.

    More variant data

  • National numbers, September 17

    National numbers, September 17

    Wastewater data from Biobot suggest that coronavirus levels in the U.S. right now are similar to this time in 2021, during the Delta surge.

    During the most recent week of data available (August 27-September 2), the U.S. reported about 18,900 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 2,700 new admissions each day
    • 5.7 total admissions for every 100,000 Americans
    • 9% more new admissions than the prior week (August 20-26)

    Additionally, the U.S. reported:

    • 14.4% of tests in the CDC’s surveillance network came back positive
    • A 10% lower concentration of SARS-CoV-2 in wastewater than last week (as of September 6, per Biobot’s dashboard)
    • 25% of new cases are caused by Omicron EG.5, 24% by XBB.1.6, 14% by FL.1.5.1 (as of September 16)

    For the second week in a row, available data suggest that the current COVID-19 surge may be turning around, or at least heading for a plateau. But there’s still a lot of coronavirus going around—and this will likely remain true through the winter respiratory virus season.

    Wastewater data from both Biobot Analytics and WastewaterSCAN suggest that coronavirus spread may be ticking down, after two months of increases. Biobot’s national trends show a 10% decline in SARS-CoV-2 levels in wastewater last week, after a 1% decline the week prior. WastewaterSCAN’s trends show a slow decline in the last week, following a slow increase over the summer.

    This decline isn’t universal across the country: according to Biobot’s regional data, the South and Northeast are reporting clearer declines in coronavirus spread, while the West is in a plateau and the Midwest is in an increase. Sewersheds in Midwestern cities like South Bend, Indiana, Coralville, Iowa, and Lincoln, Nebraska have reported major increases in SARS-CoV-2 levels in the last couple of weeks, per WastewaterSCAN.

    Test positivity data from the CDC’s respiratory virus testing network also suggest that this summer’s COVID-19 surge may be leveling off. About 14.3% of COVID-19 tests in this CDC network came back positive in the week ending September 9, compared to 14.4% and 14.6% in the prior two weeks. (Note: this network includes a sample of testing labs across the country, but is less comprehensive than our testing data were before the federal health emergency’s end.)

    Walgreens’ COVID-19 dashboard, which reports test positivity data from the pharmacy chain, shows the positivity rate leveling off as well. The share of Walgreens tests coming back positive went down slightly from 45% in late August to 40% this past week. Walgreens’ dashboard, like the wastewater data, shows that more people are testing positive in the Midwest and West regions.

    Hospitalizations for COVID-19 continue to trend up, with the CDC reporting about 2,700 new patients a day during the week ending September 2. While this number may seem small compared to the overwhelmed hospitals we saw in past surges, it’s important to remember that CDC hospitalization data are both delayed and incomplete.

    Our most recent data are from two weeks ago, and reporting standards for hospitals are more lenient now than they have been earlier in the pandemic—though the CDC does still collect data directly from facilities across the country.

    Variant estimates, also from the CDC, suggest that EG.5 and XBB.1.6 are still the dominant lineages in the U.S. Each accounted for about one in four COVID-19 cases in the last two weeks, while other versions of XBB caused the rest. BA.2.86 hasn’t appeared in the CDC’s prevalence estimates yet, but scientists have detected it in several states, suggesting it could be spreading under the radar.

    Biobot’s wastewater data suggest that COVID-19 spread in the U.S. is similar now to this time in 2021, during the Delta surge. If 2023 continues to follow trends from the last two years, we could see transmission plateau in early fall, then rise again during the holiday season.  Any lull that we do experience may be a good time to stock up on masks, rapid tests, and other tools to protect yourself and your community.

    more national numbers
  • Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows us

    Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows us

    The CDC publishes data from about 400 wastewater testing sites that are sequencing their samples. Chart shows data from the week of August 17.

    This week, the health department in New York City, where I live, announced that they’d identified new variant BA.2.86 in the city’s wastewater. (For more details about BA.2.86, see last week’s Q&A post.)

    I covered the news for local outlet Gothamist/WNYC, and the story got me thinking about how important wastewater surveillance has become for tracking variants. With less clinical testing, sewage is now a crucial source for understanding how the coronavirus is mutating and what impacts those mutations have. But there are continued barriers to obtaining and interpreting wastewater data.

    Quoting from the story:

    The declaration of the end of the public health emergency in May made COVID-19 tests less available in health care settings, and sewage monitoring has since emerged as an important way to identify new variants.

    “As the wastewater testing has gotten better, the patient surveillance has decreased,” [said Marc Johnson, a virologist at the University of Missouri]. Several variants have been found in sewage before cases were confirmed, he said.

    That list now includes BA.2.86, in New York City as well as Ohio and other countries. The CDC publishes variant data from about 400 wastewater testing sites, including the city’s.

    But wastewater data from New York City is reported unevenly, with significant delays between when samples are collected and when data is published on dashboards run by the CDC and New York state.

    Wastewater surveillance has some distinct advantages, when it comes to variant monitoring:

    • It covers thousands of people—the entire population of a sewershed—with one sample. In big cities like NYC, one sample can include data from more than one million residents.
    • Through sewage samples, scientists can look for multiple variants at once, rather than compiling data over many PCR test results. They can also track population-level trends over time.
    • Unlike traditional case data, wastewater data don’t rely on how many people are getting tested or where. This lack of testing bias is important, as people typically use rapid tests—which are not reported to health systems—over PCR these days (rapid tests are easier to access, PCR sites have closed following the end of the federal public health emergency, etc.).

    But there are also some problems, as the NYC detection this week demonstrated:

    • Public health officials are still getting used to using and sharing wastewater data, as this is a relatively novel source with novel pipelines for transmitting data. While the CDC and other organizations are working to compile these data in a standardized way, it’s still a work in progress.
    • Discrepancies and delays can sometimes occur as a result. For example, in New York, the governor’s office put out a press release on Tuesday morning claiming that BA.2.86 hadn’t been detected in the state yet—then, just hours later, the city health department announced they’d found it. State health officials weren’t aware of the detection before the city made its public announcement, I learned for my news story.
    • Health officials are also still learning how to interpret and act on wastewater data. The NYC health department failed to answer my questions about in which sewershed or from which sampling date they found BA.2.86; it’s unclear if they’re using the detection to take any specific actions, besides simply warning the public that this variant is present.
    • As wastewater surveillance captures such broad samples, it’s difficult to tie new variant detections to clinical data, such as whether an infected person went to the hospital due to their symptoms. Officials can’t contact trace from these detections, making it hard to answer questions like whether BA.2.86 causes more severe symptoms.

    For more reading on this topic, I recommend my feature for Gothamist/WNYC and MuckRock last fall about NYC’s wastewater surveillance program, as well as other past posts at the COVID-19 Data Dispatch.

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    More about wastewater surveillance

  • Variant Q&A: Why scientists are concerned about BA.2.86, and which questions they’re still investigating

    Variant Q&A: Why scientists are concerned about BA.2.86, and which questions they’re still investigating

    The CDC’s Traveler Surveillance program, which offers free PCR tests to international travelers entering the U.S., was one of the first surveillance programs to pick up BA.2.86, pictured in dark red on the right-most bar of this chart.

    Last week, I introduced you to BA.2.86, a new Omicron variant that’s garnered attention among COVID-19 experts due to its significant mutations. We’ve learned a lot about BA.2.86 since last Sunday, though there are many unanswered questions to be answered as more research is conducted.

    Here’s my summary of what we know so far—and what scientists are still working to understand. Overall, this variant has some concerning properties, but more data are needed before we know what kind of impact it will have on disease transmission and severity.

    Where did BA.2.86 come from?

    BA.2.86 was first identified in Israel earlier this month. Scientists then picked it up in Denmark, the U.S., U.K., and several other countries across multiple continents (and in people without recent travel history), suggesting that it has been spreading under the radar for a while.

    However, as I’ve noted with past variants, the country where BA.2.86 was first identified is not necessarily the country where it developed. Many countries around the world are doing fairly limited COVID-19 testing and sequencing these days, so nations like Israel and the U.S. (which have more robust surveillance, relatively speaking) are likely to catch new variants.

    Why are scientists concerned about BA.2.86?

    BA.2.86 worries experts because it has a number of mutations: about 30 in its spike protein, compared to BA.2, its closest relative. The spike protein is the part of the coronavirus that binds to and enters human cells, so mutations tend to accumulate here, enabling the virus to cause new infections in people who have already been infected or vaccinated.

    BA.2, you might remember, was a dominant variant in early 2022, so it’s unexpected to see a descendant of this lineage pop up now. Scientists hypothesize that BA.2.86 might have evolved in a single person with a persistent infection; the virus could have multiplied and mutated over the course of several months or a year in someone originally infected with BA.2. This evolution also could have occurred in an animal population, then transferred back to humans.

    Scientists have similar hypotheses about the original Omicron variant, which was also very different from circulating strains when it emerged. In fact, BA.2.86 is about as different from XBB.1.5 (a recently dominant variant globally) as Omicron BA.1 was from Delta.

    Where has BA.2.86 been identified so far?

    Surveillance efforts in many countries have now found BA.2.86, ranging from Thailand to South Africa. This variant is evidently already spreading globally; unlike Omicron’s initial emergence, however, we don’t have a singular country to watch for signals of how BA.2.86 may impact transmission trends.

    In the U.S., researchers have found BA.2.86 in three different states:

    • One case in Michigan, from a person tested in early August
    • One traveler returning to a D.C.-area airport from Japan, their infection caught through the CDC’s travel surveillance program
    • Wastewater from a sewershed in Elyria, Ohio

    As surveillance is currently fairly uneven across the U.S., we can likely assume that BA.2.86 is present in other states already. Continued testing in the next few weeks will provide a clearer picture of the situation.

    How does BA.2.86 impact transmission and disease severity?

    This is one question that we can’t answer yet, though scientists are concerned about its potential. In a risk assessment report published this past Wednesday, the CDC said that mutations present in BA.2.86 suggest that this variant may have greater capacity to “escape from existing immunity from vaccines and previous infections” when compared to recent variants.

    However, this is just a hypothesis based on genomic sequences. The CDC report cautions that it’s too soon to know how transmissible BA.2.86 is or any impact it may have on symptom severity. To answer this question, scientists will need to identify more cases caused by this variant, then track their severity and spread.

    Will our new booster shots work against BA.2.86?

    The FDA and CDC are planning to distribute booster shots this fall, based on the XBB.1.5 variant that dominated COVID-19 spread in the U.S. this spring and earlier in the summer. As Eric Topol points out in a recent Substack post, this booster choice made sense a couple of months ago, but it’s unlikely to work well against BA.2.86 if that variant takes off.

    More research is needed on this topic, of course, but the existing genomic data is concerning. Having an XBB.1.5 booster this fall, if we see a BA.2.86-driven surge, would be like having a booster based on Delta, when Omicron is spreading: better than no booster, but unlikely to provide full protection.

    “The strategy of picking a spike variant for the mRNA booster at one point in time and making that at scale, going through regulatory approval, and then for it to be given 3 or more months later is far from optimal,” Topol writes. “We desperately need to pursue a variant-proof vaccine and there are over 50 candidate templates from broad neutralizing antibodies that academic labs have published over the last couple of years.”

    Will current COVID-19 tests and treatments work for BA.2.86?

    According to the CDC’s risk assessment, current tests should still detect BA.2.86 and treatments should work against it, based on early studies of the variant’s genomic sequences. More research (from health agencies and companies) will provide further data on any changes to test or treatment effectiveness.

    Mara Aspinall points out in her testing-focused Substack that rapid tests, in particular, tend to be unaffected by variants because they test for the N protein, a different part of the coronavirus from the spike protein (which is the main area of viral evolution). However, if you’re taking a rapid test, it’s always a good idea to follow best practices for higher accuracy—testing multiple times, swabbing your throat, etc.—and get a PCR if available.

    How are scientists tracking the coronavirus’ continued evolution?

    BA.2.86 has arrived in an era of far less COVID-19 surveillance, compared to what we had available a year or two ago. Most people rely on rapid tests (if they test at all), which are rarely reported to the public health system and can’t be used for genomic surveillance. As a result, it might take longer to identify BA.2.86 cases even as this variant spreads more widely.

    However, there are still some surveillance systems tracking the virus—and all are now attuned to BA.2.86. A couple worth highlighting in the U.S.:

    • Wastewater surveillance increasingly includes testing for variants. The CDC has a dashboard showing variant testing results from sewage; this is happening in about 400 sewersheds now and will likely increase in the future.
    • The CDC also supports a travel surveillance program at major international airports, in partnership with Concentric by Ginkgo and XpressCheck. This program caught one of the first BA.2.86 cases in the U.S. (the traveler from Japan mentioned above).
    • Several major testing companies and projects continue virus surveillance, via both limited PCR samples and wastewater. These include Helix, Biobot, and WastewaterSCAN.

    What will BA.2.86 mean for COVID-19 spread this fall and winter?

    While BA.2.86 is similar to Omicron BA.1 in its level of mutations, it’s not yet driving significant disease spread at the same level that we saw from Omicron when that variant first emerged in late 2021. All warnings at this point are tentative, based on very limited data.

    In a Twitter thread last week, virologist Marc Johnson pointed to three potential scenarios for BA.2.86:

    • It could “fizzle,” or fail to outcompete currently-circulating variants and spread widely despite its concerning array of mutations.
    • It could “displace” the current variants and contribute to increased transmission, but not cause a huge wave on the same level as Omicron BA.1 in late 2021.
    • It could cause a major wave, comparable to the initial Omicron spread.

    Based on analysis from Johnson and other experts I follow, the second scenario seems most likely. But if the U.S. and other countries had meaningful public health protections in place, we could actually contribute to those odds, rather than leaving things up to evolutionary chance. Remember: variants don’t just evolve in a vacuum. We create them, by letting the virus spread.

    Sources and further reading:

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    More variant reporting

  • National numbers, August 27

    National numbers, August 27

    Biobot’s wastewater surveillance data suggest a potential plateau in COVID-19 spread, though future weeks of data will be needed to say for sure.

    During the most recent week of data available (August 6-12), the U.S. reported about 12,600 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,800 new admissions each day
    • 3.8 total admissions for every 100,000 Americans
    • 22% more new admissions than the prior week (July 30-August 5)

    Additionally, the U.S. reported:

    • 13.4% of tests in the CDC’s surveillance network came back positive
    • A 1% lower concentration of SARS-CoV-2 in wastewater than last week (as of August 23, per Biobot’s dashboard)
    • 25% of new cases are caused by Omicron XBB.1.6; 21% by EG.5; 11% by XBB.2.3; 13% by FL.1.5.1 (as of August 19)

    This week, our limited COVID-19 data picture suggests that transmission may be starting to level off. But if BA.2.86 or another newer variant enters this high-spread environment, the outlook could get less rosy.

    One sign of a possible plateau: Biobot’s national wastewater surveillance dashboard shows a very slight downward trend, with SARS-CoV-2 levels dropping by about 1% from August 16 to August 23. This is based on just one week of data, though, so we’ll have to see what further updates show.

    Biobot’s regional data similarly show potential good trends: the Midwest appears to have passed the peak during this surge, as of the last two weeks, while the South and Northeast also show slight plateaus. Coronavirus levels are still trending up in the West, but less intensely.

    Data from both Biobot and WastewaterSCAN suggest that COVID-19 spread has turned a corner in some Midwest sewersheds, such as Johnson County, Kansas; Lawrence, Kansas; Lonoke County, Arkansas; Lincoln, Nebraska; and Warren, Michigan. Still, more data are needed to see if these trends hold.

    Test positivity data from the CDC’s respiratory surveillance network also suggest that COVID-19 spread may be slowing. After a rapid rise through July, test positivity increased by just 8% in the most recent week of data (ending August 19), from 12.4% to 13.4%. This is still a high overall positivity rate, though, especially considering how difficult PCR tests are to access these days.

    Hospitalizations continue to rise as well: the CDC reported a 22% increase in new COVID-19 patients from the week ending August 5 to the week ending August 12. While hospitalizations are significantly delayed compared to other metrics, these data show one of the surge’s severe impacts. We have even less data about Long COVID, the other main severe impact.

    BA.2.86, a new variant that scientists are watching closely, isn’t yet impacting transmission in the U.S. based on our current data. But it could lead to another increase in cases, if it proves able to outcompete the now-dominant group of XBB variants. (More on BA.2.86 later in today’s issue.)

    Remember: new variants don’t appear magically out of nowhere. People encourage their evolution, by allowing the virus to continue spreading unchecked. In addition to protecting ourselves and our communities, COVID-19 safety measures help to prevent further mutation.

    more national numbers

  • BA.2.86 is the latest variant to watch; send me your questions

    Last week, several variant experts that I follow on Twitter (which I refuse to call by its new name, thanks) started posting about a new SARS-CoV-2 variant, first detected in Israel. They initially called it Omicron BA.X while waiting for more details to emerge about the sequence; it’s now been named BA.2.86.

    Scientists and health officials are concerned about BA.2.86 because it has many mutations on its spike protein, showing significant deviation from other versions of Omicron. This variant evolved from an earlier Omicron strain (BA.2) rather than XBB, which is the primary lineage spreading across the world right now—and is the primary focus of booster development for this fall.

    Here are two relevant threads with more info (the first for a more general audience, the second going into more details about mutations):

    Virologists hypothesize that BA.2.86 may have evolved in someone with a chronic infection—essentially gaining more and more mutations as the same person stayed sick for many months. Similar hypotheses apply to Delta and Omicron, though it’s hard to get definitive answers without actually finding those patients.

    Another reason for concern: as of today, BA.2.86 has been detected on three different continents. In addition to Israel, scientists have found it in Denmark and the U.S. Since most countries are not doing rigorous genomic surveillance these days, the cases found so far suggest that this variant is actually far more widespread; it just went undetected until now.

    The World Health Organization recently designated BA.2.86 as a Variant Under Monitoring, meaning that its genetic information suggests concern but little else is known at this time. The CDC has also said it’s tracking the new variant.

    I’m keeping today’s post about BA.2.86 short due to the limited information we have so far. But I’d like to dive into it more next week. So, send me your questions about this variant or about genomic surveillance more broadly, and I will answer them in next Sunday’s newsletter.

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  • National numbers, August 20

    National numbers, August 20

    While the rise in hospitalizations has been modest, test positivity is on a similar level to the last couple of surges, per the CDC. Data as of August 18.

    During the most recent week of data available (July 30 through August 5), the U.S. reported about 10,300 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,500 new admissions each day
    • 3.1 total admissions for every 100,000 Americans
    • 14% more new admissions than the prior week (July 23-29)

    Additionally, the U.S. reported:

    • 12.2% of tests in the CDC’s surveillance network came back positive
    • A 10% higher concentration of SARS-CoV-2 in wastewater than last week (as of August 16, per Biobot’s dashboard)
    • 25% of new cases are caused by Omicron XBB.1.6; 21% by EG.5; 11% by XBB.2.3; 13% by FL.1.5.1 (as of August 19)

    The summer COVID-19 surge continues. While wastewater surveillance data suggest that transmission trends may be turning around in some places, the virus is largely still increasing across the U.S. New variants are on the horizon, too.

    Nationally, coronavirus levels in wastewater are the highest they’ve been since last winter’s holiday surge, according to data from Biobot Analytics. Viral concentrations have tripled since mid-June, and continue to follow a similar pattern to the Delta surge that we experienced at about the same time in summer 2021.

    Biobot’s regional data suggest that the Midwest—which reported a serious spike last week—may have turned a corner in this surge, with viral levels going into a plateau. This pattern is based on just one week of data, though, so we’ll have to see what next week’s numbers show.

    Wastewater data from the CDC and WastewaterSCAN similarly show continued increases in COVID-19 spread. Some counties in Southern states, such as Florida, Georgia, and Alabama, are reporting particularly large upticks. Hawaii may be a state to watch, too, as residents face health access challenges following the recent wildfires.

    Test positivity also continues to increase, with the CDC reporting that about 12% of COVID-19 tests reported to its respiratory network returned positive results in the week ending August 16. Hospital admissions and emergency department visits are still going up as well, though these metrics are reported with two-week delays.

    The CDC updated its variant data this week, reporting that Omicron EG.5 continues to outcompete other XBB lineages. EG.5 doesn’t have a huge advantage in transmission, though, so it’s increasing relatively slowly amid a sea of other similar variants.

    But a new variant, called BA.2.86, may be one to watch more closely. Health officials are on the alert after seeing just a few cases in the U.S., Israel, and Denmark due to a number of mutations in this variant’s spike protein, which diverge significantly from other strains. (More on this variant later in today’s issue.)

    While the CDC says it’s monitoring this new variant, the agency’s genomic surveillance is far sparser than it was a year or two ago. The agency and its research partners are now sequencing under 5,000 coronavirus samples a week, compared to almost 100,000 a week at the height of Omicron. With this small sample pool, the CDC is less equipped to catch BA.2.86, or any other variants that may arise.

    more national numbers
  • National numbers, August 13

    National numbers, August 13

    Wastewater data from Biobot Analytics suggest that coronavirus levels in the Northeast and South may be leveling off, while the Midwest is seeing a major spike.

    During the most recent week of data available (July 23 through 29), the U.S. reported about 9,000 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,300 new admissions each day
    • 2.8 total admissions for every 100,000 Americans
    • 13% more new admissions than the prior week (July 16-22)

    Additionally, the U.S. reported:

    • 10.6% of tests in the CDC’s surveillance network came back positive
    • A 9% higher concentration of SARS-CoV-2 in wastewater than last week (as of August 9, per Biobot’s dashboard)
    • 31% of new cases are caused by Omicron XBB.1.6; 17% by EG.5; 11% by XBB.2.3; 10% by XBB.1.9 (as of August 5)

    All major COVID-19 metrics continue to increase in the U.S., as we deal with a late-summer surge. Wastewater surveillance suggests that current virus spread is on pace with the Delta surge in 2021, though other data sources are less reliable these days.

    Wastewater data from Biobot continue to show an uptick nationally, following the same upward trend that started in late June. The CDC’s wastewater surveillance system and WastewaterSCAN network report similar trends.

    Biobot’s regional data suggest that the Northeast and South, the first two regions to see COVID-19 increases this summer, might be approaching their peaks, but it’s too early to say for sure. Regional test positivity numbers, from the CDC, show no sign of slowing their rise.

    Meanwhile, COVID-19 spread is going way up in the Midwest, per Biobot and WastewaterSCAN. Some sewersheds in Iowa, Michigan, Ohio, and nearby states have reported their viral levels in wastewater more than doubling over the last couple of weeks.

    Test positivity nationwide is now over 10%, per the latest data from the CDC’s respiratory virus testing network. Walgreens’ COVID-19 dashboard, which displays testing data from its pharmacies (i.e. a smaller sample size than the CDC network), reports a record high: of about 2,400 COVID-19 tests conducted in the week ending August 6, 45% were positive.

    Hospital admissions for COVID-19 are also on the rise, with about 1,300 new hospitalizations for COVID-19 each day in the week ending July 29, per the CDC. While it’s true that these numbers are far lower than peaks during prior surges, the data are also less reliable now— with fewer hospitals reporting to the CDC and fewer measures in those hospitals (like masking) to control infections.

    A lot of articles in the last couple of weeks have connected the recent surge to EG.5, the latest Omicron subvariant gaining ground in the U.S. However, this variant is not necessarily causing the surge; it doesn’t seem to be meaningfully more contagious or more severe than other recent strains, scientists are finding.

    Rather than a variant, I would personally attribute this surge to summer travel and gatherings, combined with waning immunity—it’s been many months since most Americans had contact with the virus through vaccination or infection.

    All of the virus-spreading activities going on right now will give SARS-CoV-2 more avenues to mutate. And there are other variants circulating globally that could cause more problems in the U.S. as well, as Eric Topol outlines in a recent Substack post. The next booster can’t come soon enough.

    more national numbers
  • National numbers, July 16

    National numbers, July 16

    Wastewater surveillance data from Biobot indicate that three out of four major U.S. regions are experiencing increased COVID-19 spread.

    In the past week (July 2 through 8), the CDC did not update COVID-19 hospitalization data for unclear reasons. During the most recent week of data available (June 25 through July 1), the U.S. reported about 6,200 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 900 new admissions each day
    • 1.9 total admissions for every 100,000 Americans
    • 1% fewer new admissions than the prior week (June 18-24)

    Additionally, the U.S. reported:

    • 5.5% of tests in the CDC’s surveillance network came back positive
    • A 13% higher concentration of SARS-CoV-2 in wastewater than last week (as of July 12, per Biobot’s dashboard)
    • 32% of new cases are caused by Omicron XBB.1.6; 15% by XBB.1.9; 13% by XBB.2.3 (as of July 8)

    National COVID-19 data are showing signs of a summer uptick in infections across multiple regions. Newer variants, summer travel, and holidays are likely contributing to this increase, though it’s hard to say if we will see a real surge or a continued shifting of the U.S.’s high COVID-19 baseline.

    Wastewater surveillance data from Biobot Analytics show a significant uptick in coronavirus levels over the last month, with an increase of about 50% from June 14 to July 12. Three out of four major U.S. regions (the Northeast, South, and West Coast) report notable increases, while the Midwest reports a slower uptick.

    The CDC’s National Wastewater Surveillance System (NWSS) is not yet showing a pronounced increase. Of the testing sites in this network that reported data in the last two weeks, about half reported upticks while the others reported declines or plateaus. However, NWSS data tend to be updated on a more delayed schedule than Biobot’s dashboard, since the CDC compiles information from a number of state and local health agencies.

    As epidemiologist Caitlin Rivers points out in her Substack post describing the wastewater trend, COVID-19 summer waves in the U.S. tend to start in the South. Some experts attribute this to more indoor summer activities in the region, but there’s little data to back this up, Rivers writes. Plus, this year, the summer uptick has appeared to start in multiple regions of the country at the same time.

    In addition to the wastewater data, test positivity data from the CDCs National Respiratory and Enteric Virus Surveillance System (NREVSS) show a similar uptick in the last month: from 4.1% of COVID-19 tests returning positive results in the week ending June 10 to 5.5% in the week ending July 8. Remember, this NREVSS doesn’t share data from all PCR tests done in the U.S. (as the CDC no longer has authority to collect this information); but it is set up to provide national and regional estimates.

    According to NREVSS, COVID-19 test positivity is going up in several major regions, including New York and New Jersey, the Mid-Atlantic, the South, the Gulf Coast, and the Northwest. All of these regions are dealing with the Omicron XBB variant’s continued evolution; in the CDC’s most recent variant update on July 8, the agency listed 12 different XBB subvariants competing for hosts.

    The CDC failed to update its COVID-19 hospitalization data this week, so the most recent available data are from the week ending July 1. Typically, the agency’s data scientists will add notes to their dashboard explaining update delays or errors, but this week, I couldn’t find anything.

    As I wrote on June 25: sometimes, I wonder if the CDC doesn’t think anyone is checking their dashboard anymore. But we are! COVID-19 data may be more limited than ever, but we still have enough information to know when cases are ticking up again—and we know the measures needed to protect ourselves and our communities.

    more national numbers
  • National numbers, May 28

    National numbers, May 28

    The CDC is now updating its variant estimates every two weeks.

    In the past week (May 14 through 20), the U.S. reported about 8,300 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,200 new admissions each day
    • 2.5 total admissions for every 100,000 Americans
    • 11% fewer new admissions than last week (May 7-13)

    Additionally, the U.S. reported:

    • A 16% lower concentration of SARS-CoV-2 in wastewater than last week (as of May 24, per Biobot’s dashboard)
    • 54% of new cases are caused by Omicron XBB.1.5; 19% by XBB.1.16; 18% by XBB.1.9 (as of May 27)

    The COVID-19 plateau continues, with hospital admissions and viral levels in wastewater (the two main metrics I’m looking at these days) both trending slightly down at the national level. Newer Omicron variants are still on the rise, but don’t seem to be impacting transmission much yet.

    Hospitalizations continue to trend slightly down across the board, though hospitals are still reporting more than 1,000 new COVID-19 patients each day. The vast majority of U.S. counties have low hospitalization levels, according to the CDC, with just 14 counties in the medium or high categories.

    Coronavirus levels in wastewater are following a similar pattern: trending down very slightly, continuing the middling plateau of the last couple of months. All four major regions are still in this holding pattern, according to Biobot’s data.

    We have new variant data this week, as the CDC is now on a biweekly schedule for updates. XBB.1.5 caused just over half of new cases in the U.S. in the two weeks ending May 27, as it slowly gets outcompeted by newer versions of Omicron. XBB.1.16 and XBB.1.9 continue to rise, causing 19% and 18% of hew cases respectively.

    XBB.1.16 is most prevalent on the West Coast, the Northeast, and the Gulf Coast states, while XBB.1.9 is most prevalent in the Midwest, according to the CDC—though these estimates are becoming less reliable over time, since so few COVID-19 samples are sequenced.

    The CDC has also recently added national and regional COVID-19 test positivity data back to its dashboard, representing tests conducted by labs in the CDC’s National Respiratory and Enteric Virus Surveillance System.

    Nationally, test positivity is trending down, at just under 5% of COVID-19 tests (in this lab network) returning positive results in the most recent week of data. Test positivity is trending up slightly in the Northeast and New York/New Jersey regions; I’ll be following to see if this continues in the coming weeks.

    Finally, a bit of good news: excess deaths in the U.S. have returned to baseline in the last couple of months. While hundreds are still dying from COVID-19 every day, the excess death trend suggests that the disease is currently not causing a significant ripple effect on overall mortality the way that it did in earlier stages of the pandemic. (Of course, this could change with a new surge.)

    more national numbers