COVID-19 Data Dispatch

Tag: 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
  • New data on BA.2.86 suggest the fall booster may work well

    New data on BA.2.86 suggest the fall booster may work well

    Since BA.2.86 emerged a couple of weeks ago, scientists around the world have been racing to evaluate this variant. Several teams posted data in the last week, and the news is promising: while BA.2.86 does have an advantage over past variants, the lab findings suggest that vaccines (including the upcoming boosters) and past infections provide protection against it.

    The new studies come from research groups in the U.S., China, Japan, Switzerland, and South Africa. These scientists studied BA.2.86 by growing the variant in petri dishes and evaluating it against antibodies from blood samples. Overall, they found that BA.2.86 can infect people who were recently infected with XBB.1.5 and its relatives, but this variant isn’t as successful at getting into human cells as XBB.1.5.

    Another notable study came from researchers at Moderna, who evaluated how the company’s upcoming booster shot performs against BA.2.86. This team found that the booster—which is designed from XBB.1.5—helps the immune system prepare for XBB variants as well as BA.2.86. While lab studies like this one don’t translate perfectly to real-world effectiveness, the data do suggest that Moderna’s booster should protect well against BA.2.86 infection for a few weeks after vaccination, and against severe disease for longer.

    You might have seen the figure below shared around on social media in the last few days. This chart, from the Moderna team, shows how the new booster improves immunity toward several variants. For example, patients who received the booster had 8.7 times more neutralizing antibodies against BA.2.86 and 10 times more neutralizing antibodies against XBB.1.5 than those who had not received it.

    This figure, from a preprint by Moderna scientists, shows how the company’s upcoming fall booster performs against different variants.

    Pfizer has also tested their new booster against BA.2.86 and found similar results, according to a report from Reuters. This company’s results have yet to be shared in a scientific paper, though.

    The studies I’ve discussed here are all preprints, meaning the results have yet to be peer-reviewed (outside of the informal review process that happens on social media for this type of urgent research). It’s also worth noting that lab studies look at immune system signals, rather than actually tracking who’s getting this new variant and their disease outcomes.

    Even if BA.2.86 is not “the next Omicron,” as some scientists suggested based on its mutations, it could still contribute to a new uptick in cases this fall. And all cases carry the risk of severe illness, Long COVID, and other poor outcomes. The new boosters are likely to help reduce risk (which is good news), but other measures are still needed.

    References about the new studies:

  • 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

  • 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 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, August 6

    National numbers, August 6

    Test positivity is way up in the U.S., while hospitalizations are starting to follow this trend. Chart via the CDC.

    During the most recent week of data available (July 16 through 22), the U.S. reported about 8,000 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,150 new admissions each day
    • 2.4 total admissions for every 100,000 Americans
    • 12% more new admissions than the prior week (July 9-15)

    Additionally, the U.S. reported:

    • 8.9% 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 2, 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)

    Over the last few weeks, the signals of a summer COVID-19 surge in the U.S. have grown steadily clearer. Viral levels in wastewater, test positivity, and hospitalizations are all climbing across the country.

    Wastewater surveillance data from Biobot suggest that coronavirus levels have doubled nationally in the last month. The surge is impacting all major regions of the country; the Northeast and South saw earlier increases, but the Midwest and West Coast are now catching up.

    The CDC’s wastewater surveillance network also points to increasing COVID-19 spread, with sites across the country reporting higher viral levels. While wastewater surveillance remains uneven (some states are testing in every county, others in just a handful of locations), it still gives us enough information to identify a widespread surge.

    Test positivity from the CDC’s lab testing network shows continued increases as well. About 8.9% of COVID-19 tests reported to the agency returned positive results in the week ending July 29, compared to 4.5% in the week ending June 24. This increase, too, is consistent across regions.

    Hospitalizations for COVID-19 are also going up, according to the CDC. These data are significantly delayed, with the most recent numbers dating to about two weeks ago. So, while overall patient numbers remain low right now, I expect they will continue to rise as the surge goes on.

    The coronavirus’ continued evolution is likely playing a role in this summer’s increased spread, as are summer travel and waning immunity from past vaccinations. Omicron EG.5, a descendant of the XBB.1.9 lineage, is the latest variant to spread widely, according to the CDC’s estimates.

    No one version of XBB has yet shown a significant ability to spread much faster or cause more severe symptoms than other variants. Rather, many iterations of this Omicron lineage are spreading in tandem, continuing to mutate with every infection. And with fewer PCR tests happening, it’s harder for health agencies to keep track.

    This summer’s surge may be less visible than ever. But wastewater data suggest we’re seeing similar levels of COVID-19 spread as we saw with Delta in summer 2021. Precautions are still important!

    more national numbers
  • National numbers, July 23

    National numbers, July 23

    A wide variety of XBB-related Omicron variants are competing across the U.S. Data from the CDC, as of July 22.

    During the most recent week of data available (July 2 through 8), 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 25-July 1)

    Additionally, the U.S. reported:

    • 6.3% 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 July 19, per Biobot’s dashboard)
    • 24% of new cases are caused by Omicron XBB.1.6; 19% by XBB.1.9; 13% by XBB.2.3 (as of July 22)

    COVID-19 data in the U.S. is showing increasingly clear signs of a summer surge, with infections rising across the country. However, thanks to the federal public health emergency’s end, we have less and less data to track this trend.

    Wastewater data from Biobot Analytics show that national coronavirus levels have gone up by about 68% in the last month. Current levels are far below this time last year (when the Omicron BA.4/BA.5 surge was in full swing), but still at their highest in several months.

    Biobot’s regional data suggest that the COVID-19 uptick is hitting all major regions. But the increases have been most pronounced in the Northeast and South; coronavirus levels have doubled in both regions in the last month, per Biobot.

    The CDC’s wastewater surveillance network has picked up these increases as well, with more than half of testing sites in this network (with recent data) reporting coronavirus upticks in the last two weeks. Some major cities, such as Boston and Los Angeles, are also reflecting the increase.

    Test positivity data from the CDC also show the increasing COVID-19 spread: nationally, test positivity from the labs in the agency’s surveillance network has gone up from 4.3% one month ago to 6.3% in the most recent week of data. The most prominent increases for this metric are similarly in the Northeast and South, and in the health region including Oregon, Washington, Idaho, and Alaska.

    One metric not yet showing an increase is the CDC’s hospital admissions data. But the agency has continued to report these data with a lag: as of today, the most recent hospitalization numbers are as of July 8, two weeks ago. The CDC has yet to provide a clear explanation for this reporting lag.

    Either way, the data we do have give us sufficient warnings about this summer’s uptick in COVID-19 spread. One likely culprit is the continued evolution of Omicron XBB: about 15 different subvariants are currently competing, according to the CDC’s latest data. No variant seems to be a clear winner yet.

    Regardless of which variant comes to dominate next, the same safety measures continue to work against COVID-19.

    more national numbers

  • COVID source shout-out: Cryptic lineage investigation in Ohio

    Marc Johnson, a molecular virologist and wastewater surveillance expert at the University of Missouri, recently went viral on Twitter with a thread discussing his team’s investigation into a cryptic SARS-CoV-2 lineage in Ohio. I was glad to see the project get some attention, because I find Johnson’s research in this area fascinating and valuable for better understanding the links between coronavirus infection and chronic symptoms.

    A “cryptic lineage” is a technical term for, basically, a strange viral mutation that researchers have identified in a specific location. Unlike common variants that spread through the population (Delta, Omicron, BA.5, XBB, etc.), these lineages typically are contained in one place, or even in one person. They’re usually identified by wastewater surveillance, since that technique picks up more people’s infections than testing at doctors’ offices.

    Johnson has become a specialist in investigating these cryptic lineages over the last couple of years. His lab at the University of Missouri runs the state’s wastewater surveillance program, which includes genetic sequencing for sewage samples. And his team also collaborates on sequencing research for wastewater surveillance in other parts of the U.S. This Nature article from last year goes into more detail about how these investigations work.

    In the last few months, Johnson and his colleagues have been investigating one cryptic lineage in Ohio. The scientists have traced the lineage to Columbus and a town called Washington Court House; they believe it represents one sick person, who lives in Columbus and goes to Washington Court House for work. This individual is shedding a massive amount of coronavirus, orders of magnitude higher than the average COVID-positive person. See more details in this story by The Columbus Dispatch.

    Johnson and his colleagues would like to identify the person behind this lineage for two reasons. First, they can connect the person with doctors who can help treat their COVID-19 symptoms—it’s likely they’re having a pretty nasty gastrointestinal experience. Second, the scientists hope to better understand how viral particles that shed from a long-term infection might be related to chronic symptoms, as persistent virus in different organ systems is one of the leading hypotheses for why Long COVID occurs.

    I’ve interviewed Johnson before for stories about wastewater surveillance and I think he does fascinating work, so I was glad to see his Twitter thread get some attention. If you can help identify the Ohio resident with lots of coronavirus in their gut, get in touch with him!

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  • National numbers, May 14

    National numbers, May 14

    The CDC and its partners are sequencing far fewer coronavirus samples than they have at prior periods of the pandemic, making it harder to spot new variants of concern.

    In the past week (April 30 through May 6), the U.S. reported about 9,500 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,400 new admissions each day
    • 2.9 total admissions for every 100,000 Americans
    • 7% fewer new admissions than last week (April 22-29)

    Additionally, the U.S. reported:

    • A 14% lower concentration of SARS-CoV-2 in wastewater than last week (as of May 10, per Biobot’s dashboard)
    • 64% of new cases are caused by Omicron XBB.1.5; 13% by XBB.1.9; 14% by XBB.1.16 (as of May 13)
    • An average of 70,000 vaccinations per day

    COVID-19 spread continues to trend down in the U.S., though our data for tracking this disease is now worse than ever thanks to the end of the federal public health emergency. If newer Omicron variants cause a surge this summer, those increases will be hard to spot.

    As a result of the PHE’s conclusion this week, the CDC is no longer collecting national case counts or testing data. Instead, the agency now recommends using hospitalization data to monitor how hard COVID-19 is hitting your community—even though this metric typically lags behind actual infection patterns—while variant data and wastewater surveillance may provide warnings about new surges.

    My national updates will take a similar approach. This week, hospital admissions continue their national plateau, with a decrease of about 7% from the week ending April 29 to the week ending May 6. The CDC’s national map show that admissions are low across the country, with 99% of counties reporting fewer than 10 new admissions per 100,000 residents.

    Wastewater surveillance also suggests that, while there’s still a lot of COVID-19 in the U.S., disease spread is still on a plateau or slight decline in most of the country. Biobot’s data show a minor national downturn in recent weeks; trends are similar across the four major regions, though the decline is a bit steeper on the West Coast.

    The variant picture also hasn’t changed much: XBB.1.5 caused about two-thirds of new cases in the last two weeks, according to the CDC’s estimates. XBB.1.6 caused about 14% and XBB.1.9 caused 13%; these newer versions of Omicron are gaining ground, but fairly slowly. Regionally, XBB.1.6 is most prevalent in the Northeast and on the West Coast, while XBB.1.9 is most prevalent in the Midwest.

    It’s worth noting, though, that the CDC has switched its variant reporting from weekly to every other week, as fewer patient specimens are going through sequencing for variant identification. The agency and its surveillance partners are sequencing around 5,000 samples every week, compared to over 80,000 a week at the height of the first Omicron surge.

    Limited sequencing efforts will make it harder for the CDC to quickly identify (and respond to) new variants of concern. The same challenge is happening around the world, as PCR tests become less broadly available. Sequencing coronavirus samples from wastewater may help, but that’s only happening in a small subset of sewage testing sites right now.

    One last bit of good news: vaccine administration numbers are up in the last couple of weeks, as seniors and other eligible high-risk people get their second bivalent boosters. About 70,000 people received vaccines each day this week, compared to around half that number a few weeks ago. If you’re eligible for a second booster, this is a good time to make an appointment!

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