COVID-19 Data Dispatch

Tag: XBB

  • 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, 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 30

    National numbers, July 30

    COVID-19 is spreading more in all regions of the country, according to Biobot’s data. Data as of July 27, based on samples collected the week of July 24.

    During the most recent week of data available (July 9 through 15), the U.S. reported about 7,100 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 1,000 new admissions each day
    • 2.2 total admissions for every 100,000 Americans
    • 10% more new admissions than the prior week (July 2-8)

      Additionally, the U.S. reported:

    • 7.6% of tests in the CDC’s surveillance network came back positive
    • A 17% higher concentration of SARS-CoV-2 in wastewater than last week (as of July 26, 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)

    Several major metrics continue to point to a summer increase in COVID-19 spread. Coronavirus levels in wastewater are up in all major regions, as is test positivity from the CDC’s network. Hospitalizations have started ticking up as well.

    Nationally, coronavirus levels in wastewater have doubled in the last month, according to Biobot Analytics. Viral levels are on par with this period in summer 2021, at the start of that year’s Delta surge, and are the highest they’ve been since this year’s holiday surge concluded.

    Data from the WastewaterSCAN network similarly shows COVID-19 upticks in the last month, though the team’s latest national update notes that current levels are still low compared to the start of 2023. WastewaterSCAN recently added national wastewater levels to its dashboard, making it easier to track broad trends from this sewage testing network.

    Test positivity data from the CDC’s respiratory lab network are still increasing as well. National test positivity was 7.6% in the week ending July 22, compared to 4.5% about a month ago, an increase of about 70%.

    The CDC’s hospitalization data are also showing an increase now: new COVID-19 patients admitted to hospitals went up by about 10% from the week ending July 8 to the week ending July 15. These are the most recent hospitalization numbers available, as the CDC is still reporting this metric with a delay.

    Wastewater and positivity data suggest that COVID-19 spread is increasing in all major regions of the country. All regions are also dealing with the virus’ continued evolution, as a variety of XBB lineages circulate and compete with each other.

    Several national publications reported on these COVID-19 increases in the last week, pointing to the potential for a summer surge. I personally liked this article from Dylan Scott at Vox, which also covers implications for COVID-19 this winter.

    But the COVID-19 Data Dispatch was on this potential surge weeks before any mainstream media news site. If you appreciate our early warnings, please donate to support this work!

    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
  • 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
  • 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!

    more national numbers
  • National numbers, April 23

    National numbers, April 23

    Coronavirus concentrations are trending down in Boston’s wastewater, a promising signal.

    In the past week (April 13 through 19), the U.S. officially reported about 94,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 13,000 new cases each day
    • 7% fewer new cases than last week (April 6-12)

    In the past week, the U.S. also reported about 12,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 1,700 new admissions each day
    • 3.7 total admissions for every 100,000 Americans
    • 8% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 1,200 new COVID-19 deaths (170 per day)
    • 74% of new cases are caused by Omicron XBB.1.5; 11% by XBB.1.9; 10% by XBB.1.16 (as of April 22)
    • An average of 35,000 vaccinations per day

    Across the U.S., COVID-19 spread continues at a moderately high plateau as newer versions of Omicron compete with XBB.1.5. Officially-reported cases and new hospitalizations declined by 7% and 8% respectively, compared to the prior week.

    Wastewater surveillance data from Biobot and from the CDC similarly show that COVID-19 spread is at a plateau. Nationally, coronavirus concentrations in sewage are higher than they were at this point in 2021 (when the initial vaccine rollout was in full swing), but lower than at this point in 2022 (when BA.2 had started spreading widely).

    Of course, it’s important to flag that official case counts are becoming even more unreliable these days, as PCR testing becomes increasingly difficult to access and state health departments no longer prioritize timely reporting to the CDC. According to CDC, five states didn’t report COVID-19 cases and deaths last week: Arkansas, Florida, Iowa, Mississippi, and Pennsylvania. (Iowa has permanently stopped reporting.)

    These case reporting issues are likely to continue—and perhaps accelerate—when the federal public health emergency ends next month. I’m thinking about how to adjust these National Numbers reports when that happens; that will likely involve foregrounding wastewater data and hospitalizations rather than cases.

    Regionally, Biobot’s surveillance shows a slight uptick in coronavirus spread on the West Coast and declines in the other major regions. Some counties in California have reported recent increases in wastewater, according to Biobot and WastewaterSCAN, but it’s currently tough to tell if this is a sustained surge or isolated outbreaks.

    The West Coast and Midwest continue to be hotspots for newer versions of Omicron, according to the CDC’s estimates, with XBB.1.9 still most prevalent by far in the region including Iowa, Kansas, Missouri, and Nebraska. Nationwide, the CDC estimates that XBB.1.9 caused about 11% of new cases in the last week and that XBB.1.16 caused 10% of new cases.

    XBB.1.16 (also called “Arcturus”) was recently classified as a variant of interest by the World Health Organization because it can spread significantly faster than other Omicron lineages. The variant is likely to “spread globally and contribute to an increase in case incidence,” according to the WHO.

    While I’m wary of the new variants, I have been heartened to see coronavirus levels in wastewater remain mostly at plateaus—or even decline—in many places across the U.S. In Boston, for example, coronavirus levels have been on a downward trend since early 2023. I hope to see this trend continue. 

    more national numbers
  • National numbers, April 16

    National numbers, April 16

    New subvariants XBB.1.16, XBB.1.9.1, and XBB.1.9.2 are on the rise, according to the CDC’s estimates.

    In the past week (April 6 through 12), the U.S. officially reported about 100,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 15,000 new cases each day
    • 17% fewer new cases than last week (March 30-April 5)

    In the past week, the U.S. also reported about 13,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 1,900 new admissions each day
    • 3.9 total admissions for every 100,000 Americans
    • 14% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 1,300 new COVID-19 deaths (190 per day)
    • 78% of new cases are caused by Omicron XBB.1.5; 9% by XBB.1.9; 7% by XBB.1.16 (as of April 15)
    • An average of 35,000 vaccinations per day (CDC link)

    COVID-19 spread appears to be at a continued plateau nationally, with slight declines in cases, hospitalizations, and viral concentrations in wastewater. New variants are on the horizon, though, at a time when data are becoming increasingly less reliable. 

    The CDC reported about 100,000 new cases this week, the lowest this number has been since early summer 2021. Unlike that period, however, PCR tests are much less available and reporting infrastructures are being dismantled.

    Wastewater surveillance data from Biobot show that transmission is actually several times higher now than it was at that previous low point. We’re in an undercounted plateau, rather than a real lull. Even so, less COVID-19 is spreading now than we’ve seen throughout the last few months.

    To get a more accurate picture of potential COVID-19 case counts in your area, I recommend going to the Iowa COVID-19 Tracker, an independent dashboard run by Sara Anne Willette. Willette has mapped out “likely cases per 100,000 people” by county, by multiplying the CDC’s data by 20 to account for underreporting.

    Wastewater data suggest that most parts of the U.S. are seeing steady (though slight) declines in transmission, with the exception of the West coast. Some counties in California have reported increased coronavirus levels in wastewater in the last week, according to Biobot and WastewaterSCAN, including parts of the Bay Area.

    One culprit for the increases could be newer Omicron subvariants, particularly XBB.1.9 and XBB.1.16. The CDC added XBB.1.16—which has drawn international concern, due to its connection with a recent surge in India—to its variant proportion estimates, along with XBB.1.9.2, a relative of XBB.1.9.1. (Yes, we’re getting into alphabet soup territory again here.)

    Nationally, the CDC estimates that XBB.1.16 caused about 7% of new cases in the last week, while the XBB.1.9s together caused 9%. At the regional level, XBB.1.16 is more prevalent in the West and Southwest (at over 20% of new cases in the region including Texas and other Gulf coast states), while the XBB.1.9s are more prevalent in the Midwest.

    The CDC published its second-to-last data update yesterday (which is still called the “Weekly Review,” even though it is far from weekly at this point). According to this update, most of the CDC’s public COVID-19 data “won’t be affected by the end of the public health emergency,” though the agency says it’ll provide more details in its final update on May 12.

    I personally expect that, while the national data systems might remain in place, more state and local health agencies will stop reporting, as we saw from Iowa recently. This will, of course, make the numbers less and less reliable.

    more national numbers
  • National numbers, April 9

    National numbers, April 9

    COVID-19 spread is at a plateau in all four major regions of the U.S., according to wastewater data from Biobot.

    In the past week (March 30 through April 5), the U.S. officially reported about 120,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 17,000 new cases each day
    • 37 total new cases for every 100,000 Americans
    • 12% fewer new cases than last week (March 23-29)

    In the past week, the U.S. also reported about 15,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 2,100 new admissions each day
    • 4.5 total admissions for every 100,000 Americans
    • 12% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 1,800 new COVID-19 deaths (250 per day)
    • 88% of new cases are caused by Omicron XBB.1.5; 5% by XBB.1.9.1; 2% by XBB.1.5.1; 0.4% by CH.1.1 (as of April 8)
    • An average of 40,000 vaccinations per day

    COVID-19 spread in the U.S. remains at a high plateau, according to reported cases, hospitalizations, and wastewater surveillance. Experts are watching new variants that mutated from XBB as potential drivers of more transmission this spring.

    While the case numbers may seem low, remember that cases are now severely undercounted—potentially by up to 20 times. So, when the CDC reported about 37 new cases per 100,000 people last week, the true number could be closer to 700 new cases per 100,000. It’s becoming harder and harder to get a PCR test, as sites shut down and the federal health emergency’s end approaches, which will further drive undercounting.

    Wastewater data, on the other hand, continue to show that coronavirus levels in the U.S. are significantly higher than they were at this time in 2022 and 2021. Last week, I wrote that Biobot’s dashboard showed a slight increase in COVID-19 spread across the country; after this week’s data updates, that appears to have been a blip, with the company’s national surveillance again showing a plateau.

    Biobot’s regional data also indicates that COVID-19 spread has remained relatively consistent in the last few weeks. The Northeast and Midwest have slightly higher coronavirus levels than the South and West, but there aren’t significant differences between these regions.

    As I wrote last week, new subvariant XBB.1.9.1 remains more prevalent in the Midwest, particularly the region including Iowa, Kansas, Missouri, and Nebraska (where it caused about 18% of new cases in the last week, per CDC estimates). Some wastewater testing sites in these states have reported increases recently, but there isn’t a consistent increase across the board.

    Nationally, the CDC estimates that XBB.1.9.1 caused about 5% of new cases nationwide in the week ending April 8, compared to 88% caused by XBB.1.5. XBB.1.9.1 has been growing relatively slowly, so it may be a few more weeks before we see it either outcompete XBB.1.5 or die out at low levels. Experts are also watching XBB.1.16, which drove a surge in India recently but has not shown up in large numbers in the U.S. yet.

    Will the U.S. see a new surge this spring? It seems possible, thanks to Omicron’s continued evolution and our lack of collective safety measures. But continued declines in data reporting will make it harder to see this surge than it’s ever been.

    In this environment, wastewater surveillance is growing more and more valuable. It’s also probably a good idea to keep taking some basic precautions (like masking in public indoor spaces, or regularly testing) no matter how low the reported cases get in your community.

    more national numbers