COVID-19 Data Dispatch

Author: Betsy Ladyzhets

  • National numbers, June 25

    National numbers, June 25

    Wastewater data from Boston show some small increases and decreases in transmission this spring, reflecting our uncertain baseline.

    In the past week (June 11 through 17), the CDC did not update COVID-19 hospitalization data due to changes in its reporting process.

    During the most recent week of data available (June 4 through 10), the U.S. reported about 6,600 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 950 new admissions each day
    • 2.0 total admissions for every 100,000 Americans
    • 8% fewer new admissions than the prior week (May 28-June 3)

    Additionally, the U.S. reported:

    • 4.0% of tests in the CDC’s surveillance network came back positive
    • A 16% lower concentration of SARS-CoV-2 in wastewater than last week (as of June 21, per Biobot’s dashboard)
    • 30% of new cases are caused by Omicron XBB.1.6; 24% by XBB.1.9; 11% by XBB.2.3 (as of June 24)

    The CDC failed to update its primary COVID-19 metrics this week, so I have no national updates to share about hospital admissions, deaths, or test positivity. The most recent available data from the agency and wastewater surveillance sources suggest that the U.S. is still experiencing a transmission plateau.

    According to the CDC’s dashboard, the agency didn’t update its hospitalization data “due to a change in required reporting cadence from daily to weekly,” following the end of the public health emergency in May. The dashboard note is a bit unclear, but I’m assuming this refers to a change in requirements for state public health departments reporting to the CDC, as the national agency lost its authority to require daily data reporting when the PHE ended.

    Still, it’s confusing to me that the CDC’s dashboard note only refers to hospitalization data, because deaths, test positivity, and other metrics also weren’t updated this week. These data points don’t rely on state reporting systems, so they shouldn’t be impacted by the reporting change.

    Either the note is incomplete, or the CDC staff in charge of this dashboard took an issue with one metric as an excuse not to update several metrics. I don’t love the outcome either way. Like, do they think nobody is checking this dashboard? Because we still are.

    Anyway, the CDC’s most recent data (from the week of June 10, now about three weeks ago), suggested that the U.S. was in a continued COVID-19 plateau, with hospital admissions and test positivity from the CDC’s surveillance network declining very slightly. 

    Wastewater data from Biobot Analytics indicates a similar plateau at the national level. Regionally, the Northeast and West coast experienced slight upticks in COVID-19 spread in the last few weeks, but the coronavirus levels in their wastewater now appear to be trending back down. (These are small changes, though, compared to what we’ve seen in past surges.)

    The sewage in Boston and New York City, two large Northeast cities that are often bellwethers for larger COVID-19 trends, similarly slow slight viral increases in May followed by downturns in June. NYC data are delayed by up to two weeks, though, so take this with a grain of salt.

    The CDC did update its variant estimates this week, showing that XBB.1.5 is now causing less than one-third of cases nationwide. XBB.1.6 and its relatives are now the most popular lineages in the U.S., causing a combined 30% of new cases in the two weeks ending June 24. Other XBB variants, including XBB.1.6 and XBB.2.3, are also on the rise.

    As health agencies put fewer and fewer resources into tracking COVID-19, the data we still have show continued severe ramifications for this disease’s unchecked spread. This disease still kills over 100 people per day.

    more national numbers

  • COVID source shout-out: Advocating for masks in healthcare

    A reader recently sent me this petition to the Illinois state legislature, which asks lawmakers to request that the state health department reconsider its position on masks in healthcare settings. This petition is one of many advocacy efforts that have pushed for healthcare organizations to continue prioritizing COVID-19 safety.

    In Illinois: the state health department ended its mask requirement in healthcare settings on May 11, timed with the end of the public health emergency. This petition, authored by patients, doctors, and researchers in Illinois, requests that legislators tell the health department that this choice was a mistake. Illinois residents can sign onto it here.

    For readers outside Illinois who’d like to get involved with these efforts, Mandate Masks US, the COVID Advocacy Initiative, and COVID Safe Campus have compiled a toolkit to advocate for masks in healthcare with political and healthcare organizations. The People’s CDC offers some resources in this area as well. While the advocacy groups’ Week of Action on this issue may have passed (it took place in mid-May), there are still many ways to help push for safer healthcare settings.

    more source spotlights

  • Sources and updates, June 18

    • New York Times COVID-19 tracker is back: After shutting down ahead of the ending federal public health emergency, the New York Times COVID-19 tracker has now resumed updates. Since the tracker is based on CDC data, case numbers and other major metrics are no longer available; but readers can find hospital admissions, deaths, and vaccinations nationally and by state, along with some local data based on hospital service areas. The NYT website doesn’t give much information about why they resumed updates—if anyone reading this can share what happened, please let me know! (And thank you to reader Robin Lloyd who flagged the renewed updates.)
    • CDC Director calls for more data authority: CDC Director Rochelle Walensky appeared in front of Congress this week, speaking to Republican lawmakers for a hearing about her time leading the agency before she steps down at the end of June. One notable trend from the hearing, according to reporting by Rachel Cohrs at STAT News: Walensky acknowledged that the CDC wasn’t able to collect some key COVID-19 data points, such as vaccination rates for COVID-19 patients in hospitals. Walensky called for Congress to give the CDC more authority in collecting data from state and local health departments.
    • CDC expanding its wastewater testing targets: Another CDC update for this week: the agency’s National Wastewater Surveillance System is expanding the pathogens that it will look for in sewage, Genome Web reports. NWSS plans to test for several respiratory viruses (COVID-19, flu, RSV), foodborne infections such as E. coli and norovirus, antimicrobial resistance genes, mpox, and other pathogens that may warrant concern. CDC scientists are working with the company GT Molecular to develop and test new assays. Other wastewater research groups are similarly developing tests to expand the health data that we get from sewage, I’ve learned in reporting for an upcoming story (which will be out later this summer).
    • Genomic surveillance to keep tabs on Omicron’s evolution: CDC researchers invovled with tracking coronavirus variants shared some updates in a study published this week by the agency’s Morbidity and Mortality Weekly Report. As fewer people are getting PCR tests across the U.S., the CDC has access to fewer samples for sequencing than it did at prior points in the pandemic. As a result, scientists have had to update their analytical procedures for using available data to estimate how much different variants are spreading. According to the CDC, Omicron has dominated the U.S. since early 2022, with earlier BA lineages giving way to XBB.
    • Fungal infections increased during the pandemic: In recent years, hospital patients have become increasingly at risk of infection with fungi, which can spread widely in healthcare settings. A new paper from the CDC adds evidence to this trend: fungal infections in hospitals have increased steadily from 2019 through 2021, the researchers found. The researchers also found that patients hospitalized with COVID-19 and a fungal infection had high mortality rates, with almost half of these patients dying in 2020-2021. COVID-19 can disrupt patients’ immune systems and make them more vulnerable to fungi, the researchers suggested. This is a major threat that’s likely to continue in coming years.

  • Updated COVID-19 vaccines are coming this fall

    This past Thursday, the FDA’s advisory committee on vaccines and similar biological products met to discuss COVID-19 boosters for this fall. They voted in favor of updating the vaccines based on Omicron XBB, a variant lineage that has dominated both in the U.S. and globally this year.

    Here are a few key points from the meeting, citing from Your Local Epidemiologist and the Associated Press’ coverage:

    • The fall boosters will be monovalent, meaning they’ll only include the XBB strain—unlike our most recent boosters, which were bivalent (including BA.4/BA.5 and the original, Wuhan strain). The FDA has recommended this switch because research suggests monovalent vaccines may be more effective, and because the original coronavirus strain is no longer circulating; we’re mostly seeing XBB right now.
    • The FDA has not yet decided which exact variant will be used for this fall’s boosters. While experts generally agree that it should be an XBB lineage, the FDA will make a final call on this closer to the fall respiratory virus season. XBB.1.5, XBB.1.9, and XBB.1.16 are all major contenders right now.
    • This fall’s vaccination campaign is likely to prioritize at-risk populations, including seniors and those with medical conditions that damage their immune systems, similar to the bivalent booster shot rollouts. Ongoing vaccine effectiveness research suggests that these groups benefit most from the protection of an additional booster shot, though people not in these groups obviously benefit as well.
    • The CDC will make final decisions about which groups will most need the fall boosters, as well as whether some groups may be eligible for more than one of the shots. Children may also become eligible for new boosters; that’ll be up to the CDC as well.
    • In choosing XBB for the fall boosters, the FDA is standardizing with recommendations from the World Health Organization and European Union, which have also suggested that XBB be the target for the next boosters. Last year, the WHO recommended BA.1, while the U.S. used BA.4/BA.5. Standardizing will be helpful for ongoing data collection, since…
    • Data problems persist: I’ve written a lot about the U.S.’s disadvantages in tracking vaccine effectiveness, particularly compared to other countries with more standardized health systems. This problem has persisted through all rounds of boosters, including the shots planned for this fall; in fact, it’s even harder now for U.S. agencies to monitor how well the vacines work, as the federal public health emergency’s end led to fewer data collection authorities for the CDC. (Safety monitoring systems will continue, though.)

    It’s also worth noting that the boosters this fall will be the first major COVID-19 vaccine rollout following the end of the federal public health emergency. While the Biden administration has devoted some funding for getting vaccines to uninsured Americans, most people will now be getting vaccinated through their health insurance.

    This is certain to make the process more complicated and more challenging for many. I’ve already seen stories of people who are eligible for a second bivalent booster having a hard time getting that shot. (See this recent Death Panel episode, for example.) The federal government is doing very little to improve this situation in time for the fall boosters to arrive—and no matter how well XBB vaccines work in theory, they’ll do little in practice if nobody can actually get them.

    more vaccine coverage
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  • Resources from last week’s community event

    Thank you to everyone who logged onto Slack for last Sunday’s community event! I really appreciated the opportunity to hear your COVID-19 questions and concerns, and I hope the discussion was helpful for those who attended.

    One thing I loved about the event was that it didn’t just consist of me answering questions. The readers who attended also helped answer each other’s questions and shared resources, such as information about air filters and local COVID-safe meet-up groups.

    To bring those resources outside those who attended the event, I’ve compiled the list here:

    For both readers who attended the event and those who didn’t, I would love to hear your feedback. Should I host more of these? If yes, what would you like to discuss at events—general COVID-19 questions, or more focus on specific topics? Is Slack a good platform to use? (I.e., would it be worthwhile to pay for pro options on the server?)

    Let me know what you’re thinking: email me, comment on this blog post, etc. And thank you again to those who attended last Sunday, I learned a lot from all of you.

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  • National numbers, June 18

    National numbers, June 18

    COVID-19 hospital admissions and test positivity (from a select number of labs) are both trending slightly down. Chart from the CDC.

    In the past week (June 4 through 10), the U.S. reported about 6,600 new COVID-19 patients admitted to hospitals, according to the CDC. This amounts to:

    • An average of 950 new admissions each day
    • 2.0 total admissions for every 100,000 Americans
    • 8% fewer new admissions than last week (May 28-June 3)

    Additionally, the U.S. reported:

    • 4.0% of tests in the CDC’s surveillance network came back positive (a 5% decrease from last week)
    • A 5% lower concentration of SARS-CoV-2 in wastewater than last week (as of June 14, per Biobot’s dashboard)
    • 40% of new cases are caused by Omicron XBB.1.5; 26% by XBB.1.16; 21% by XBB.1.9 (as of June 10)

    Overall, the national COVID-19 picture remains fairly similar to what we’ve seen for the last few weeks. The U.S. is at a plateau of COVID-19 spread; we could see an increase this summer, but limited data make it hard to say for sure.

    New hospitalizations for COVID-19 continue to trend slightly down, with just under 1,000 patients admitted each day nationwide. This is the first time that the U.S. has passed this low benchmark since early in the pandemic, and suggests the protective value of vaccinations and prior infections for preventing severe symptoms.

    Biobot Analytics resolved the data issue I mentioned last week and provided updated wastewater numbers, also showing a continued (though slight) downward trend. Current national coronavirus levels are far below this time last year, when Omicron BA.2 variants were spreading widely, though they’re still above prior low points in 2020 and 2021.

    Biobot’s regional data also show mostly plateaus, though coronavirus levels may be increasing very slightly in the Northeast. The CDC’s wastewater data also suggest some places in the Northeast may be seeing increased viral spread, but it’s difficult to identify a clear regional trend.

    Trends from the CDC’s lab testing network similarly show a potential increase in COVID-19 spread in the Northeast over the last couple of weeks, though this testing trend has yet to translate to higher hospitalizations. In New York City, some of the sewersheds that reported recent coronavirus upticks now appear to be trending back down.

    Is a summer surge coming for the Northeast, and then the rest of the country? Right now, it’s quite hard to say; signals from wastewater and testing data are mixed, sometimes delayed, and tough to interpret in the short term. I’ll be watching closely to see how this changes in the coming weeks.

    Meanwhile, it’s important to remember that data are especially limited when it comes to Long COVID, one of the most severe (and most likely) impacts of coronavirus infection. As testing becomes less and less accessible, fewer people will recognize their infections—and, as a result, they may be less likely to recognize later symptoms as Long COVID. But those symptoms can still occur, and cause lasting damage.

    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!

    more source spotlights

  • Sources and updates, June 11

    • Quantifying Long COVID’s impact on day-to-day life: A new study published this week in the BMJ is one of the first I’ve seen to focus not on Long COVID’s symptoms, but on how it impacts quality of life for patients. Researchers at University College London assessed life impacts for about 3,700 Long COVID patients using surveys in an online health platform. The surveys found that “Long COVID can leave people with worse fatigue and quality of life than some cancers, yet the support and understanding is not at the same level,” study coauthor Dr. William Henley said in a statement about the research. This study confirms what I’ve heard from many long-haulers in interviews over the last couple of years.
    • Long COVID and ME/CFS similarities: Another notable Long COVID paper: two leading experts on chronic illness, Dr. Anthony Komaroff at Harvard Medical School and W. Ian Lipkin at Columbia University, wrote a detailed review identifying commonalities between Long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), a debilitating condition with symptoms similar to Long COVID that often occurs after infection. ME/CFS has long been under-recognized and understudied, but there are still lessons from this condition that can inform Long COVID research and lead to answers for both diseases. The review paper points to directions for future study.
    • Metformin for Long COVID: One more Long COVID paper: a study published this week in The Lancet shares results from a Long COVID clinical trial at the University of Minnesota, which found that the diabetes drug metformin reduces the risk of developing long-term symptoms when patients take it early in the course of a COVID-19 case. I shared this study when it was first posted as a preprint in March, and also spoke to one of its authors for my STAT/MuckRock story about the RECOVER initiative. I’m glad to see that the major findings haven’t changed in this peer-reviewed version; metformin appears to be a promising treatment option, though more study is needed.
    • At-home test receives FDA approval: This week, the FDA approved an at-home, rapid COVID-19 test made by the company Cue Health. It’s the first at-home test to receive full approval, as these tests have previously received Emergency Use Authorization under public health emergency rules. With the federal emergency over, the FDA is encouraging test companies to apply for full approval so that at-home COVID-19 tests can be distributed (and marketed) like other commonly-available health products. The emerency authorizations still apply for tests that don’t have full approval yet, though.
    • COVID-19 Medicaid rules led to more coverage for children: For the first three years of the pandemic, federal rules tied to the public health emergency forbid states from kicking their residents off of Medicaid. The policy led to a significant increase in Americans with health insurance—and that includes children, according to a new paper published this week in Health Affairs. For states that changed their Medicaid rules for children due to the pandemic policy, coverage increased by about 5% from 2019 to 2021, representing thousands of kids who were able to get healthcare more easily. Of course, these kids and their family members are now likely to lose their health insurance, as the federal policy ended in April.
    • Animal behaviors changed during 2020 lockdowns: Remember when, in the early days of the pandemic, big cities with more stringent lockdowns saw more wild animals than normal? A new paper from a large coalition of scientists, published this week in Science, finds that this pattern wasn’t just anecdotal: animal behavior really did change. The scientists compiled a large dataset of animals tracked with GPS, representing 2,300 individuals from 43 different mammal species, and compared their behaviors in spring 2020 to the same period in 2019. Animals living in areas under strict lockdowns were more likely to travel outside their normal ranges, the researchers found.

  • Clean air has value beyond COVID-19, the wildfire smoke shows us

    Clean air has value beyond COVID-19, the wildfire smoke shows us

    I left some free masks outside my apartment for my neighbors this week. That orange tint on the photo is from the poor air quality in NYC.

    This week, much of the eastern U.S. was inundated with wildfire smoke that traveled south from Canada. While fires have been blazing across the country for several weeks, some recent particularly-intense wildfires in Quebec led to smoke so full of pollutants, it set poor air quality records in the U.S.

    Americans living in California and other Western states have grown accustomed to wildfire smoke over the last few years; you might remember the orange skies over West Coast cities in fall 2020. But for people on the East Coast (myself included), this week’s smoke was a rude reminder that climate disasters have no borders or boundaries.

    The smoke also reminded us how important clean air is for our health. The same public health measures that help reduce COVID-19 risk can also reduce the impacts of wildfire smoke. High-quality masks filter out both the pollution in smoke and coronavirus particles at the individual level; ventilation improvements do this at the collective level. And these health measures help with other respiratory viruses, other types of pollution, chronic conditions like asthma… the list goes on.

    For COVID-cautious folks like me who still wear masks in public spaces, the smoke situation this week demonstrated that yes, many people are willing to put a mask on if they understand why it’s needed—and if the masks are widely available. In New York City this week, I saw more people wearing masks than I have since the height of the Omicron wave in winter 2021-2022. Public officials encouraged masking and even gave out masks in large numbers.

    In addition to broader mask use, more people have become interested in cleaning the air in their homes and in public spaces. Air filter sales spiked on Amazon this week, CNN reported, as did Google searches for these items. My Twitter feed has been full of recommendations for air-cleaning devices and instructions for building DIY filters.

    This is all great to see, but I hope it’s not just a one-week trend. If we invest in cleaner air now—both individually and collectively—we’ll be more prepared for the next round of wildfire smoke. (While the worst has likely passed for now, we’re likely to see more events like this in the future.) And we’ll be more protected against COVID-19 and other respiratory diseases.

    With that in mind, here are some suggestions that apply to both COVID-19 and air pollution:

    • Stock up on high-quality masks, i.e. N95s and KN95s. This STAT article has some helpful information about which masks work well for COVID-19 protection as compared to air pollution. Notably, for COVID-19 protection, it’s more important to mask inside, while for air pollution protection, it’s more important to mask outside.
    • Buy or make air filters for your home. Air filters can dramatically improve air quality in an indoor space, and you don’t have to spend hundreds of dollars to get one. Corsi-Rosenthal boxes can be easily constructed with less than $100 of materials.
    • Monitor your local air quality. This can include buying a monitor to measure CO2 or pollutants, or following air quality data through public sources. I’ve personally started checking AirNow.gov, a site run by the U.S. government, and IQAir, a crowdsourced air quality tracking site. Checking local air quality data can inform your behavioral choices, similar to checking local COVID-19 statistics.
    • Get involved with mask distribution. This week has shown many people are willing to put on a mask, if they understand why it’s needed and can access one. You can help share information and resources, whether that’s getting involved with a mask distribution group in your area or simply donating individually to friends and neighbors. (For example, I left some free masks outside my apartment building this week.)
    • Advocate for clean air in public spaces. Public buildings can do a lot to improve their air, such as updating HVAC systems and adding air filters to high-traffic spaces. There are already many groups advocating for this, such as parents organizing for ventilation upgrades at their kids’ schools; I hope the recent wildfire smoke adds new motivation to those efforts.

    Do you have other suggestions or resources that you’d like to share with other COVID-19 Data Dispatch readers? Email me, and I’ll send your suggestions in a future newsletter issue.

    More about air quality

  • National numbers, June 11

    National numbers, June 11

    Some NYC sewershed have reported substantial increases in coronavirus levels in recent weeks. Screenshot from the New York State wastewater dashboard.

    In the past week (May 28 through June 3), the U.S. reported about 7,200 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
    • 6% fewer new admissions than last week (May 21-27)

    Additionally, the U.S. reported:

    • 4.2% of tests in the CDC’s surveillance network came back positive (an 8% decrease from last week)
    • 40% of new cases are caused by Omicron XBB.1.5; 26% by XBB.1.16; 21% by XBB.1.9 (as of June 10)
    • (Biobot update delayed)

    Nationally, the COVID-19 situation in the U.S. is similar to where we’ve been for the last few weeks. Major metrics (such as we have them) show an overall plateau in disease spread. Wastewater trends in a few places suggest a summer surge might be coming, but it’s hard to say for sure.

    Hospital admissions and test positivity (from the specific network of labs reporting to the CDC) are trending slightly down at the national level. But there are still about 1,000 people being hospitalized with COVID-19 every day.

    Biobot Analytics, my usual go-to source for wastewater surveillance data, did not update their dashboard this week due to a tech issue. The company’s most recent data, as of May 29, show plateaus in all four major regions.

    The CDC’s National Wastewater Surveillance System (NWSS) shows a similar picture. Among about 1,100 sewage testing sites that recently reported to the CDC, 60% reported decreases in coronavirus levels in the last two weeks while 40% reported increases.

    New York City is one of the places seeing wastewater increases, as I noted last week. Patterns differ somewhat across the city’s fourteen sewersheds, with some reporting more than 1000% increases in wastewater levels in recent weeks while others are still in plateaus.

    Both the New York/New Jersey and New England regions are reporting slight upticks in their test positivity, according to the CDC’s surveillance network. This (along with the trends in NYC’s sewage) could be a precursor of more COVID-19 spread this summer, but it’s currently hard to say for sure.

    The CDC updated its variant estimates (now reported every other week) this past Friday. XBB.1.5 is still the most common lineage, causing an estimated 40% of cases, the CDC reports. XBB.1.16 and XBB.1.9 continue to outcompete it, causing about 26% and 21% of cases respectively.

    These newer lineages have yet to contribute to a significant shift in transmission, from what I can tell. We have yet to see if past immunity in the U.S. can hold off against the ever-evolving Omicron variants this summer.

    more national numbers