COVID-19 Data Dispatch

Category: Federal data

  • New wastewater surveillance report highlights need for expansion, standardization

    New wastewater surveillance report highlights need for expansion, standardization

    Nearly a year after the CDC’s National Wastewater Surveillance System began reporting public data, the system still has very unequal representation across the U.S.

    This week, the National Academies of Sciences, Engineering, and Medicine (NASEM) released a major report about the state of wastewater surveillance for infectious diseases in the U.S. The report, written by a committee of top experts (and peer-reviewed before its release), is an extensive description of the promise and the challenges of wastewater testing.

    Its authors describe how a grassroots network of researchers, public officials, and wastewater treatment plant staff developed strategies for sewage testing, analysis, and communicating results. Now, as committee chair Guy Hughes Palmer writes in the report’s introduction, broader collaboration and resources are needed to “solidify this emergency response to the COVID-19 pandemic into a national system” that continues to monitor COVID-19 as well as other public health threats. To this end, the report includes specific recommendations for the CDC’s National Wastewater Surveillance System.

    Here are some key findings from the report, taken from its summary section and a NASEM webinar presentation last Thursday:

    • Overall, the report finds that wastewater surveillance data “are useful for informing public health action and that wastewater surveillance is worthy of further development and continued investment.” The authors recommend that public agencies at all levels keep funding and promoting this monitoring tool.
    • Wastewater surveillance is not a new technology; it’s been used for decades to monitor the spread of polio. But COVID-19 led to widespread adoption of this technology and innovation into how it could be used, driven by some municipalities and universities that were early to embrace wastewater.
    • As a population-level tool, wastewater surveillance provides data on how diseases spread through a community without relying on access to clinical testing. This surveillance is becoming more important for COVID-19 as people opt for at-home tests over PCR tests, and should be used specifically to track new variants.
    • Community sewersheds that may be tested range in size from serving hundreds of people to serving millions; they also differ based on geography, demographics, and many other factors. As a result, early researchers in this space developed testing and analysis methods that were specific to their communities.
    • Now, however, the CDC faces a challenge: “to unify sampling design, analytical methods, and data interpretation to create a truly representative national system while maintaining continued innovation.” In other words, standardize the system while allowing local communities to keep doing what works best for them.
    • Sites in the CDC’s National Wastewater Surveillance System (NWSS) are currently not representative of the U.S. as a whole, as the system is based on wastewater utilities and public health agencies choosing to participate.
    • The CDC needs to expand this system to be more equitable across the country, with targeted outreach, offering resources to sites not currently participating, and other similar tactics. This expansion process should be open and transparent, the report’s authors write.
    • As NWSS expands, the CDC should select and prioritize “sentinel sites” that can help detect new coronavirus variants and other new emerging health threats early on. These sites might include international airports as well as zoos and livestock farms, where potential animal-to-human transmission may be monitored.
    • Better public communication is needed: the CDC (and other agencies) should improve its public outreach about wastewater data, including addressing any privacy concerns that people may have. The report specifically recommends that the CDC “convene an ethics advisory committee” to assist with privacy concerns and data-sharing concerns.
    • In assessing potential new targets for wastewater surveillance, the report recommends three criteria: “(1) public health significance of the threat, (2) analytical feasibility for wastewater surveillance, and (3) usefulness of community-level wastewater surveillance data to inform public health action.”
    • NWSS needs more funding from the federal government to expand its sites, continue its COVID-19 tracking efforts, fund projects at state and local levels, and pivot to new public health threats as needed. This funding needs to be “predictable and sustained,” the report’s authors write.

    In related news: I just updated the COVID-19 Data Dispatch’s resource page for wastewater data dashboards in the U.S.

    • The dashboard now includes information on four national dashboards, 24 state dashboards, seven local dashboards, and four regional dashboards.
    • New states added in this update: Illinois (see last week’s source shout-out for more details), as well as Vermont and New Hampshire.

    As always, please reach out if you see any errors on the page or would like to recommend a new source!

    More wastewater data

  • Looking ahead to the big COVID-19 stories of 2023

    Looking ahead to the big COVID-19 stories of 2023

    The number of sites reporting to the National Wastewater Surveillance System (see the black line) has declined in recent weeks. This may be a worrying trend going into 2023.

    It’s the fourth year of the pandemic. I’ve written this statement in a few pitches and planning documents recently, and was struck by how it feels simultaneously unbelievable—wasn’t March 2020, like, yesterday?—and not believable enough—haven’t we been doing this pandemic thing for an eternity already?

    As someone who’s been reporting on COVID-19 since the beginning, a new year is a good opportunity to parse out that feels-like-eternity. So this week, I reflected on the major trends and topics I hope to cover in 2023—both building on my work from prior years and taking it in new directions.

    (Note: I actually planned to do this post last week, but then XBB.1.5 took higher priority. Hence its arrival two weeks into the new year.)

    Expansions of wastewater, and other new forms of disease surveillance

    As 2022 brought on the decline of large-scale PCR testing, wastewater surveillance has proven itself as a way to more accurately track COVID-19 at the population level—even as some health departments remain wary of its utility. We also saw the technology’s use for tracking monkeypox, polio, and other conditions: the WastewaterSCAN project, for example, now reports on six different diseases.

    This year, I expect that wastewater researchers and public agencies will continue expanding their use of this surveillance technology. That will likely mean more diseases as well as more specific testing locations, in addition to entire sewersheds. For example, we’re already seeing wastewater testing on airplanes. I’m also interested in following other, newer methods for tracking diseases, such as air quality monitors and wearable devices.

    At the same time, these surveillance technologies will continue to face challenges around standardization and public buy-in. The CDC’s big contract with Biobot expires this month, and I’ve already noticed a decline in sites with recent data on the agency’s dashboard—will CDC officials and local agencies step in to fill gaps, or will wastewater testing become even more sporadic?

    New variants, and how we track them

    For scientists who track the coronavirus’ continued evolution, 2022 was the year of Omicron. We didn’t see all-new virus lineages sweeping the world; instead, Omicron just kept mutating, and mutating, and mutating. It seems likely that this pattern will continue in 2023, but experts need to continue watching the mutation landscape and preparing for anything truly concerning.

    With declining PCR testing, public agencies and companies that track variants have fewer samples to sequence. (This led to challenges for the CDC team tracking XBB.1.5 over the holidays.) As a result, I believe 2023 will see increased creativity in how we keep an eye on these variants—whether that’s sequencing wastewater samples, taking samples directly from healthcare settings, increased focus on travel surveillance, or other methods.

    Public health experts—and journalists like myself—also need to rethink how we communicate about variants. It’s no longer true that every new, somewhat-more-contagious variant warrants alarm bells: variants can take off in some countries or regions while having relatively little impact in others, thanks to differences in prior immunity, seasonality, behavior, etc. But new variants still contribute to continued reinfections, severe symptoms, Long COVID, and other impacts of COVID-19. Grid’s Jonathan Lambert recently wrote a helpful article exploring these communication challenges.

    Long COVID and related chronic diseases

    As regular readers likely know, Long COVID has been an increased topic of interest for me over the last two years. I’ve covered everything from disability benefits to mental health challenges, and am now leading a major project at MuckRock that will focus on government accountability for the Long COVID crisis.

    Long COVID is the epidemic following the pandemic. Millions of Americans are disabled by this condition, whether they’ve been pushed out of work or are managing milder lingering symptoms. Some people are approaching their three-year anniversary of first getting sick, yet they’ve received a fraction of the government response that acute COVID-19 got. Major research projects are going in the wrong directions, while major media publications often publish articles with incorrect science.

    For me, seeing poor Long COVID coverage elsewhere is great motivation to continue reporting on this topic myself, at MuckRock and other outlets. I’m also planning to spend more time reading about (and hopefully covering) other chronic diseases that are co-diagnosed with Long COVID, like ME/CFS and dysautonomia.

    Ending the federal public health emergency.

    Last year, we saw many state and local health agencies transition from treating COVID-19 as a health emergency to treating it as an endemic disease, like the many others that they respond to on a routine basis. This transition often accompanied changes in data reporting, such as shifts from daily to weekly COVID-19 updates.

    This year, the federal government will likely do the same thing. POLITICO reported this week that the Biden administration is renewing the federal public health emergency in January, but will likely allow it to expire in the spring or summer. The Department of Health and Human Services has committed to telling state leaders about this expiration 60 days before it happens.

    I previously wrote about what the end of the federal emergency could mean for COVID-19 data: changes will include less authority for the CDC, less funding for state and local health departments, and vaccines and treatments controlled by private markets rather than the federal government. I anticipate following up on this reporting when the emergency actually ends.

    Transforming the U.S. public health system

    Finally, I intend to follow how public health agencies learn from—or fail to learn from—the pandemic. COVID-19 exposed so many cracks in America’s public health system, from out-of-date electronic records systems to communication and trust issues. The pandemic should be a wakeup call for agencies to get their act together, before a new crisis hits.

    But will that actually happen? Rachel Cohrs has a great piece in STAT this week about the challenges that systemic public health reform faces, including a lack of funding from Congress and disagreements among experts on what changes are necessary. Still, the window for change is open right now, and it may not be at this point in 2024.

    More federal data

  • How official death data underestimate COVID-19’s inequities

    How official death data underestimate COVID-19’s inequities

    In the last week of December, I had a major story published at MuckRock, USA TODAY, and local newsrooms in Arizona, Oregon, and Texas. The story explains that official COVID-19 statistics underestimate the pandemic’s true toll—particularly on people of color, who are more likely to have their deaths inaccurately represented in mortality data.

    This story was part of Uncounted, MuckRock’s broader project to investigate death certificate errors and other death reporting issues uncovered by looking at all excess deaths during the pandemic, not just those deaths officially marked as COVID-19. It relies on data from the CDC’s provisional mortality statistics and excess death estimates by a team of demography researchers at Boston University led by Andrew Stokes.

    I’ve copied the introductory section of the story here, because I don’t think anything else I write would do a better job at summarizing it. I encourage you to read the full piece; it is the biggest (and likely most important) story that I wrote in 2022.

    It’s not always easy to identify a COVID-19 death.

    If someone dies at home, if they have symptoms not typically associated with the disease or if they die when local health systems are overwhelmed, their death certificate might say “heart disease” or “natural causes” when COVID-19 is, in fact, at fault.

    New research shows such inaccuracies also are more likely for Americans who are Black, Hispanic, Asian or Native.

    The true toll of the COVID-19 pandemic on many communities of color – from Portland, Oregon, to Navajo Nation tribal lands in Arizona, New Mexico and Utah, to sparsely populated rural Texas towns – is worse than previously known.

    Incorrect death certificates add to the racial and ethnic health disparities exacerbated by the pandemic, which stem from long-entrenched barriers to medical care, employment, education, housing and other factors. Mortality data from the Centers for Disease Control and Prevention point to COVID-19’s disastrous impacts, in a new analysis by the Documenting COVID-19 Project at Columbia University’s Brown Institute for Media Innovation and MuckRock, in collaboration with Boston University’s School of Global Public Health; the USA TODAY Network; the Arizona Center for Investigative Reporting; Willamette Week in Portland; and the Texas Observer.

    The data shows that deaths from causes the CDC and physicians routinely link to COVID– including heart disease, respiratory illnesses, diabetes and hypertension–have soared and remained high for certain racial and ethnic groups.

    In Arizona’s Navajo and Apache counties, which share territory with Navajo Nation, COVID deaths among Native Americans drove nation-leading excess death rates in 2020 and 2021. While COVID death rates among Natives dropped during the second year of the pandemic thanks to local health efforts, other causes of death such as car accidents and alcohol poisoning increased significantly from 2020 to 2021.

    In Portland, deaths from causes indirectly related to the pandemic went up in 2021 even as official COVID deaths remained relatively constant. Black residents were disproportionately impacted by some of these causes, such as heart disease and overdose deaths – despite a county-wide commitment to addressing racism as a public health threat.

    In Texas, smaller, rural counties served by Justices of the Peace were more likely to report potential undercounting of COVID deaths than larger, urban counties served by medical examiners. Justices of the Peace receive limited training in filling out death certificates and often do not have sufficient access to postmortem COVID testing, local experts say.

    Experts point to several reasons for increased inaccurate death certificates among non-white Americans. These include resources available for death investigations, the use of general or unknown causes on death certificates, and how the race and ethnicity fields of these certificates are filled out.

    Such barriers to accurate death reporting add on to existing health disparities that made non-white Americans more susceptible to COVID in 2021, despite widespread vaccination campaigns and health equity efforts.

    “Even if you try to level the playing field, from the jump, certain populations are dealing with things that put them at greater risk,” said Enrique Neblett, a health equity expert at the University of Michigan’s School of Public Health. These issues include higher exposure to COVID, as people of color are overrepresented among essential workers, as well as higher rates of chronic conditions that confer risk for severe disease. “Those things aren’t eliminated just by increasing access to a vaccine,” Neblett said.

    It is critical to improve data collection and reporting for deaths beyond those officially labeled as COVID because data is a “major political determinant of health,” said Daniel Dawes, executive director of the Satcher Health Leadership Institute at the Morehouse School of Medicine. Information on how people are dying in a particular community can shape priorities for local public health departments and funding for health initiatives.

    “If there is no data, there is no problem,” Dawes said.

  • COVID source callout: CDC archives public datasets

    COVID source callout: CDC archives public datasets

    The CDC has archived a couple of major datasets providing COVID-19 cases and deaths by state and county.

    The CDC is now updating its COVID-19 cases and deaths data weekly, instead of daily, as I covered last week. This shift goes beyond the agency’s public dashboard: the CDC has also archived datasets with state- and county-level data providing COVID-19 cases and deaths, which were previously updated daily on data.cdc.gov.

    These datasets previously included the underlying numbers behind the CDC’s dashboard, allowing data-savvy Americans to produce their own analysis and visualizations. I learned about the archiving via a Twitter thread by Iowa data expert Sara Anne Willette, who uses the CDC’s data to update an independent dashboard tracking COVID-19 in her state.

    https://twitter.com/amethystarlight/status/1585760819320872961

    To replace these daily datasets, the CDC has posted a new dataset, “Weekly COVID-19 County Level of Community Transmission Historical Changes.” It appears to provide COVID-19 cases and test positivity rates by county, by week—but the data aren’t actually available yet. This dataset currently includes zero rows while the CDC resolves a “processing issue.”

    None of this is particularly surprising, considering that the CDC is clearly deprioritizing COVID-19 tracking and allocating its data analysis resources elsewhere. But it remains frustrating for those of us who still want to know what’s going on with COVID-19 in our communities.

    more source spotlights
  • The U.S.’s flu and RSV surveillance is insufficient for tracking this fall’s outbreaks

    The U.S.’s flu and RSV surveillance is insufficient for tracking this fall’s outbreaks

    The CDC’s FluView dashboard does not provide precise case numbers, only an approximation of “activity level.”

    I recently received a question from a reader, asking how to follow both COVID-19 and the flu in the county where she lives. For COVID-19, county-level data sources aren’t too hard to find: the CDC still provides some clinical data—though case numbers are now updated weekly, instead of daily—and many counties have wastewater surveillance available. (See last week’s post for more details.)

    But following flu transmission is much harder: there’s no county-level tracking of this virus. The same thing goes for respiratory syncytial virus (RSV), a virus currently sending record cases to children’s hospitals across the country. There are a few data sources available, which I’ll list later in this post, though nothing as comprehensive as what we’ve come to expect for COVID-19.

    As I’ve previously written, the COVID-19 pandemic inspired nationwide disease surveillance at a level the U.S. has never seen before. The healthcare and public health systems had not previously attempted to count up every case of a widely-spreading virus and share that information back to the public in close-to-real-time.

    It’s unlikely that flu, RSV, and other diseases will get the same resources as COVID-19 did for intensive tracking—at least not in the near future. But the scale of data we’ve had during the pandemic reveals that our current surveillance for these diseases is pretty inadequate, even for such basic purposes as giving hospitals advanced warning about new surges. 

    Insufficient RSV data

    A recent CNN story by Deidre McPhillips and Jacqueline Howard explains how data gaps have hindered preparation for the current RSV surge. The reporters explain that the CDC’s RSV data are “based on voluntary reporting from a few dozen labs that represent about a tenth of the population.” The CDC uses these reports to provide weekly estimates about RSV cases, though recent data tend to be incomplete due to reporting delays.

    Here’s a helpful quote from the story (though I recommend reading the whole piece):

    “For hospitals [using CDC data], it’s a little like looking through the rearview mirror. They’ve already begun to experience that uptick in cases themselves before it’s noticeable in the federal data,” said Nancy Foster, vice president for quality and patient safety with the American Hospital Association.

    “We’re talking about data that are collected inside hospitals, transmitted through a data trail to get to the federal government, analyzed there and then fed back to hospitals.”

    In other words, it’s not surprising that we saw plenty of stories about higher-than-normal RSV cases in children’s hospitals before national data actually picked up the surge. For more details on why RSV is spreading this fall and how it’s impacting children’s hospitals, I recommend this piece by Jonathan Lambert at Grid.

    Insufficient flu data

    Meanwhile, this year’s flu season is clearly starting earlier than normal; but current data aren’t able to tell us how severe the season might get or who, exactly, is being hit the hardest. According to the CDC’s flu surveillance report for this week, the agency estimates that the U.S. has seen “at least 880,000 flu illnesses, 6,900 hospitalizations, and 360 deaths from flu” so far this fall.

    The CDC’s estimates come from networks of testing labs, hospitals, and outpatient healthcare providers that participate in the agency’s flu surveillance networks. National flu data tend to be imprecise estimates, clearly labeled as “preliminary” by the CDC, while state-by-state data are estimates reported with delays. Note, for example, that the CDC’s map of “influenza-like-activity” by state and by metro area provides only general categories of activity (ranging from “minimal” to “very high”) rather than actual case numbers.

    The flu data we have so far aren’t sufficient for making predictions about how the rest of this fall and winter will go, explains STAT’s Helen Branswell in a recent story. “The virus is maddeningly unpredictable,” she writes. U.S. experts often look to the flu season in the Southern Hemisphere, which precedes ours, for clues, but this can be unreliable (just as the U.S. shouldn’t rely on other countries for all its vaccine effectiveness data).

    For both flu and RSV, one major problem with our surveillance methods is that our systems overly rely on healthcare centers. When public health agencies have to wait for hospitals and clinics to report cases of these viruses before starting to analyze data, they miss the opportunity to warn healthcare providers at the very beginning of a surge—and give them time to prepare.

    In the future, expanding non-clinical surveillance methods like wastewater and population surveys to these diseases would provide more data, more quickly; both for healthcare providers and for the general public. (I provided some more specific ideas here.)

    Existing sources

    With all the above caveats in mind, here are a few sources you can look at to track flu and RSV:

    • CDC’s weekly flu surveillance report: This page is updated once a week with national estimates of flu activity, hospitalizations, flu virus variants, and more. Data tend to be preliminary.
    • CDC’s FluView dashboard: Information from the CDC’s flu surveillance system also appears on this dashboard in a more interactive format; for example, you can see how flu activity by state has changed over time.
    • CDC’s RSV trends report: Similar to its flu reports, the CDC provides weekly updates of estimated RSV tests and cases, including national, regional, and state-by-state trends.
    • Walgreens flu index: Walgreens tracks prescriptions for antiviral medications at its pharmacies as a proxy for flu activity, by state and for select metro areas. For more information on the index, see this press release.
    • WastewaterSCAN: The SCAN network, run by researchers at Stanford University and Emory University, tests wastewater for flu, RSV, and monkeypox in addition to COVID-19 in select counties across the U.S. So far, this network is the first I know of to publicly share flu and RSV wastewater data, though other researchers are working in this area.

    Please let me know if I missed any data sources! (You can email me or comment below.)

    More federal data

  • Interpreting COVID-19 data as the CDC goes weekly and a fall surge approaches

    Interpreting COVID-19 data as the CDC goes weekly and a fall surge approaches

    As of this week, the CDC has switched to reporting COVID-19 cases and deaths on a weekly basis.

    As of this Thursday, the CDC is updating COVID-19 case and death data every week instead of every day. Here are some thoughts on interpreting COVID-19 data in the wake of this change, citing an article I recently wrote for The Atlantic.

    To me, the CDC’s shift to weekly updates feels like the end of an era for tracking COVID-19. While I understand the change, considering both our less-complete case information and other data analysis needs for the agency, I can’t help but wish we had a national public health agency with enough resources to continue providing us with frequent, reliable information on this ongoing pandemic. After all, shouldn’t that be the CDC’s job?

    The CDC has clearly deprioritized two major metrics (cases and deaths) that used to be the first places people looked to see the pandemic’s impact on their communities. Instead, the agency now points us to hospitalization metrics, variant surveillance, and wastewater—all metrics that are certainly useful, but may be harder for the average user to interpret.

    And even the case data we do have are quite unreliable at this point, as PCR tests become less and less accessible compared to rapid tests. Case numbers may be underreported by twenty times or more; it’s difficult to even get a good estimate of how far off the numbers are. Public communications like the CDC’s “Weekly Review” report fail to acknowledge this problem, and the agency does not appear to be making any effort to determine the true infection rates right now. 

    Through its current data communication choices, the CDC seems to be saying, “If you still care about keeping track of COVID-19, you’re on your own.” Even though we are likely heading for a fall surge and many people need to keep track of this disease in order to keep their communities safe.

    In absence of useful information from our public health leaders, it falls on us to survey the best available data sources and help others interpret them. My article in The Atlantic takes on this question, focusing on wastewater surveillance and population surveys as particularly useful sources we should consider right now.

    Interpreting wastewater data

    Wastewater data, unlike case data, don’t require people to actively go out and get tested: if their public sewer system is getting sampled for COVID-19, they will automatically be included in the data. You can look for wastewater surveillance in your area on Biobot’s dashboard, the CDC’s dashboard, or other state and local dashboards, depending on where you live. (I have a list of state dashboards here.)

    But interpreting wastewater data can be pretty different from interpreting case data. Here are a couple of key tips for approaching this source, based on my interview with Biobot president and cofounder Newsha Ghaeli:

    • Look at “directionality” and “magnitude.” “Directionality” means whether viral levels are going up or down, and “magnitude” means how they compare with earlier points in the pandemic. To quote from the story: “A 10 percent uptick when levels are low is less concerning than a 10 percent uptick when the virus is already spreading widely.”
    • If you do not have public wastewater data for your county, data from a neighboring county still provides useful info. When we talked, Ghaeli gave the example of a New York City resident looking at data from New Jersey or Connecticut counties neighboring the city: as people from these areas commute into NYC, a surge in one place could quickly drive a surge in the other.
    • Wastewater data are not a perfect proxy for infections. Scientists are still learning about how to best use this newer surveillance tool. Unlike clinical metrics (like cases), wastewater data can differ based on local environmental factors, and it often takes a long time for researchers to build useful interpretations of their communities. (See my past FiveThirtyEight story for more detail on this.)
    • These data can’t tell you who is getting sick. To comprehensively answer demographic questions, we need to actively survey people in our communities and ask them about their experiences with COVID-19. (See the story for more about how this works.)

    Other interpretation tips

    Beyond looking at wastewater data, here are a couple of tips I received from experts for readers seeking to watch their local COVID-19 numbers this fall:

    • “Look as local as you can,” said Pandemic Prevention Initiative expert Sam Scarpino. In other words, if you can find data for your individual county or even ZIP code, go there. 
    • Check multiple sources, and try to “triangulate” between them, said City University of New York epidemiologist Denis Nash. (I’ve provided similar advice in past posts like this one.)
    • Consider local events and behavior, Scarpino said. Quoting from the story: “If a popular community event or holiday happened recently, low case numbers might need to be taken with a grain of salt.”

    I also wanted to give a quick shout-out here to the People’s CDC, a volunteer science communication and advocacy organization. If you’re looking for more thoughtful analysis of national COVID-19 data, their weekly “weather reports” are a really helpful and accessible source. The organization also provides resources to help people push for more COVID-19 safety measures in their communities. 

    “People do want layers of protection, they do want to keep themselves in each other safe from COVID,” said Mary Jirmanus Saba, a geographer and volunteer with the People’s CDC whom I interviewed (with a couple of other volunteers) for my story. The weather reports and other similar initiatives help the organization’s followers “see that we really are there for each other,” she said.

    More wastewater reporting

  • COVID source callout: CDC shifts to weekly updates

    This week, the CDC announced a big change to its COVID-19 data reporting: instead of updating case and death numbers daily, the figures will be updated weekly. The change comes into effect on October 20.

    Under the new schedule, data updates will be cut off on Wednesdays, though it’s unclear if the CDC will actually update its dashboard on Wednesdays or if this will happen on a day later in the week.

    According to the CDC’s data FAQ page, this change was made “to allow for additional reporting flexibility, reduce the reporting burden on states and jurisdictions, and maximize surveillance resources.” To me, this makes a lot of sense: as case data become increasingly less reliable (thanks to increased at-home testing, closing PCR sites, etc.), daily updates can be more misleading than they are valuable. Most states are not reporting daily data either.

    Also, much as it pains me to say this, the CDC’s COVID-19 dashboard is very likely not getting the views and attention that it received one or two years ago. If this change frees up agency data scientists to work on new tracking mechanisms that will be more useful, that seems like a fair trade-off to me. But it’s still a bummer to see the daily data go, especially at a time when we really need information to track a potential fall surge.

    Worth noting: the HHS Community Profile Reports are updating on a weekly cadence now as well.

    more source spotlights
  • Orders of free at-home COVID-19 tests varied widely by state

    Orders of free at-home COVID-19 tests varied widely by state

    On September 2, 2022, the federal government stopped taking orders for free at-home COVID-19 tests. The distribution program, which launched during the first Omicron surge in early 2022, allowed households to order free tests up to three times, with either four or eight tests in each order.

    The day this program ended, I sent a public records request to the federal government asking for data on how many tests were distributed. I filed it through MuckRock’s portal, so both the original request and my correspondence with the U.S. Postal Service’s records office are publicly available.

    Last week, the USPS fulfilled my request. While I’d requested data by state, county, and/or ZIP code, the agency only sent over at-home test orders and distribution numbers by state. According to the formal response letter they sent, more granular data would (somehow) count as “commercial information” and is therefore exempt from FOIA.

    https://twitter.com/betsyladyzhets/status/1574410510476496897/

    Now, obviously, I think that far more data on the test distribution program should be publicly available. As I wrote back in January when the program started, in order to truly evaluate the success of this program, we need test distribution numbers by more specific geographies and demographic groups.

    Still, the state-by-state data are better than nothing. With these data, we can see that states with the highest volume of at-home test orders fall on the East and West coasts, with people living in the South and Midwest less likely to use the program.

    (The population data that I used to calculate these per capita rates are from the HHS Community Profile Report.)

    With the data from my FOIA request, we can see that states with higher vaccination rates also had more people taking advantage of the free COVID-19 test program. States like Vermont and Hawaii rank high up for both metrics, while states like North Dakota and Wyoming are on the lower end for both.

    At the same time, many of the states where fewer people ordered the free tests are also states that saw higher COVID-19 death rates in 2022. In Mississippi, for example, about 433 people died of COVID-19 for every 100,000 residents since the year started—the highest death rate of any state. But people in the state ordered free tests at a rate under 0.3 per capita.

    These charts basically confirm what many public health experts suspected about the free COVID-19 test program: Americans who already were more protected against COVID-19 (thanks to vaccination) were most likely to order tests. Just as we’re seeing now with the Omicron-specific booster shots, a valuable public health measure went under-utilized here.

    I invite other journalists to report on these data; if you do, please link back to my original FOIA request on MuckRock!

    More testing data

  • 12 statistics showing the pandemic isn’t over

    12 statistics showing the pandemic isn’t over

    Long COVID and ME/CFS patients protest in front of the White House, telling Biden that the pandemic is not over and demanding action on their conditions. Image courtesy of ME Action.

    Last Sunday, 60 Minutes aired an interview with President Joe Biden in which he declared the pandemic is “over.”

    “The pandemic is over,” Biden said, while walking through the Detroit Auto Show with 60 Minutes correspondent Scott Pelley. “We still have a problem with COVID. We’re still doing a lot of work on it. But the pandemic is over. If you notice, nobody’s wearing masks, everybody seems to be in pretty good shape.”

    Most of the debate and dissection of this interview has focused on Biden’s statement that the “pandemic is over.” Is it, actually? (Epidemiologists say no.) Does he have the authority to declare it over? (No, that’s a job for the WHO.) Was his statement just reflecting what most Americans are already thinking? (Depends on who you call “most Americans.”)

    See, I think the key part of Biden’s quote here actually comes at the end: “everybody seems to be in pretty good shape.” Seems to be is doing a lot of work here. In the interview, Biden is strolling through the auto show, through groups of unmasked people looking at car exhibits.

    He is not actually talking to these bystanders, asking them whether they’ve lost loved ones to COVID-19, lost work during the pandemic, or faced any lingering symptoms after catching the virus themselves. Biden also isn’t considering the people who were excluded from this auto show: the Americans who were left disabled with Long COVID, and those still taking safety precautions due to other health conditions.

    Images of the auto show, like those of packed indoor restaurants or maskless stadiums, seem to suggest that, yeah, Americans no longer care about COVID-19. But there are plenty of other images that don’t make it into high-profile media settings like Biden’s interview. 

    Today, I invite you to consider a few of the images that Biden isn’t seeing. Here are 12 statistics showing how the COVID-19 pandemic continues to have a massive impact on Americans:

    • At least 400 Americans are dying with COVID-19 every day, about 47,000 deaths total between June and September 2022. Daily death data tend to be underestimates, because it can take weeks to process death certificates (and numbers are often retroactively edited up). But we can still see that hundreds of people are dying each day. As Sarah Zhang points out in The Atlantic, this is several times the threshold experts set in early 2021 for calling the pandemic at an end.
    • About 25,000 people are currently hospitalized with COVID-19 cases. Yes, many of the people included in this statistic probably entered the hospital for another reason, then tested positive as part of routine screening. But incidental coronavirus infections still put pressure on the hospitals caring for these patients, and can intersect with a wide variety of other health conditions, potentially causing long-term issues for patients.
    • About 7.6% of adults are currently experiencing some form of Long COVID, as of early August. This estimate, which I pulled from the Census and CDC’s Household Pulse Survey, rises for certain demographics: almost 10% of women, 11% of transgender adults, 11% of adults with less than a high school diploma, and 15% of adults with a disability are currently experiencing Long COVID.
    • Hundreds of Long COVID and ME/CFS patients protested at the White House and online on Monday. Biden’s statement coincidentally landed the night before a planned protest, in which patient-advocates called for the president to declare a national emergency around Long COVID and ME/CFS. The protest was covered in the New York Times, MedPage Today, the BMJ, and other outlets.
    • 19 patients, patient-advocates, and experts testified at a New York City Council hearing about Long COVID and gender on Thursday. Long COVID patients and those with related conditions (like ME/CFS and HIV) talked about dismissals from doctors and inability to return to their pre-COVID lives. They called for more comprehensive medical care and other forms of financial and social support for patients. I covered the hearing for Gothamist/WNYC.
    • About 2.5 million adults were recently out of work due to a COVID-19 case, either because they were sick themselves or were caring for a sick person. Another 1.6 million adults were out of work due to concern about getting or spreading COVID-19. These statistics come from the most recent iteration of the Household Pulse Survey, conducted from July 27 to August 8, 2022.
    • About 2.2 million adults were recently laid off or furloughed due to the COVID-19 pandemic. Another one million had their employers go out of business due to the pandemic, and 900,000 had their employers close temporarily due to COVID-19. These data are from the same Household Pulse Survey.
    • Over 50 million adults experienced symptoms of anxiety for at least half the days in the last two weeks, at the time of the most recent Household Pulse Survey. Almost 40 million adults experienced symptoms of depression for at least half the days in the same two-week period.
    • Over 80% of Americans still support the federal government providing free COVID-19 vaccines, treatments, and tests to anyone who needs them, according to an Axios-Ipsos poll conducted in early September. A past iteration of that poll, from March 2022, found that 74% of Americans reported they were “likely to wear a mask outside the home if COVID-19 cases surge again in their area.”
    • About 3% of Americans, or around 12 million people, are immunocompromised and still have reason to take intense COVID-19 precautions. Immunocompromised people have been eligible for extra vaccine doses, but are still more vulnerable to both severe COVID-19 symptoms and Long COVID.
    • Over one million seniors live in nursing homes, and almost one million more live in assisted living and other forms of long-term care facilities. Seniors in long-term care have represented a hugely disproportionate share of deaths from COVID-19, and the CDC just made its mask recommendations for these facilities much more lenient—putting many vulnerable adults at risk.
    • 2.5 billion people worldwide still haven’t been vaccinated, according to estimates from Our World in Data. Bloomberg’s vaccine tracker estimates that, at the current pace of first doses administered, it will take another 10 months for just 75% of the global population to have received at least one COVID-19 shot. As long as COVID-19 continues to spread anywhere in the world, new variants can be a threat everywhere.

    More on Long COVID

  • Potential data fragmentation when the federal COVID-19 public health emergency ends

    Potential data fragmentation when the federal COVID-19 public health emergency ends

    About half of U.S. states have D or F grades on their breakthrough case reporting, according to the Pandemic Prevention Institute and Pandemic Tracking Collective. Other metrics could be heading in this direction next year.

    COVID-19 is still a public health emergency. At the moment, this is true according to both the general definition of this term and official declarations by the federal government. But the latter could change in the coming months, likely leading to more fragmentation in U.S. COVID-19 data.

    A reader recently asked me about the federal government’s ability to compile and report COVID-19 data, using our new anonymous Google form. They asked: “Will the CDC at some point stop reporting COVID data even though it may still be circulating, or is it a required, reportable disease?”

    It’s difficult to predict what the CDC will do, as we’ve seen in the agency’s many twists and turns throughout the pandemic. That said, my best guess here is that the CDC will always provide COVID-19 data in some form; but the agency could be severely limited in data collection and reporting based on the disease’s federal status.

    The CDC’s authority

    One crucial thing to understand here is that the CDC does not actually have much power over state and local public health departments. It can issue guidance, request data, distribute funding, and so forth, but it isn’t able to require data collection in many circumstances.

    Here’s Marc Lipsitch, an epidemiologist at Harvard’s public health school and interim director of science at the CDC’s Center for Forecasting and Outbreak Analytics, explaining this dynamic. This quote is from an interview that I conducted back in May for my FiveThirtyEight story on the new center:

    Outside of a public health emergency, CDC has no authority to require states to share data. And even in an emergency, for example, if you look on the COVID Data Tracker, there are systems that have half the states or some of the states. That’s because those were the ones that were willing to share. And that is a very big handicap of doing good modeling and good tracking… Everything you’re trying to measure, for any decision, is better if you measure it in all the states.

    Consider breakthrough cases as one example. According to the Pandemic Prevention Institute’s scorecard for breakthrough data reporting, about half of U.S. states have D or F grades, meaning that they are reporting zero or very limited data on post-vaccination COVID-19 cases. The number of states with failing grades has increased in recent months, as states reduce their COVID-19 data resources. As a result, federal agencies have an incomplete picture of vaccine effectiveness.

    Wastewater data is another example. While the CDC is able to compile data from all state and local public health departments with their own wastewater surveillance systems—and can pay Biobot to expand the surveillance network—the agency has no ability to actually require states to track COVID-19 through sewage. This lack of authority contributes to the CDC’s wastewater map still showing many empty spaces in states like Alabama and North Dakota.

    The COVID-19 public health emergency

    According to the Department of Health and Human Services (HHS), a federal public health emergency gives the HHS and CDC new funding for health measures and the authority to coordinate between states, among other expanded powers.

    During the COVID-19 pandemic, the federal emergency was specifically used to require data collection from state health departments and individual hospitals, POLITICO reported in May. According to POLITICO, the required data includes sources that have become key to our country’s ability to track the pandemic, such as:

    • PCR test results from state and local health departments;
    • Hospital capacity information from individual healthcare facilities;
    • COVID-19 patients admitted to hospitals;
    • COVID-19 cases, deaths, and vaccination status in nursing homes.

    The federal COVID-19 public health emergency is formally controlled by HHS Secretary Xavier Becerra. Becerra most recently renewed the emergency in July, with an expiration date in October. Health experts anticipate that it will be renewed again in October, because HHS has promised to give states a 60-day warning before the emergency expires and there’s been no warning for this fall. That leaves us with a new potential expiration date in January 2023.

    CDC officials are seeking to permanently expand the agency’s authority to include this data collection—with a particular priority on hospitalization data. But that hasn’t happened yet, to the best of my knowledge. So, what might happen to our data when the federal emergency ends?

    Most likely, metrics that the CDC currently requires from states will become voluntary. As we see right now with breakthrough cases and wastewater data, some states will probably continue reporting while others will not. Our federal data will become much more piecemeal, a patchwork of reporting for important sources such as hospitalizations and lab test results.

    It’s important to note here that many states have already ended their own public health emergencies, following a trend that I covered back in February. Many of these states are now devoting fewer resources to free tests, contact tracing, case investigations, public data dashboards, and other data-related efforts than they were in prior phases of the pandemic. New York was the latest state to make such a declaration, with Governor Kathy Hochul letting her emergency powers expire last week.

    How the flu gets tracked

    COVID-minimizing officials and pundits love to compare “endemic” COVID-19 to the flu. This isn’t a great comparison for many reasons, but I do think it’s helpful to look at how flu is currently tracked in the U.S. in order to get a sense of how COVID-19 may be tracked in the future.

    The U.S. does not count every flu case; that kind of precise tracking on a large scale was actually a new innovation for COVID-19. Instead, the CDC relies on surveillance networks that estimate national flu cases based on targeted tracking.

    There are about 400 labs nationwide (including public health labs in all 50 states) participating in flu surveillance via the World Health Organization’s global program, processing flu tests and sequencing cases to track viral variants. Meanwhile, about 3,000 outpatient healthcare providers in the U.S. Outpatient Influenza-like Illness Surveillance Network provide the CDC with flu-related electronic health records. You can read more about both surveillance programs here.

    Sample CDC flu reporting from spring 2020. The agency provides estimates of flu activity rather than precise case numbers.

    The CDC reports data from these surveillance programs on a dashboard called FluView. As you can see, the CDC provides estimates about flu activity by state and by different demographic groups, but the data may not be very granular (eg. no estimates by county or metro area) and are provided with significant time delays.

    Other diseases are tracked similarly. For example, the CDC will track new outbreaks of foodborne illnesses like E. coli when they arise but does not attempt to log every infection. When researchers seek to understand the burden of different diseases, they often use hospital or insurance records rather than government data.

    One metric that I’d expect to remain unchanged when the COVID-19 emergency ends is deaths: the CDC’s National Center for Health Statistics (NCHS) comprehensively tracks all deaths through its death certificate system. But even provisional data from NCHS are reported with a delay of several weeks, with complete data unavailable for at least a year.

    Epidemiologists I’ve interviewed say that we should be inspired by COVID-19 to improve surveillance for other diseases, rather than allowing COVID-19 to fall into the flu model. Wastewater data could help with this; a lot of wastewater researchers (including those at Biobot) are already working on tracking flu and other diseases. But to truly improve surveillance, we need more sustained investment in public health at all levels—and more data collection authority for the CDC and HHS.

    More federal data