COVID-19 Data Dispatch

Tag: Federal data

  • Tips for following COVID-19 trends this winter

    Tips for following COVID-19 trends this winter

    This chart from Biobot Analytics shows that current coronavirus levels in wastewater (the light green line) have followed a similar pattern to fall 2021 (light blue).

    The U.S. is heading into our first winter since the end of the federal public health emergency for COVID-19. Those of us still following COVID-19 trends might need to change which data sources we use to track the disease this winter, and how we think about trends.

    The pandemic certainly hasn’t ended: COVID-19 still leads to hundreds of hospitalizations and deaths each day, not to mention millions with Long COVID. Since the U.S. government ended its emergency response to this disease, we now have significantly less information—but not zero information—about how it’s spreading.

    To recap the key changes to COVID-19 data following the emergency’s end (see this post from May for more details):

    • The CDC is no longer collecting case data, as it lost authority to require reporting from PCR testing labs.
    • Following the CDC’s lead, many state and local health departments have also stopped tracking COVID-19 cases.
    • The CDC is still tracking COVID-19 hospitalizations, though these data are more delayed and less comprehensive following the PHE’s end.
    • Death reporting is also more delayed and less comprehensive.
    • The CDC is using networks of testing labs and healthcare centers (like the National Respiratory and Enteric Virus Surveillance System) to estimate COVID-19 trends, similar to its strategies for tracking flu and RSV.
    • To track variants, the CDC is relying on a mix of continued PCR samples, wastewater testing, and travel surveillance.
    • Vaccinations are no longer reported directly to the CDC, leading the agency to track the 2023-24 vaccines through other means.

    In short, we lost a few of the primary data sources that people have used to follow COVID-19 over the last three years. But there’s still a lot of data available, primarily from wastewater surveillance, the CDC’s sentinel networks, and local health agencies.

    Here are my tips for tracking COVID-19 this winter.

    Look at multiple sources for your community.

    Following COVID-19 in your city or state used to be easy: you could just look at case numbers. Now, with that metric unavailable in many places, I would recommend having two or three go-to data sources that you check in tandem. Don’t be certain about a trend (like a new surge) until you’ve seen it in multiple sources at once. These sources might be local wastewater pages, local health department pages, and regional trends from the CDC.

    For example, when I want to check on COVID-19 spread in New York City (where I live), I look at:

    Wastewater is the best early indicator.

    It’s pretty universally acknowledged among epidemiologists and public health experts at this point in the pandemic that, without case data, wastewater surveillance is now our best way to spot new changes in COVID-19 spread. When a new surge occurs, coronavirus levels in wastewater tend to go up days or weeks before other metrics, like hospitalizations.

    So, as you track COVID-19 for your community, I would highly recommend that one of your top sources is a wastewater surveillance dashboard.

    Test positivity is still helpful for trends.

    Test positivity—the rate of COVID-19 tests that returned positive results—was a popular indicator early in the pandemic, with policy decisions like whether students could attend school in-person tied to this metric. While test positivity numbers are less available now, people are still getting tested for COVID-19: these tests mostly occur in healthcare settings among people who present with COVID-like symptoms or had recent exposures to the virus.

    I still find test positivity to be a helpful metric for watching trends in COVID-19 spread. When the positivity rate goes up, more people are getting COVID-19; and when the rate goes over 10%, that’s a decent indicator that the disease is spreading in significant magnitudes.

    Two places to find test positivity data:

    Acknowledge data delays, especially around holidays.

    Many COVID-19 dashboards used to update on a daily basis. Now, we get weekly updates from most health agencies—and even less frequency in some places. With these update schedules, all data are inevitably delayed by at least a few days. So, when you look at a dashboard, it’s important to keep the update schedule in mind and ask yourself how a trend might have continued following the most recent data available.

    Data delays become particularly prominent after holidays: remember, public health officials take days off just like the rest of us. Holiday reporting delays often lead to appearances of low COVID-19 during the immediate week of a holiday, followed by appearances of higher COVID-19 in the weeks after as cases (and other metrics) are retroactively reported. The weeks around Christmas and New Year’s are particularly bad, as most people take both of those holidays off.

    Compare current trends to past surges and lulls.

    With interpreting COVID-19 data, context is everything. Spread of the virus is usually either rising or falling; comparing current numbers to historical data can help you understand the magnitude of those recent patterns. Is your community seeing as much COVID-19 as it has at past times commonly recognized as surges? Or are you in more of a lull between waves?

    One helpful tool that I often use for such context is a chart on Biobot’s COVID-19 dashboard that provides year-over-year comparisons between coronavirus levels in wastewater in the U.S. Right now, for example, you can see that current viral levels have followed a similar trendline to what we observed in the fall 2021 Delta surge (before Omicron appeared), but lower than this time last year (when different BA variants were spreading quickly).

    The original Omicron surge in winter 2021-22 is often a popular point for these comparisons, as pundits love to assure us that a new variant won’t cause as intense a wave as we saw with Omicron’s first appearance. While this can be reassuring, I think it’s important to not just look at the highest peaks for comparison. The summer/fall of Delta in 2021 wasn’t a great time either, and we’re on track to repeat it right now even if no wildly competitive new variants appear.

    Keep an eye on variants.

    As we watch for a likely COVID-19 surge this winter, viral variants could have an impact on how much the virus is able to spread during our holiday travel and gatherings. You can keep an eye on variant development through a couple of CDC data pages:

    • The CDC’s variant proportions, which estimate levels of different variants based on PCR testing;
    • Variant patterns from wastewater, which the CDC and local health departments track from select sewage testing sites (many state and local wastewater dashboards include these data as well);
    • Travel-based genomic surveillance, a CDC program in which international travelers can opt into PCR testing as they return to U.S. airports, contributing to the agency’s understanding of variants circulating globally.

    If you have further data tracking questions or suggestions, please reach out via email or in the comments below.

  • Paxlovid will be far more expensive and covered by private insurance in 2024, likely leading to access issues

    Paxlovid will be far more expensive and covered by private insurance in 2024, likely leading to access issues

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    Starting in 2024, the antiviral drug Paxlovid will be a private—and expensive—treatment for COVID-19. The Department of Health and Human Services (HHS) announced about a week ago that it’s reached a deal with Pfizer, the pharmaceutical company that produces Paxlovid, to “transition” this drug into the commercial market within the next few months. The transition will lead to Paxlovid becoming even less accessible than it is now and will exacerbate health inequities that we’ve seen with this drug. 

    A few days ago, news outlets reported that Pfizer will charge about $1,400 per course as the list price for Paxlovid upon this transition. This is about double the price that HHS previously paid for the drug, which was about $530 per course.

    HHS previously purchased about 24 million courses of Paxlovid, of which about 17 million have been distributed and 11 million have been administered, according to the agency’s data. Under the privatization agreement, HHS will return about 8 million courses back to Pfizer, which will serve as a credit for covering continued free supply to people who have Medicare, Medicaid, or who are uninsured.

    According to HHS, people who have public insurance or no health insurance should continue to receive free Paxlovid through the end of 2024. And after that, Pfizer will run a patient assistance program for people who are uninsured or underinsured. Still, the transition is likely to cause health equity issues, as people who have public insurance or no insurance will have to jump through more hoops to receive free Paxlovid under these programs, as opposed to the current situation where everyone can get it for free. We’ve all seen how chaotically this fall’s vaccine rollout went, after all.

    The HHS’s data for Paxlovid administration (shown above) demonstrate that states where healthcare is more easily accessible and/or where patient populations are wealthier tend to have higher rates of receiving Paxlovid over the nearly two years that it’s been available. We also know from scientific studies looking at Paxlovid that this drug has followed access issues similar to the COVID-19 vaccines and tests.

    Considering these prior patterns, combined with the increasing price, it unfortunately seems like a foregone conclusion that Paxlovid will get harder to access in 2024. This will be a huge issue for preventing severe disease and death from COVID-19 as well as limiting risks of Long COVID, which research suggests Paxlovid can do as well.

    If you are a reader who’s had a hard time getting Paxlovid, or if you want to share more comments or questions on this issue, please reach out.

    more federal data
  • How is the CDC tracking the latest round of COVID-19 vaccines?

    How is the CDC tracking the latest round of COVID-19 vaccines?

    The CDC’s vaccination data pages all stopped updating in May 2023. How is the agency tracking our current round of shots?

    It’s now been a couple of weeks since updated COVID-19 vaccines became available in the U.S. At this point in prior COVID-19 vaccine rollouts, we would know a lot about who had received those vaccines: data would be available by state, for different age groups, and other demographic categories.

    This time, though, the data are missing on a national scale. Following the end of the federal public health emergency in May, the CDC has lost its authority to collect vaccination data from all state and local health agencies that keep immunization records. As a result, the CDC is no longer providing comprehensive vaccination numbers on its COVID-19 dashboards.

    But we still have some information about this year’s vaccination campaign, thanks to continued CDC efforts as well as reporting by other health agencies and research organizations. In fact, last week, the federal Department of Health and Human Services (HHS) told reporters that more than seven million Americans have received updated COVID-19 vaccines so far this fall.

    HHS also said that about 14 million doses have been shipped to vaccination sites, primarily pharmacies. In addition, 710,000 vaccines for children have been ordered through a federal program that provides these shots.

    Vaccine distribution numbers are slightly easier for the CDC and HHS to collect, as they can work directly with vaccine manufacturers. To understand how many people are getting the shots, though, is more challenging—requiring a mix of data from state and local agencies, surveys, and other surveillance mechanisms.

    What changed with the PHE’s end:

    Early in the pandemic, the CDC established data-sharing agreements with the health agencies that keep immunization records. This includes all states, territories, and a few large cities (such as New York City and Philadelphia) that have separate records systems from their states; you can see a full list of records systems here.

    Through those agreements, the CDC collected vaccine administration numbers, standardized the data (as much as possible), and reported them on public dashboards. The CDC wasn’t able to collect as detailed demographic information as many health experts would’ve liked—for example, they never reported vaccinations by race and ethnicity below the national level. But the data were still useful for tracking who got vaccinated across the U.S.

    These data-sharing agreements concluded with the end of the public health emergency (PHE) in May 2023. According to a CDC report published at that time, the CDC was able to extend agreements with some jurisdictions past the PHE’s end. Still, the report’s authors acknowledged that “future data might not be as complete” as during the emergency period. Even if 40 out of 50 states keep reporting, the remaining 10 represent data gaps.

    Notably, the May report also claims that the CDC would continue to provide data on COVID-19 vaccination coverage on the CDC’s COVID-19 dashboard and a separate vaccination dashboard. But neither of those dashboards has been updated with any information from this fall’s vaccine campaign, as of this publication.

    In addition to compiling data from state and local systems, the CDC has other mechanisms for tracking vaccinations. According to CBS News reporter Alexander Tin, CDC officials highlighted a couple during a briefing on October 4:

    • The National Immunization Survey, a phone survey conducted by CDC officials to estimate national vaccination coverage based on a representative sample of Americans. This survey is currently the CDC’s method for tracking flu vaccinations.
    • CDC’s Bridge Access and Vaccines for Children (VFC) programs, both of which buy vaccines to distribute to Americans who may not have health insurance or face other financial barriers to vaccination. The Bridge Access program was specifically set up for COVID-19 vaccines, while the VFC program covers other childhood vaccines.
    • Contact with vaccine manufacturers and distributors, i.e. the pharmaceutical companies that make the vaccines and the pharmacies and healthcare organizations that give them out. These companies share data with the CDC, offering insights into how many vaccines have been distributed to different locations; though the data may not be comprehensive if not all distributors are included (i.e. just big pharmacy chains, not smaller, independent stores).

    Other places to look for vaccination data:

    Outside of the CDC, there are a few other places where you can look for vaccination data. Here are a couple that I’m monitoring:

    • State and local public health agencies: Some agencies that track immunizations have their own dashboards, reporting on vaccinations in a specific state or locality. For example, New York City’s health department tracks COVID-19 vaccinations among city residents, although the agency hasn’t yet published data for this fall’s vaccines. I have a list of state vaccination dashboards here; this doesn’t currently represent data on the fall 2023 vaccines, but I aim to do that update in the coming weeks.
    • Outside surveys, such as KFF’s COVID-19 Vaccine Monitor: Like the CDC’s National Immunization Survey, other health organizations conduct surveys to track vaccinations. The Kaiser Family Foundation’s COVID-19 Vaccine Monitor is one well-known project, which has been doing regular surveys on COVID-19 vaccine uptake since December 2020.
    • Scientific reports answering specific vaccination questions: Public health researchers may use surveys, immunization records, or other data systems to study specific questions about vaccination, such as the impact that vaccination has on lowering a patient’s risk of severe disease. These studies are often published in the CDC’s Morbidity and Mortality Weekly Report and other journals.

    If you have other questions about vaccination data—or want to share a data source I didn’t mention here—please reach out: email me or leave a comment below.

    more vaccine coverage
  • The CDC has a new wastewater surveillance contract; here’s what this means for public data sources

    The CDC has a new wastewater surveillance contract; here’s what this means for public data sources

    The number of wastewater testing sites that recently reported to the CDC’s national surveillance system has dropped in recent weeks, likely in time with a contract switch.

    Editor’s note, October 15: This article has been updated with comments from Verily.

    This week, the CDC and life sciences company Verily announced that the agency awarded a five-year wastewater surveillance contract to Verily. The announcement marks a shift in the U.S. sewage monitoring landscape and will impact our public COVID-19 data, with short-term gaps and changing coverage in a couple of sources—but ultimate improvements in the long term.

    First, some background:

    In fall 2020, the CDC launched the National Wastewater Surveillance System (NWSS), a network of sewage testing sites around the country all reporting data to a central location. While some state and local health agencies quickly developed in-house systems for testing wastewater and reporting their data to NWSS, others lacked the resources (staff, lab capacity, data infrastructure, etc.) to start doing this new type of health surveillance.

    As a result, the CDC began working with private testing companies to fill gaps in the NWSS network and expand surveillance more quickly across the country. The first contactor was a diagnostic company headquartered in Canada called LuminUltra. Then, last spring, the CDC awarded a contract to Biobot Analytics, a startup focused on wastewater surveillance. Biobot did a lot of work to extend the NWSS, helping bring the total CDC network up to nearly 1,400 sites; but the contractor switch initially led to a few weeks of missing data for about 150 sites covered by the CDC contract, as they transitioned from one set of testing protocols to another. (See my coverage at the time for more details.)

    One advantage of Biobot working with the NWSS, if you’re someone who cares about public wastewater data, is that the company added data from many CDC contract sites to its COVID-19 wastewater dashboard, making that dashboard more comprehensive in its view of national COVID-19 patterns. You couldn’t view the CDC sites in Biobot’s county-level visualizations; those present data from other sites that have individual contracts with the company or are participating in the free Biobot Network program. But Biobot added CDC sites that opted into data-sharing to its national and regional visualizations, a company spokesperson told me last year.

    What’s changing with the new contract:

    Biobot’s contract with the CDC ended last month. The CDC’s new contract with Verily replaces it. Verily’s contract covers five years (as opposed to shorter periods for prior CDC wastewater testing contracts), and includes additions of more pathogens that may be tested through NWSS, in addition to SARS-CoV-2. These are both great improvements, adding to the surveillance system’s longevity and expanding its capacity beyond COVID-19—though additional federal funds will likely be needed past this contract.

    However, in the short term, we will see data gaps on NWSS as contracted sites change over to Verily from Biobot. These testing sites may have to adjust how they collect samples, how they package and ship samples, and other logistical changes. The CDC NWSS dashboard already indicates a reporting dip in the last couple of weeks, coinciding with the contract change.

    Meanwhile, Biobot will no longer have the same direct access to the CDC contract testing sites. While all the sites’ data will still be published publicly by the CDC, the Biobot-Verily switch will likely lead to changes in sample processing and analysis that make data from those sites no longer directly comparable with the hundreds of other sites covered by Biobot. My guess here is that Biobot may no longer be able to include the CDC contract sites in its national and regional visualizations.

    I reached out to Biobot for comment about this shift, and haven’t heard back from them yet. I’ve also reached out to Verily asking about the contract changeover and any data-sharing plans they may have, and haven’t heard back there yet either. I will update this post with more details from the companies as I receive them.

    How this new contract may impact major data sources:

    • CDC NWSS: Data from all sites participating in NWSS will continue to be available on the CDC’s dashboard, though the sites covered by the CDC’s national testing contract (previously with Biobot, now with Verily) may have missing data for a couple of weeks. NWSS continues to be the most comprehensive place to find wastewater data in the U.S., but unfortunately doesn’t share national or regional trends because it is compiling from many different testing programs with different methodologies.
    • Biobot Analytics: County-level data won’t change. National and regional data will still be available, but are likely to be less comprehensive pictures of wastewater trends across the U.S., if I’m right about Biobot no longer including CDC contract sites in those visualizations. Also worth noting, Biobot shifted its update schedule recently to once a week on Mondays (with a longer delay in data, but likely less retroactive updating).
    • WastewaterSCAN: No changes due to this contract switch, though WastewaterSCAN has been working with Verily for a while to test sewage samples from its network. This project also recently announced that it’s adding six more disease targets to its program: parainfluenza, rotavirus, adenovirus group F, enterovirus D68, Candida auris, and hepatitis A. See the statement from WastewaterSCAN below for more details.
    • In the long-term: The CDC’s new five-year contract will enable continued expansion of the NWSS, potentially with both more sites and more disease targets. I also expect public data offerings will continue to improve as scientists and public health officials learn more about how to interpret wastewater surveillance data.

    Statement from WastewaterSCAN about the new contract

    WastewaterSCAN was pleased to learn that the CDC selected Verily to support the National Wastewater Surveillance System (NWSS). As our lab partner, Verily has an important role managing sample collection logistics from wastewater treatment plants participating in the WastewaterSCAN network, processing samples, and supporting our research to advance the science of wastewater-based epidemiology.

    WastewaterSCAN continues to demonstrate that wastewater monitoring can provide comprehensive, efficient, community-wide tracking of seasonal and emerging diseases. We recently added six disease targets to our program and are helping many communities prepare for the respiratory virus season with a public data dashboard to communicate what wastewater is telling us about the diseases circulating in our communities.

    At this time, only data from our program will appear on WastewaterSCAN’s data dashboard. WastewaterSCAN will continue to make our methods public and to collaborate and share data with NWSS and contribute to its important, mission-critical work.

    Statement from Verily, responding to COVID-19 Data Dispatch questions

    CDD: Will the WastewaterSCAN dashboard start including data from wastewater testing sites included in the CDC contract, as they come online? Or is Verily planning to launch its own dashboard that will share data from those sites (perhaps in aggregate, national trends, similar to the current Biobot dashboard)?

    Verily: WastewaterSCAN representatives have responded.
    On the question of sharing aggregated, national trends data from these sites: This is a CDC decision for the NWSS testing program.

    CDD: Besides public dashboards, will there be alignment between WastewaterSCAN and Verily in how wastewater data are processed, analyzed, and interpreted?

    Verily: There are many methods for analyzing the concentration of pathogens in wastewater. Verily offers several methods for wastewater analysis to its customers and ones chosen by the CDC NWSS and WastewaterSCAN programs differ primarily in what part of the wastewater is analyzed and how the pathogens are concentrated and extracted before measurement of pathogen concentrations. Beyond these initial steps, Verily’s lab processes all samples similarly.

    The liquid fraction (of influent samples) will be concentrated and tested for the CDC NWSS program, similar to the approach previously used for NWSS contract testing.

    The solid fraction of samples (from the primary clarifier or influent) has been shown to concentrate many pathogens and is tested for the WastewaterSCAN program.

    Results from methods have shown agreement with case data in the literature. However, differences between the methods make them complementary to each other.

    CDD: When the CDC previously switched contractors in spring 2022, some testing sites covered by the contract didn’t report to NWSS for several weeks while they transferred to a new process. What is Verily doing to help transition sites during the current switch?

    Verily: Verily has an established system and team dedicated to onboarding new sites with the ability to rapidly initiate testing. This is informed by our previous experience providing logistics and lab services to over 200 sites in wastewater monitoring programs.

    As we receive information from the CDC NWSS program about which sites will transition, we will get sites up and running as soon as possible. Our goal is to have up to 200 sites testing within the first four weeks of the contract.

    More on wastewater surveillance
  • This summer, COVID-19 safety is more individualized than ever

    This summer, COVID-19 safety is more individualized than ever

    Current coronavirus levels in wastewater are close to the summer 2021 Delta surge, according to Biobot.

    COVID-19 metrics have been on the rise in the U.S. for about a month now, indicating that we’re experiencing a summer surge. This is pretty unsurprising for many public health experts, as the country has experienced increased transmission during the last three summers.

    Unlike past years, though, this summer’s surge comes after the end of the federal public health emergency. We now have less data than ever to follow COVID-19 trends, combined with less access to health measures than ever.

    We’re also dealing with continued minimization of the problem. Coverage of the current surge in mainstream media sources tends to downplay any concerns, suggesting that hospitalizations are low (even though those data are delayed), or that masking isn’t necessary (even though this tool works best as a preventative measure), or that all infections are now mild (even though Long COVID remains a risk for any case). The People’s CDC offers more critique here.

    Despite these challenges, enough information is out there that anyone committed to safety can keep up with COVID-19 news and protect themselves. Unfortunately, this practice now requires much more individual effort—a far cry from the collective measures that we took back in 2020. But we still have opportunities to show leadership, by sharing information and resources with our communities.

    Here are a few things I’m doing in the current surge, and recommendations to consider sharing:

    • Assume all data are delayed and undercounted. COVID-19 data sources are sparser than ever, so the trends we see are likely to be small reflections of larger issues. Biobot’s wastewater dashboard, for example, provides results from a sample of sewersheds across the U.S.; the same increases are likely happening in places where we aren’t tracking them.
    • Watch your local wastewater numbers. Despite the uneven coverage of wastewater surveillance, this is still the best tool for advanced warnings on COVID-19 now that case data are no longer available. If your city or county doesn’t have a wastewater testing site, you can likely find a nearby one to follow for trends. See the CDD’s resource page for links to dashboards.
    • Stock up on high-quality masks. N95s and KN95s are really necessary to protect yourself from the ever-evolving Omicron variants. There are a lot of places to buy these online; Project N95 is my personal favorite, as you can get masks directly from their manufacturers and contribute to mask donations for less-resourced communities.
    • Consider a higher-value respirator for riskier activities. If you’re traveling or going to a higher-risk event this summer, a reusable respirator might be helpful. I wrote more about why I bought one in this post last summer.
    • Stock up on rapid tests. Most health insurance plans no longer cover these (following the end of the federal health emergency), but some local governments are still giving them out for free in public spaces, like libraries in NYC. You might also buy tests in bulk online. I personally use iHealth Labs, because they sell packs of five tests that are easy to bring while traveling and frequently run sales.
    • Make a plan for isolation/quarantine. In case you or a member of your household gets sick, it can be helpful to have an advance plan on where you might isolate, how to keep air clean in shared spaces, where to get Paxlovid, etc. Your Local Epidemiologist has more tips on how to deal with a positive test.
    • Share information and resources. Surveys have suggested that many Americans would mask and take other public health measures during surges, but those people might not know about the current rise in transmission. Sharing information with your community (along with masks, rapid tests, and other tools, if you have surplus) can help broaden safety measures.
    • Remember why you’re taking precautions. During increased social pressures against COVID-19 safety, I personally find it helpful to remember why I find these behaviors important. Some reasons are selfish (for example, taking a week or two off work would be difficult) while others are more philosophical (such as a dedication to the principles of broader public health)—but all of them are valuable.

    If you have questions or additional suggestions, please share them below.

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  • New pandemic preparedness office at the White House

    The White House has launched a new office focused on high-level pandemic preparedness, about six months after Congress requested this. The new Office of Pandemic Preparedness and Response Policy will be a permanent office in the executive branch, according to a fact sheet from the Biden administration.

    This announcement is good news; it’s a small step towards improving the U.S.’s infrastructure for responding to future disease threats. But we shouldn’t just be focusing on pandemic preparedness—the U.S. also needs better infrastructure for many health issues impacting the country now, including the continued impacts of COVID-19.

    According to the White House, the new office’s responsibilities include:

    • Coordinating the executive branch’s “domestic response to public health threats that  have pandemic potential or may cause significant disruption.” Current notable threats include COVID-19, mpox, polio, flu, and RSV.
    • Coordinating federal science and technology efforts related to pandemic preparedness, such as developing next-generation vaccines and treatments. A current focus here is next-gen vaccines for COVID-19, though it’s unclear how this new office will coordinate with other federal agencies on that initiative, per reporting by Sarah Owermohle at STAT.
    • Develop pandemic preparedness reports for Congress, including a shorter review every two years and more in-depth reports every five years.

    The Biden administration has appointed retired Major General Paul Friedrich (MD), currently the senior director for global health security at the National Security Council, to lead the new office. Friedrich has decades of experience leading global health initiatives in the military and for the federal government; he advised the Pentagon in the early months of COVID-19.

    Between this new office and Congress’ work on reauthorizing the Pandemic and All-Hazards Preparedness Act, there’s been a lot of discussion on preventing future pandemics in the last couple of weeks. This is obviously good news; COVID-19 has taught U.S. officials at all levels that they will need more resources for the next big health threat.

    But at the same time, the focus on pandemic preparedness can potentially distract us from the many current health threats that we face now. That includes COVID-19 and Long COVID, along with many common diseases, chronic conditions, and other health issues that could be managed better. For example, our seasonal flu surveillance could use an upgrade! 

    The U.S. has plenty of resources to devote to present and future health threats; we could be doing much more on both fronts.

    more federal data

  • Debt ceiling deal will mean even less COVID-19 funding

    You’ve probably seen the news that last weekend, President Joe Biden and Congressional leaders reached a deal to raise the U.S. government’s debt ceiling. The deal passed both houses and Biden signed it yesterday.

    In order to reach this bipartisan deal, Biden had to make a lot of compromises—including limiting funding for COVID-19 and other public health needs. The deal could make it harder for state and local governments to distribute COVID-19 vaccines, track disease through programs like wastewater surveillance, and prepare for future health threats.

    The federal government is essentially taking back $27 billion of COVID-19 funds that it provided to various federal agencies, according to reporting by Ximena Bustillo and Tamara Keith at NPR. The move focuses on funds for programs that concluded or have “no immediate demands,” per a White House document shared by NPR.

    But programs with “no immediate demands” could easily have demands in the coming months. One of NPR’s examples is funding for the federal Department of Health and Human Services (HHS) to research and distribute vaccines, which can be distributed to other agencies (the CDC, NIH, FDA, state and local health departments, etc.). Vaccine distribution might not be a big need right now, but it likely will be in the fall, when new COVID-19 boosters become available.

    Another potential need could be wastewater surveillance for COVID-19 and other health threats. The CDC’s National Wastewater Surveillance System (NWSS) was funded through 2025 by the American Rescue Plan, but it’s possible some of those funds could be in the HHS money pulled back by the debt ceiling deal. This would obviously be a huge loss for the U.S.’s ability to get early warning about future COVID-19 surges, as well as warnings about other pathogens. (Shout-out to Sean Kennedy for pointing this one out.)

    In addition, the debt ceiling deal may lead to a smaller budget for the NIH, as Sarah Owermohle reports in STAT News. This could have implications for the agency’s ability to fund research into many pressing diseases, including Long COVID. The NIH has already wasted a lot of its Long COVID funding so far, according to my reporting, so it would be pretty bad news if more support for this research is not available.

    The White House has claimed that Biden’s deal preserves funds for some key COVID-19 issues, according to NPR, including next-generation vaccines and Long COVID research. It’s hard to verify this, though, because of how convoluted federal COVID-19 funding has been. From a recent brief by the Association of State and Territorial Health Officials:

    “Given the way Congress appropriated COVID-19 funding, and the way funding was later transferred between federal accounts and agencies, it is extremely difficult to discern which federal public health programs are affected by the rescissions.”

    Public health funding often follows a cycle of “panic and neglect.” When a crisis occurs, governments panic and put tons of money into the immediate response. But after that crisis fades, it falls into neglect, with less money devoted to preparedness—even though preparedness efforts could help avert the next crisis. We’re clearly in that neglect part of the cycle for COVID-19 now; the debt ceiling deal is just the latest example.

    More federal data

  • The CDC’s new COVID-19 dashboard hides transmission risk

    The CDC’s new COVID-19 dashboard hides transmission risk

    The CDC’s new COVID-19 dashboard suggests that the national situation is totally fine, because hospitalizations are low. But is that correct?

    On Thursday, the CDC revamped its COVID-19 dashboard in response to changing data availability with the end of the federal public health emergency. (For more details on the data changes, see my post from last week.) The new dashboard downplays continued COVID-19 risk across the U.S.

    Overall, the new dashboard makes it clear that case counts are no longer available, since testing labs and state/local heath agencies aren’t sending those results to the CDC anymore. You can’t find case counts or trends on the homepage, at the top of the dashboard, or in a county-level map.

    Instead, the CDC is now displaying data that shows some of COVID-19’s severe impacts— hospitalizations and deaths—without making it clear how widely the virus is still spreading. Its key metrics are new hospital admissions, currently-hospitalized patients, emergency room visits, and the percentage of recent deaths attributed to COVID-19. You can find these numbers at national and state levels in a revamped “trends” page, and at county levels in a “maps” page.

    The “maps” page with county-level data has essentially replaced the CDC’s prior Community Level and Transmission Level page, where users were previously able to find COVID-19 case rates and test positivity rates by county. In fact, as of May 13, the URL to this maps page is still labeled as “cases” when you click into it from the main dashboard.

    While these changes might be logical (given that case numbers are no longer available), I think the CDC’s design choices here are worth highlighting. By prioritizing hospitalizations and deaths, the CDC implicitly tells users of this dashboard that the virus should no longer be a concern for you unless you’re part of a fairly small minority of Americans at high risk of those severe outcomes.

    But is that actually true, that COVID-19 is no longer a concern unless you’re going to go to the hospital? I personally wouldn’t agree. I’d prefer not to be out sick for a week or two, if I can avoid it. And I’d definitely like to avoid any long-term symptoms—or the long-term risks of heart problems, lung problems, diabetes, etc. that may come after a coronavirus infection.

    These outcomes still persist after a mild COVID-19 case. But the current CDC data presentation makes it hard to see those potential outcomes, or your risk of getting that mild COVID-19 case. The agency still has some data that can help answer these questions (wastewater surveillance, variant surveillance, Long COVID survey results, etc.) but those numbers aren’t prioritized to the same degree as hospitalizations and deaths.

    I’m sure the CDC data scientists behind this new dashboard are doing the best they can with the information they have available. Still, in this one journalist’s opinion, they could’ve done more to make it clear how dangerous—and how widely prevalent—COVID-19 still is.

    For other dashboards that continue to provide updates, see my list from a few weeks ago. I also recommend looking at your state and local public health agencies to see what they’re doing in response to the PHE’s end.

    More federal data

  • The federal public health emergency ends next week: What you should know

    The federal public health emergency ends next week: What you should know

    A chart from the CDC’s recent report on surveillance changes tied to the end of the federal public health emergency.

    We’re now less than one week out from May 11, when the federal public health emergency (or PHE) for COVID-19 will end. While this change doesn’t actually signify that COVID-19 is no longer worth worrying about, it marks a major shift in how U.S. governments will respond to the ongoing pandemic, including how the disease is tracked and what public services are available.

    I’ve been writing about this a lot in the last couple of months, cataloging different aspects of the federal emergency’s end. But I thought it might be helpful for readers if I compiled all the key information in one place. This post also includes a few new insights about how COVID-19 surveillance will change after May 11, citing the latest CDC reports.

    What will change overall when the PHE ends?

    The ending of the PHE will lead to COVID-19 tests, treatments, vaccines, and data becoming less widely available across the U.S. It may also have broader implications for healthcare, with telehealth policies shifting, people getting kicked off of Medicaid, and other changes.

    Last week, I attended a webinar about these changes hosted by the New York City Pandemic Response Institute. The webinar’s moderator, City University of New York professor Bruce Y. Lee, kicked it off with a succinct list of direct and indirect impacts of the PHE’s end. These were his main points:

    • Free COVID-19 vaccines, tests, and treatments will run out after the federal government’s supplies are exhausted. (Health experts project that this will likely happen sometime in fall 2023.) At that point, these services will get more expensive and harder to access as they transition to private healthcare markets.
    • We will have fewer COVID-19 metrics (and less complete data) to rely on as the CDC and other public health agencies change their surveillance practices. More on this below.
    • Many vaccination requirements are being lifted. This applies to federal government mandates as well as many from state/local governments and individual businesses.
    • The FDA will phase out its Emergency Use Authorizations (EUAs) for COVID-19 products, encouraging manufacturers to apply for full approval. (This doesn’t mean we’ll suddenly stop being able to buy at-home tests—there’s going to be a long transition process.)
    • Healthcare worker shortages may get worse. During the pandemic emergency, some shifts to work requirements allowed facilities to hire more people, more easily; as these policies are phased out, some places may lose those workers.
    • Millions of people will lose access to Medicaid. A federal rule tied to the PHE forbade states from kicking people off this public insurance program during the pandemic, leading to record coverage. Now, states are reevaluating who is eligible. (This process actually started in April, before the official PHE end.)
    • Telehealth options may become less available. As with healthcare hiring, policies during the PHE made it easier for doctors to provide virtual care options, like video-call appointments and remote prescriptions. Some of these COVID-era rules will be rolled back, while others may become permanent.
    • People with Long COVID will be further left behind, as the PHE’s end leads many people to distance themselves even more from the pandemic—even though long-haulers desperately need support. This will also affect people who are at high risk for COVID-19 and continue to take safety precautions.
    • Pandemic research and response efforts may be neglected. Lee referenced the “panic and neglect” cycle for public health funding: a pattern in which governments provide resources when a crisis happens, but then fail to follow through during less dire periods. The PHE’s end will likely lead us (further) into the “neglect” part of this cycle.

    How will COVID-19 data reporting change?

    The CDC published two reports this week that summarize how national COVID-19 data reporting will change after May 11. One goes over the surveillance systems that the CDC will use after the PHE ends, while the other discusses how different COVID-19 metrics correlate with each other.

    A lot of the information isn’t new, such as the phasing out of Community Level metrics for counties (which I covered last week). But it’s helpful to have all the details in one place. Here are a few things that stuck out to me:

    • Hospital admissions will be the CDC’s primary metric for tracking trends in COVID-19 spread rather than cases. While more reliable than case counts, hospitalizations are a lagging metric—it takes typically days (or weeks) after infections go up for the increase to show up at hospitals, since people don’t seek medical care immediately. The CDC will recieve reports from hospitals at a weekly cadence, rather than daily, after May 11, likely increasing this lag and making it harder for health officials to spot new surges.
    • National case counts will no longer be available as PCR labs will no longer be required to report their data to the CDC. PCR test totals and test positivity rates will also disappear for the same reason, as will the Community Levels that were determined partially by cases. The CDC will also stop reporting real(ish)-time counts of COVID-associated deaths, relying instead on death certificates.
    • Deaths will be the primary metric for tracking how hard COVID-19 is hitting the U.S. The CDC will get this information from death certificates via the National Vital Statistics System. While deaths are reported with a significant lag (at least two weeks), the agency has made a lot of progress on modernizing this reporting system during the pandemic. (See this December 2021 post for more details.)
    • The CDC will utilize sentinel networks and electronic health records to gain more information about COVID-19 spread. This includes the National Respiratory and Enteric Virus Surveillance System, a network of about 450 laboratories that submit testing data to the CDC (previously established for other endemic diseases like RSV and norovirus). It also includes the National Syndromic Surveillance Program, a network of 6,300 hospitals that submit patient data to the agency.
    • Variant surveillance will continue, using a combination of PCR samples and wastewater data. The CDC’s access to PCR swab samples will be seriously diminished after May 11, so it will have to work with public health labs to develop national estimates from the available samples. Wastewater will help fill in these gaps; a few wastewater testing sites already send the CDC variant data. And the CDC will continue offering tests to international travelers entering the country, for a window into global variant patterns.
    • The CDC will continue tracking vaccinations, vaccine effectiveness, and vaccine safety. Vaccinations are generally tracked at the state level (every state health agency, and several large cities, have their own immunization data systems), but state agencies have established data sharing agreements with the CDC that are set to continue past May 11. The CDC will keep using its established systems for evaluating how well the vaccines work and tracking potential safety issues as well.
    • Long COVID notably is not mentioned in the CDC’s reports. The agency hasn’t put much focus on tracking long-term symptoms during the first three years of the pandemic, and it appears this will continue—even though Long COVID is a severe outcome of COVID-19, just like hospitalization or death. A lack of focus on tracking Long COVID will make it easier for the CDC and other institutions to keep minimizing this condition.

    On May 11, the CDC plans to relaunch its COVID-19 tracker to incorporate all of these changes. The MMWR on surveillance changes includes a list of major pages that will shift or be discontinued at this time.

    Overall, the CDC will start tracking COVID-19 similar to the way it tracks other endemic diseases. Rather than attempting to count every case, it will focus on certain severe outcomes (i.e., hospitalizations and deaths) and extrapolate national patterns from a subset of healthcare facilities with easier-to-manage data practices. The main exception, I think, will be a focus on tracking potential new variants, since the coronavirus is mutating faster and more aggressively than other viruses like the flu.

    What should I do to prepare for May 11?

    If you’ve read this far, you’re probably concerned about how all these shifts will impact your ability to stay safe from COVID-19. Unfortunately, the CDC, like many other public agencies, is basically leaving Americans to fend for themselves with relatively little information or guidance.

    But a lot of information sources (like this publication) are going to continue. Here are a few things I recommend doing this week as the PHE ends:

    • Look at your state and local public health agencies to see how they’re responding to the federal shift. Some COVID-19 dashboards are getting discontinued, but many are sticking around; your local agency will likely have information that’s more tailored to you than what the CDC can offer.
    • Find your nearest wastewater data source. With case counts basically going away, wastewater surveillance will be our best source for early warnings about surges. You can check the COVID-19 Data Dispatch list of wastewater dashboards and/or the COVIDPoops dashboard for sources near you.
    • Stock up on at-home tests and masks. This is your last week to order free at-home/rapid tests from your insurance company if you have private insurance. It’s also a good time to buy tests and masks; many distributors are having sales right now.
    • Figure out where you might get a PCR test and/or Paxlovid if needed. These services will be harder to access after May 11; if you do some logistical legwork now, you may be more prepared for when you or someone close to you gets sick. The People’s CDC has some information and links about this.
    • Contact your insurance company to find out how their COVID-19 coverage policies are changing, if you have private insurance. Folks on Medicare and Medicaid: this Kaiser Family Foundation article has more details about changes for you.
    • Ask people in your community how you can help. This is a confusing and isolating time for many Americans, especially people at higher risk for COVID-19. Reaching out to others and offering some info or resources (maybe even sharing this post!) could potentially go a long way.

    That was a lot of information packed into one post. If you have questions about the ending PHE (or if I missed any important details), please email me or leave a comment below—and I’ll try to answer in next week’s issue.

    More about federal data

  • CDC shifts away from COVID-19 Community Levels with the federal emergency’s end

    CDC shifts away from COVID-19 Community Levels with the federal emergency’s end

    The CDC’s Community Levels suggest (perhaps inaccurately!) that the U.S. has little to worry about from COVID-19 right now. The agency is set to stop calculating these metrics next month.

    As we’ve gotten closer to May 11, the official ending of the federal public health emergency for COVID-19, I’ve tried to collect news on how this change will impact COVID-19 data availability. We know, for example, that the CDC will lose some of its authority to collect data from state and local health agencies, and that PCR testing numbers will become even less accurate.

    This week, another key change became public: the CDC will stop reporting COVID-19 Community Levels, according to reporting by Brenda Goodman at CNN. The agency is overall planning to shift from using case data to hospitalizations and wastewater surveillance.

    The CDC’s Community Levels are county-level metrics based on cases and hospitalizations. In February 2022, the agency switched to these metrics from its prior Transmission Levels (which were based on cases and test positivity), and essentially changed its national COVID-19 map from bright red to pastel green-yellow-orange overnight.

    Community Levels have generally made the U.S.’s COVID-19 situation look better than it really is over the last year, since these metrics relied on hospitalizations, a lagging indicator, and were set to high thresholds for recommending safety measures. Even so, the metrics gave Americans an easy way to look at the COVID-19 situation in their county or region.

    On May 11, that county-level information will no longer be available, according to Goodman’s reporting. When the public health emergency ends, the CDC will no longer be able to require COVID-19 testing labs to report their results—so this already-spotty information will become even less accurate. While test results at the national level might still be helpful for following general trends, it will be harder to interpret more local data.

    “We’re not going to lose complete surveillance, but we will lose that hyperlocal sensitivity to it perhaps,” an anonymous source at the CDC told Goodman. These more local metrics “simply cannot be sustained” due to reporting changes, the source said.

    In absence of county-level case data, the CDC plans on utilizing hospitalizations and wastewater surveillance to track COVID-19, according to the CNN report. The agency might focus on tracking COVID-19 at specific healthcare settings in a reporting network, similar to its surveillance for endemic diseases like flu and RSV, rather than trying to count every single severe COVID-19 case.

    Hospitalization data tend to lag behind cases, so wastewater surveillance will be important to provide early warnings about potential new coronavirus variants or surges. However, the country’s wastewater surveillance network is still patchy: some states have a sewage testing site in every county, while others only have a handful. Our data will be biased, based on which health departments have invested in this technology.

    It’s unsurprising to see the CDC plan this COVID-19 reporting change, given the powers it will lose on May 11. But I’m still disappointed. I’ve followed the U.S.’s incomplete surveillance for endemic diseases, and I hoped that continued COVID-19 tracking would provide an opportunity for improvement. Instead, it looks like we’re going to revert to something like our flu tracking, with wastewater surveillance unevenly tacked on.

    The May 11 changes will inevitably have a huge impact on the Americans who are still trying to stay safe from COVID-19, especially those with health conditions that make them more vulnerable to severe symptoms. Without reliable data, people will be unable to identify when spread is high or low in their community. I expect some will simply shrug off the risks (but may regret that choice later), while others will anticipate that COVID-19 is everywhere, all the time, and retreat from public activities.

    And from the public health perspective, less data will make it harder to identify concerning new variants or potential surges. For more on these challenges, I recommend this article by KFF Health News reporter Sam Whitehead, published in CNN and other outlets.

    “We’re all less safe when there’s not the national amassing of this information in a timely and coherent way,” Anne Schuchat, former principal deputy director of the Centers for Disease Control and Prevention, told Whitehead.

    More on federal data