COVID-19 Data Dispatch

Tag: Wastewater

  • 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

  • National numbers, January 15

    National numbers, January 15

    New hospital admissions for COVID-19 are starting to trend down, according to the CDC, though we’ll need more data to see if this trend persists.

    In the past week (January 5 through 11), the U.S. officially reported about 420,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 59,000 new cases each day
    • 126 total new cases for every 100,000 Americans
    • 13% fewer new cases than last week (December 29-January 4)

    In the past week, the U.S. also reported about 40,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 5,800 new admissions each day
    • 12.3 total admissions for every 100,000 Americans
    • 12% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 3,900 new COVID-19 deaths (560 per day)
    • 43% of new cases are caused by Omicron XBB.1.5; 45% by BQ.1 and BQ.1.1 (as of January 14)
    • An average of 150,000 vaccinations per day (CDC link)

    Last week, I wrote that a combination of holiday travel/gatherings and the latest Omicron subvariant, XBB.1.5, was driving a winter surge. This week, COVID-19 metrics suggest that the surge may have peaked, though we’ll need more data to say for sure—and XBB.1.5 remains a concern.

    After reporting a significant increase in coronavirus levels through the end of December, Biobot’s wastewater dashboard is now showing downturns nationally and for all four U.S. regions. The CDC’s wastewater dashboard similarly shows that about two-thirds of sites in the National Wastewater Surveillance System have reported decreasing COVID-19 levels in the last two weeks, as of January 10.

    “Importantly, this data is subject to change as we update 2x weekly,” Biobot’s Twitter shared on Thursday, when the company’s dashboard was most recently updated. “Stay tuned for Tuesday’s update.”

    Official COVID-19 cases and hospital admissions are also trending down, according to CDC data: new cases dropped by 13% from the week ending January 4 to the week ending January 11, while newly hospitalized patients dropped by 12%. But this trend isn’t universal; five states and Washington D.C. reported increased hospitalizations this week, with the biggest upticks in Rhode Island, Louisiana, and Maine.

    XBB.1.5, the latest and most contagious Omicron subvariant, caused an estimated 43% of new cases nationwide in the week ending January 14, per the CDC. It’s clearly outcompeting BQ.1 and BQ.1.1 as well as a number of other strains in the “Omicron soup” we currently face, but is not taking over as quickly as we saw the original Omicron do in late 2021.

    This strain continues to dominate the Northeast—particularly New England and New York/New Jersey—where COVID-19 spread is trending down. But it’s just starting to pick up in other parts of the country; to me, it seems likely that the Northeast had a holidays-and-XBB.1.5 combined surge, while other areas may face a second COVID-19 increase as this variant spreads more widely.

    Meanwhile, other respiratory viruses continue to place additional burden on our health system. For example, the CDC recently released estimates about this year’s flu season, finding that the flu may have caused up to 560,000 hospitalizations and 48,000 deaths since fall 2022.

    more national numbers

  • Sources and updates, January 8

    • NIH launches at-home testing telehealth program: This week, the National Institutes of Health announced the first location for “Home Test to Treat,” a new program that will make it easier for people in vulnerable communities to receive Paxlovid after testing positive on at-home, rapid tests. The Biden administration first announced this program in September, but it’s formally launching now with Berks County, Pennsylvania as the first participating community. As Paxlovid shifts to a drug that must be privately purchased instead of provided for free by the federal government, more programs like this one will be needed to fill access gaps.
    • Study estimates global Long COVID prevalence: A large team of researchers, led by population health scientists at the University of Washington, conducted an extensive review of Long COVID symptoms. The analysis used 54 prior studies and two medical record databases, incorporating data from 1.2 million people in total. Overall, about 6% of patients reported at least one class of Long COVID symptoms three months after their initial infections, with the vast majority of cases occurring in people who had mild acute cases. The study was published in JAMA in October, but gained attention this week thanks to an article that its leading authors wrote in The Conversation.
    • China’s COVID-19 data are unreliable: It’s been about a month since China loosened its COVID-19 protocols in the wake of protests and contagious Omicron subvariants, and the country is now facing a massive surge—with as many as one million new cases a day according to some modeling estimates. Yet COVID-19 deaths reported in the country have been very low, fewer than five a day. This discrepancy suggests that China’s authorities are not correctly counting their COVID-19 deaths, while the country’s dismantled testing infrastructure has also led to less reliable case numbers. Officials from the World Health Organization have formally called on the country to “be more forthcoming with information” about its COVID-19 surge, reports Helen Branswell at STAT News.
    • CDC testing airplane wastewater on flights from China: In response to surveillance concerns, the CDC is working to test wastewater on flights arriving from China in select U.S. airports. This method is, of course, more efficient than testing every single traveler from the country in the interest of identifying any new variants that might arise. (Though it’s worth noting that some experts are skeptical about the potential of new variants arising in China.) Scientists from Concentric, a company that works with the CDC on traveler surveillance, previously talked about plane wastewater testing during our interview in November.
    • Race/ethnicity differences among child vaccination rates: Finally, a notable study in this week’s CDC Morbidity and Mortality Weekly Report: researchers at the CDC and collaborators examined vaccination rates among children ages five to 17 using data from the National Immunization Survey. They found vaccination coverage (with at least one dose) was highest among Asian children (at about 75%), followed by Hispanic or Latino children (49%), white children (45%), and Black children (43%). The researchers also noted differences among vaccination rates by other socioeconomic factors, and by parents’ mask-wearing habits.

    All featured sources
  • National numbers, January 8

    National numbers, January 8

    Wastewater surveillance in Boston suggests COVID-19 transmission has reached levels not seen since last winter.

    In the past week (December 29 through January 4), the U.S. officially reported about 470,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 67,000 new cases each day
    • 143 total new cases for every 100,000 Americans
    • 16% more new cases than last week (December 22-28)

    In the past week, the U.S. also reported about 46,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 6,500 new admissions each day
    • 13.9 total admissions for every 100,000 Americans
    • 16% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,700 new COVID-19 deaths (390 per day)
    • 28% of new cases are caused by Omicron XBB.1.5; 56% by BQ.1 and BQ.1.1; 5% by XBB (as of January 7)
    • An average of 150,000 vaccinations per day

    Well, here we are: the winter COVID-19 surge. It may have happened later than some experts predicted, but the U.S. is clearly now experiencing an uptick in virus transmission as the latest, most contagious Omicron subvariants collide with holiday travel and gatherings.

    You might notice that the CDC’s official case numbers didn’t rise too dramatically this week (though the national count is up 16% compared to last week). That’s unsurprising: case increases after holidays are always delayed, because many testing sites and public health officials take time off from processing new data. Christmas and New Year’s tend to deliver the worst of this trend—and in 2022, limited access to PCR testing made case numbers even less reliable.

    Wastewater surveillance, on the other hand, clearly shows a significant rise in coronavirus spread from early December through early January—building on another rise that followed Thanksgiving. Biobot’s dashboard suggests that the U.S. as a whole is seeing about as much COVID-19 transmission now as we saw at the peak of the summer BA.5 wave. In some places, transmission is the highest it’s been since last January (during the original Omicron surge.)

    The CDC’s wastewater data similarly show increasing COVID-19: out of 600 sites with available recent data, more than half were reporting upticks in the two-week period ending January 2. 117 of those sites reported an increase between 100% and 999%, and 87 reported an increase over 1,000%.

    Regionally, the Northeast has reported the biggest recent COVID-19 spike in wastewater, though the trend may already be turning around. We see this both in Biobot’s regional data and in individual cities and counties, like Boston and New York City. The Northeast is also a hotspot for XBB.1.5, a homegrown Omicron subvariant that’s spreading faster than other lineages. (More on that later in the issue.)

    In addition to the wastewater surveillance, hospitalization data have remained uninterrupted by the holidays with clear increases in COVID-19 patients through December and into this week. This week, about 6,600 new COVID-19 patients were admitted to hospitals nationwide, a 16% increase from the prior week and about twice the number of people admitted during the week before Thanksgiving.

    Washington D.C., Connecticut, Massachusetts, and West Virginia reported the highest rates of new COVID-19 patients in the week ending January 3, according to the latest Community Profile Report. They were followed by other Northeast states New Jersey, New York, and Delaware. But states reporting the highest increases in hospitalization are in the South: Louisiana, Mississippi, Florida, Texas.

    Two pieces of good news for this week: the flu and RSV are both trending down after their surges earlier in the fall. High levels of influenza-like activity remain in the majority of states, though. And we may see a second flu peak driven by a second strain, as Katelyn Jetelina reports in Your Local Epidemiologist.

    All the same safety measures we know and love—masks, testing, vaccinations, etc.—continue to help reduce the risk of COVID-19 and other viruses. But uptake of these measures remains low. As of January 5, only 15% of the eligible U.S. population has received an Omicron-specific booster dose, per the CDC.

    more national numbers

  • Sources and updates, December 18

    • Federal government opens up at-home test orders: The Biden administration has revived its program to mail out free COVID-19 at-home rapid tests, just in time for the holidays. Every household can now order four more tests. This feels pretty minimal (and late in the season) for a surge already overwhelming hospitals, but it’s better than nothing. Also, remember to report your results from these tests to the National Institutes of Health’s new portal!
    • COVID-19 vaccines saved millions of lives: A new report from the Commonwealth Fund estimates the hospitalizations and deaths saved by two years of COVID-19 vaccines, in honor of the two-year anniversary of those shots first becoming available. About 80% of Americans have received at least one vaccine dose, the authors write, “with the cumulative effect of preventing more than 18 million additional hospitalizations and more than 3 million additional deaths.” The modeling data underlying this analysis are available for download.
    • Congressional COVID-19 subcommittee issues final report: House Democrats on the Select Subcommittee on the Coronavirus Crisis recently released their final report, a 200-page document outlining how the U.S. should prepare for the next public health emergency. The report sums up information from three years of research and hearings, including some new findings from more recent investigations. It was released in time with the Subcommittee’s final hearing last Wednesday, which also focused on preparedness. Next year, the Republican-controlled House will have new COVID-19 priorities.
    • Helix and CDC build multi-disease surveillance program: This week, leading viral surveillance company Helix announced that its partnership with the CDC has expanded to include sequencing other respiratory viruses, beyond COVID-19. The company will work with major health systems in Minnesota and Washington to track viral variants for the coronavirus, flu, RSV, and other pathogens—and will build infrastructure connecting that sequencing data to electronic health records. That second piece is particularly intriguing, as variant data usually aren’t connected back to health records in the U.S.
    • State-level wastewater surveillance expansions: The University of Minnesota is working on a process to test wastewater for the coronavirus, flu, and RSV simultaneously, according to reporting by local outlet KARE11. A team of researchers at the university’s medical school currently test wastewater from 44 sewage treatment plants in Minnesota, and is working to broaden this work with grants from the CDC and state health department. Across the country, New Hampshire’s state health department has announced that it will start publishing results of its COVID-19 wastewater testing program online in the coming weeks. The New Hampshire program includes 14 plants across the state.

    All featured sources

  • NYC’s wastewater program models the challenges facing local public health agencies

    NYC’s wastewater program models the challenges facing local public health agencies

    In 2022, wastewater data in NYC have more accurately reflected COVID-19 spread in the city than case data. See the full story (on MuckRock or Gothamist) for the interactive chart; links are below.

    My second big story this week is a detailed report about New York City’s wastewater surveillance program, highlighting its lack of transparency. You can read the story on Gothamist and/or on MuckRock. I’m particularly excited to share this one with NYC-based readers, as it uncovers a public program that’s been running under our feet for nearly three years.

    Longtime readers might remember that, back in April, I noticed that NYC wastewater data had disappeared from the CDC’s national dashboard. And the city’s data stayed unavailable even when other locations (which were similarly interrupted by the CDC’s switch between wastewater contractors) resumed reporting to the dashboard.

    That observation piqued my curiosity about how, exactly, NYC agencies are testing our wastewater—and what they’re doing with the data. So, I started investigating, with the support of MuckRock and Gothamist/WNYC. My project eventually revealed the answers to my questions: while NYC has set up an impressive, novel program to test all 14 city wastewater treatment plants for COVID-19, the health department doesn’t appear to be taking advantage of these results.

    In a joint statement, NYC’s health and environmental protection agencies said that they still see wastewater surveillance as a “developing field” and are skeptical about its utility for public health. Even though NYC’s program has been running since early 2020 and cost over $1 million. And even though other wastewater programs across the U.S. and internationally have demonstrated the potential of this type of data.

    Here are the story’s main findings, as drafted for MuckRock’s version of the article:

    • New York City’s Department of Environmental Protection created a brand-new program to test city wastewater for COVID-19 in 2020, working with limited lab equipment and personnel to sample from 14 sewage treatment plants across the city. In doing so, the city brushed off assistance offered from “multitudes of academics” and private sector researchers, and set up its program in-house. It has cost more than $1 million over the past three years.
    • But the city didn’t publicly post any wastewater data until January 2022, almost two years after testing started. Unlike other large cities, such as Boston, New York City lacks a public dashboard for wastewater data. The city’s data available on dashboards run by the Centers for Disease Control and Prevention and New York State are often delayed by a week or more, making it less useful for New Yorkers seeking advanced warning about potential new surges.
    • In other parts of the U.S. — and at Columbia University in uptown Manhattan — wastewater surveillance is used for public health strategies, such as encouraging people to get PCR tests or sending extra resources to hospitals before a surge. However, New York City’s health and environmental agencies say they still consider wastewater research a “developing field” and aren’t using it for policy decisions.
    • In response to our questions, city health and environment agency officials argued that wastewater results “do not generally provide a complete picture” of how COVID-19 is spreading and said, unlike in other parts of the country, trends in city wastewater data tend to align with case counts rather than predicting them. But wastewater has shown a higher level of COVID-19 spread than PCR testing, as the latter became less available in 2022, according to Gothamist and MuckRock analyses. This pattern suggests that the sewage numbers may more accurately reflect actual disease patterns.
    • A bill introduced to the New York City Council in August would make the wastewater surveillance program permanent, expand it to other public health threats as needed, and require the health department to report data on a public dashboard.

    For readers outside NYC, I think this story provides an informative case study of the hurdles that wastewater surveillance for COVID-19 (and other diseases) will need to clear.

    First, you have the resource challenges. If the NYC Department of Environmental Protection, which oversees the largest municipal water network in the country, had a hard time getting equipment and personnel for testing—imagine the challenges facing small, rural public health departments.

    Next, after testing is set up, you have to interpret the data. NYC’s health department seems to be somewhat stuck on this step, with no public dashboard and its insistence that city residents should look at clinical case data—which we know are a significant undercount of true infections—rather than wastewater data. To be fair, wastewater data are new terrain for public health experts, with a lot of analytical issues. (See my MuckRock/FiveThirtyEight story from the spring for more details on this.)

    And finally, you have to communicate the data. How do you share wastewater results with the public in a way that is clear, real-time, local—and acknowledging necessary caveats? This is a tough challenge that health agencies across the U.S. are just starting to tackle, in tandem with the private companies that work on wastewater analysis.

    As I said in the radio story accompanying my piece, I hope that, someday, we can get wastewater surveillance updates as easily and regularly as we get weather updates. That future feels a long way off right now, but I intend to keep reporting on the journey in 2023.

    If you live somewhere with a thriving (or faltering) wastewater surveillance program, reach out and tell me about it!

    More on wastewater data

  • National numbers, December 18

    National numbers, December 18

    Biobot’s wastewater surveillance data suggest that COVID-19 spread is trending down in the West coast and plateauing in other regions. Data as of December 15.

    In the past week (December 8 through 14), the U.S. reported about 460,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 65,000 new cases each day
    • 139 total new cases for every 100,000 Americans
    • 3% fewer new cases than last week (December 1-7)

    In the past week, the U.S. also reported about 35,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 5,000 new admissions each day
    • 10.7 total admissions for every 100,000 Americans
    • 2% more new admissions than last week

    Additionally, the U.S. reported:

    • 2,700 new COVID-19 deaths (390 per day)
    • 69% of new cases are caused by Omicron BQ.1 and BQ.1.1; 5% by BF.7; 7% by XBB (as of December 17)
    • An average of 250,000 vaccinations per day (CDC link)

    After a significant post-Thanksgiving spike, COVID-19 transmission in the U.S. appears to be in a high plateau, according to trends in cases and wastewater. Official case counts stayed fairly steady this week compared to the week following the holiday, according to the CDC, while wastewater data from Biobot show coronavirus concentrations leveling out.

    COVID-19 hospital admissions are similarly at a high plateau: about 5,000 new people with COVID-19 were admitted to hospitals every day last week, per the CDC. That’s a 2% increase from last week.

    Going beyond the national trends, though, we see that some places are experiencing dips in COVID-19 spread while others are spiking. In Boston, for example, wastewater data suggest that COVID-19 is at its most prevalent since the surge in early summer. Across the country in Los Angeles, coronavirus levels in wastewater are trending down after increasing through November.

    New York and New Jersey had the highest official COVID-19 case rates in the last week, according to the latest Community Profile Report, followed by Illinois, California, and Rhode Island. But these data may be more a product of which states still have somewhat-available PCR testing than actual case comparisons.

    And even in places where COVID-19 is declining, the combined threat of this virus, flu, and RSV is still putting a lot of strain on healthcare systems. Take Los Angeles: while it might not be seeing record COVID-19 cases, the city currently has fewer free hospital beds available than at any other point in the pandemic, per reporting by the Los Angeles Times.

    Flu might be peaking in some parts of the country, Helen Branswell wrote in STAT on Friday, based on CDC data. But it’s still early in the typical flu season, and hard to tell how COVID-19 and the flu (and RSV) might impact each other.

    As we gear up for another week of holiday travel and gatherings—and as highly contagious Omicron subvariants, the BQs and XBB, continue to outcompete other versions of the virus—this is an important time to take all possible safety precautions.

    That includes getting your flu shot and the new Omicron-specific COVID-19 booster, which further CDC studies have shown is highly effective at preventing hospitalization. And it includes masking, testing before and after events, and gathering outdoors (or otherwise improving ventilation) to reduce your risk of spreading all kinds of viruses.

    more national numbers

  • Sources and updates, December 11

    • 2022 America’s Health Rankings released: This week, the United Health Foundation released its 2022 edition of America’s Health Rankings, a comprehensive report providing data for more than 80 different health metrics at national and state levels. The 2022 report includes new metrics tailored to show COVID-related disparities; for example, Black and Hispanic Americans had higher rates of losing friends and family members to COVID-19 compared to other groups. I’ve used data from past iterations of this report in stories before, and I’m looking forward to digging into the 2022 edition.
    • FDA authorizes bivalent boosters for young kids: This week, the FDA revised the emergency use authorizations (EUAs) of both Pfizer’s and Moderna’s updated, Omicron-specific booster shots to include children between six months and five years old. Kids who previously got two shots of Moderna’s vaccine for this age group can receive a bivalent booster two months later, while kids who got two shots of Pfizer’s vaccine can receive a bivalent booster as their third dose. (Remember, Pfizer’s vaccine for this age group includes three doses.) The updated EUAs will help protect young children from Omicron infection, though uptake will likely be low.
    • CDC updates breakthrough case data: Speaking of the updated boosters: the CDC recently added data on these shots to its analysis of COVID-19 cases and deaths by vaccination status. In September, people who had received a bivalent, Omicron-specific boosters had a 15 times lower risk of dying from COVID-19 compared to unvaccinated people; and in October, bivalent-boosted people had a three times lower risk of testing positive compared to the unvaccinated. The CDC will update these data on a monthly basis.
    • Director Walensky discusses authority challenges: One bit of coverage from the Milken Future of Health Summit that caught my attention: CDC Director Dr. Rochelle Walensky talked about the agency’s limitations in collecting data from states, reports Rachel Cohrs at STAT News. Walensky specifically highlighted the challenges that the CDC might face in collecting data when the public health emergency for COVID-19 ends, something I’ve previously covered in this publication.
    • Boston establishes neighborhood-level wastewater testing: Finally, one bit of wastewater surveillance news: the city of Boston is setting up 11 new sites to test wastewater, giving local public health officials more granular information about how COVID-19 is spreading in the region. The new initiative is a partnership with Biobot Analytics, the same wastewater testing company that has long worked with Boston, the CDC, and public health institutions across the country. (Boston was one of the first cities to start doing this testing.) Also, speaking of Biobot: the company just added a nice chart of coronavirus variants in U.S. wastewater over time to its dashboard.

    All featured sources
  • Answering reader questions about data interpretation, good masking

    Answering reader questions about data interpretation, good masking

    As this chart from Biobot shows, trends in wastewater and case data often look a bit different. But how do you compare wastewater numbers to true infection numbers?

    This week, I’m sharing answers to three questions from readers that came in recently, through emails and the COVID-19 Data Dispatch Google form. The questions discuss interpreting wastewater and case data, and an interesting masking conundrum.

    Q1: Comparing wastewater trends to case trends

    I would love to know if there is any data on what levels of COVID in wastewater equals what risk level—are there any guidelines that could be used to turn masking policies on or off, for example? We know going up is bad and that the data is noisy but, if there’s any information on what concentrations in sewage corresponds to what level of cases I would love to know.

    I would love to be able to point you to specific guidelines about matching wastewater levels to cases, but unfortunately this isn’t really available right now. And if it were available, you would likely need to tailor the analysis pretty closely to where you live.

    An ongoing challenge with using wastewater surveillance data, as I wrote about for FiveThirtyEight and MuckRock in the spring, is that this type of environmental information is categorically pretty different from traditional case data. When a public health agency provides case numbers, they are adding up results from tests done in hospitals, doctors’ offices, and other healthcare settings. Each test result generally represents one person and can be interpreted with that framework.

    But with wastewater data, figuring out exactly what your test results represent can be more complicated. The data generally include people sick with COVID-19 who shed the coronavirus in their waste, but different people might shed different amounts of virus depending on what stage of illness they’re at, the severity of their symptoms, and possibly other factors that scientists are still working to figure out. Environmental factors like a big rainstorm or runoff from nearby agriculture could also interfere with the data. Population shifts, like college students returning to their campus after a break, can cause noise, too.

    As a result, public health experts who interpret wastewater data generally need a lot of data—like, a year or more of testing’s worth of data—from a specific location in order to analyze how wastewater trends correlate with case trends. And the data has to be consistent; if your wastewater collection team switches their sample processing methods halfway through the year, that might interrupt the analysis.

    A few institutions have figured out the wastewater-to-cases correlation for their communities. For examples, see the section on San Diego in this story and this paper by researchers in Gainesville, Florida. But for most research groups and health departments, it’s still a work in progress.

    All of that said, I don’t think this complexity should stop individuals or organizations from using wastewater data to recommend turning mask policies (or other policies) on or off. This surveillance might be less precise, but a sustained increase in coronavirus concentrations in the sewer is still certainly cause for concern and can be used to inform public health guidance.

    Q2: Estimating case underreporting

    How do you estimate how undercounted COVID testing is? Asking because I work for Whentotest.org—our COVID Risk Quiz assumes that COVID testing is undercounted by 7x, but I believe I’ve seen you estimate that it could be undercounted by as much as 20x. Wondering how you get to that number—we want to keep our Quiz as up to date as possible, and that number is a moving target.

    It is definitely a moving target, since COVID-19 testing (especially the lab-based PCR testing that generally contributes to official case numbers) can go up or down depending on people’s access to tests, perceptions of how much transmission is going on, and so many other factors.

    That said, I would personally put undercounting in the 10 times to 20 times range for this fall, likely with different levels of undercounting for different locations. I have two sources for the 20 times number: the first is an estimate from the Institute for Health Metrics and Evaluation made in September, suggesting that 4% to 5% of infections in the U.S. were reported at that time. (If 5% of infections are reported, case counts are 20 times higher than reported cases.)

    My second source is a paper from epidemiologist Denis Nash and his team at the City University of New York, released as a preprint earlier this fall. The researchers surveyed a representative sample of 3,000 U.S. adults, finding that about 17% of the respondents had Omicron during a two-week period in the summer BA.5 surge. Extrapolating from the survey findings, the researchers estimated that about 44 million people across the country had COVID-19 in this timeframe—compared to 1.8 million reported cases. This estimate suggests reported cases were undercounted by a factor of 24.

    Unfortunately, I have to use months-old estimates here because the U.S. does not have a regular data source comparing cases to true infections. The Census and CDC’s Household Pulse Survey comes close to this, as it includes questions about whether survey respondents have recently received a COVID-19 diagnosis; but it doesn’t ask about rapid tests, recent exposure, or other factors needed to determine the true infection rate, so the numbers here are also underestimates.

    Personally, I keep a close eye out for survey studies like those done by Nash and his team at CUNY and use those results to inform how I interpret national case data. I’ll make sure to flag any future studies like this for readers.

    Q3: Nose-only masking

    I follow some masking subs on Reddit and folks periodically suggest to others or refer to hacking masks that only cover their nose (KN95, N95s, etc.) for dental appointments or unavoidable indoor eating scenarios. Assuming they’re successful in creating a proper seal for these “half masks,” would there actually be any scientific backing this is helpful in minimizing risk?

    I wasn’t sure how to answer this question, so I shared it on Twitter, tagging a couple of masking and ventilation experts I know.

    Overall, the consensus that emerged from my replies is that it could be helpful to wear a mask over one’s nose for short periods of time, but it’s hard to say for sure due to a lack of rigorous research in this area. Behavior also plays a big role in how effective such a mask might be in alleviating risk.

    One expert, Devabhaktuni Srikrishna, pointed out that having a sealed filter over one’s nose could reduce the amount of virus that gets inhaled, if the coronavirus is present in the space. (This “inhalation dose” might correlate with one’s chances of infection and/or severity of symptoms if infected, though research is still ongoing on these questions.)

    Achieving a sealed filter over the nose is easier said than done, though. You can’t just use a standard mask, since that’s designed for the nose and mouth. One commenter shared a system that he uses, an elastomeric nose mask held in place with a headband. Another suggested using nasal filters designed to block allergens. As far as I know, there hasn’t been any research showing what might be most successful—unlike the extensive research that has gone into showing the value of high-quality face-masks and respirators.

    In addition to the discussion of designing a nose-only mask, this reader’s question led to some discussion about the careful behavior needed to use it successfully. One commenter pointed out that, if you’re eating alone, it’s easier to stay focused on breathing patterns than if you’re eating in a group and engaged in conversation. I also appreciated this reply from a Louisiana-based behavioral scientist:

    So, to summarize, I’d say that a nose filter could be helpful for situations like a dentist appointment and could be helpful (but trickier) for indoor dining—but it’s hard to say for sure. A much easier conclusion: avoid indoor dining as much as possible during COVID-19 surges like the one we’re in right now.

    More reader responses

  • COVID source shout-out: Variant data from wastewater

    COVID source shout-out: Variant data from wastewater

    New York City is one of a few jurisdictions contributing variant sequencing data from wastewater to CDC NWSS.

    I recently learned that the CDC is publishing a limited amount of variant surveillance data from its National Wastewater Surveillance System (NWSS).

    While NWSS is mostly focused on tracking coronavirus concentrations in wastewater as a proxy for transmission patterns, about 100 sites in the national network are also sequencing their wastewater samples and providing variant data. These data are available on the “Variant Summary” page of the CDC’s COVID Data Tracker, along with data from the CDC’s clinical specimen and traveler surveillance systems.

    The NWSS variant data is not very representative of the entire country (as a relatively small number of jurisdictions are sending the CDC this information), but this is still a helpful starting point for expanding wastewater surveillance to include sequencing. I hope to see this program expand in the coming months.

    more source spotlights