Author: Betsy Ladyzhets

  • National numbers, April 23

    National numbers, April 23

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

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

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

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

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

    Additionally, the U.S. reported:

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

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

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

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

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

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

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

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

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

  • COVID source callout: Montana ends its dashboard

    Last week, I wrote about the Iowa health department’s move to end COVID-19 case reporting requirements for labs, and in turn stop reporting these data to the CDC. Well, Montana just became the next state to follow this trend.

    The state’s public health agency announced that it will stop updating its COVID-19 dashboard on May 5, the week before the federal public health emergency ends, in a note on the dashboard and a statement to local media outlets.

    Unlike Iowa, Montana will continue reporting COVID-19 numbers to the CDC; so residents of that state will still be able to find information on the CDC’s dashboard. But the discontinuation of Monatana’s own dashboard shows how the state is taking resources out of pandemic response and treating COVID-19 as an endemic virus—even though it’s not.

  • Sources and updates, April 16

    • Long COVID care access challenges: A new paper, published this week in JAMA Network Open, shares the results of a survey by the Urban Institute think tank. The researchers surveyed about 9,500 adults, including 800 with self-reported Long COVID, about their experiences accessing medical care. The long-haulers were more likely to report difficulties with accessing and paying for care, compared to adults who don’t have the condition. To address this issue, the healthcare system needs to develop clinical guidelines for Long COVID, train workers about it, address insurance barriers, and more, the researchers said.
    • PolyBio announces Long COVID research agenda: Speaking of Long COVID: the PolyBio Research Foundation, a nonprofit devoted to Long COVID, ME/CFS, and other chronic conditions, has announced several research projects that it’s supporting. The projects will evaluate potential biological mechanisms underlying Long COVID symptoms, such as virus persisting in different parts of the body, changes in T cell activity, microclots, and more. PolyBio has a great reputation for pushing ahead post-viral disease research, and I’m looking forward to seeing the results of these studies.
    • Bivalent boosters hold up against XBB variants: Another new study that caught my attention this week: researchers at the University of North Carolina and North Carolina state health department reported on how well the bivalent, Omicron-specific boosters worked, based on the agency’s surveillance data. The study examined data from September 2022 through February 2023, a period when the BQ and XBB subvariants were dominating coronavirus spread. North Carolina residents who received the bivalent boosters were significantly less likely to experience severe COVID-19 symptoms, the researchers found, but their protection started to wane within a month after receiving the shots.
    • Resources on indoor air quality in schools: Journalist’s Resource recently updated this list of research and resources for journalists interested in covering indoor air quality in K-12 schools. The update follows a CDC report showing that many public schools across the U.S. have failed to upgrade their ventilation, despite federal funding to do so (which I covered last week). School air quality is a topic that deserves more reporting, especially from local journalists who can dig into how their school districts are doing.
    • Arizona county starts monitoring for a fungus in wastewater: I’m always on the lookout for new uses of wastewater surveillance, and one promising application could be tracking Candida auris, a fungal pathogen that’s resistant to common drugs and spreads quickly in healthcare settings. The Arizona state health department and a lab at the University of Arizona recently launched a pilot program to track this fungus through Yuma County’s wastewater. Arizona and neighboring southwest states have been a hotbed for C. auris; if this pilot is successful, other states could start similar efforts.

  • Mainstream media’s COVID-19 failure

    It’s pretty clear, at this point, that the U.S.’s political leaders would like for us all to pretend that the pandemic is over. President Biden says he doesn’t think about it (even though everyone in his orbit is still PCR-tested regularly), Congress hasn’t passed any new COVID-19 funding since spring 2021 (but sends billions to the military), state and local governments end their final mask mandates (yes, the ones in healthcare settings), and so on.

    And the mainstream media—tasked with holding these powerful people accountable—has let them do it. Most news outlets these days barely want to include the word “COVID-19” in their headlines, let alone give you an honest picture of the risks that this disease still poses. Many individual journalists are doing their best to get the important news out, but they have to push back against shrinking editorial budgets, colleagues who spread misinformation, weariness from sources, and other structural barriers.

    Personally, as a freelancer still covering this topic, I would love to write about only COVID-19, all the time. But in order to keep working, I’ve had to branch out. Even when I write COVID-related stories, these days, the headlines often aren’t directly about the coronavirus; they focus on broader issues like health surveillance or chronic disease that are easier to give broader appeal (or at least, what my editors see as broader appeal).

    I’m eternally grateful to have the COVID-19 Data Dispatch and its community of readers, as a place where I can keep prioritizing this topic and sharing my honest perspectives, rather than watering them down for more mainstream outlets. But this is a pretty small fish in the sea of media coverage—I know my work only goes so far.

    So, I was really glad to see an excellent article in Neiman Lab this week that captures exactly how mainstream media has failed on covering COVID-19 over the last two years. Climate journalist Kendra Pierre-Louis explains that yes, COVID-19 is still a major health threat, and publications have failed their duty to the public by largely ignoring it.

    I highly recommend reading the full story, but here’s one section that exemplifies Pierre-Louis’ argument:

    Outlets like The New Yorker, The Washington Post, and NPR, to name just a few, have amplified voices and arguments that helped create a narrative that not only pathologizes those who remain cautious about the disease, but also fails to adequately convey the risks associated with Covid such that many people are unwittingly taking on potentially lifelong risks.

    In the process, we’ve failed at our field’s core tenets — to hold power to account and to follow the evidence. Our failures here could last a generation. As reporters, it’s our responsibility to accurately represent the needs of diverse perspectives and avoid an ableist bias that diminishes the real and lasting health concerns not only of those who are keenly at risk but those who are cautious about repeatedly catching a virus that scientists are still grappling to understand.

    I hope this article inspires some reflection among other journalists, if not some real changes in editorial priorities.

  • Next-generation COVID-19 vaccines: what you should know

    Next-generation COVID-19 vaccines: what you should know

    Low uptake of the Omicron-specific boosters does not inspire confidence in the government’s ability to distribute next-gen vaccines. Data from the CDC.

    This week, the White House announced that it’s setting up a $5 billion program to support next-generation COVID-19 vaccines and treatments. The program, called Project Next Gen, is essentially a follow-up to Operation Warp Speed (which launched our current COVID-19 vaccines in 2020).

    Project Next Gen is a big step toward actually ending the pandemic, not just pretending it’s over. The federal government can support large-scale clinical trials and speed up regulatory approval in a way that no research group or company could. Still, the U.S.’s prior vaccine campaigns don’t inspire confidence that this project will lead to widespread adoption of new shots when they become available.

    What are the “next-gen” vaccines under development?

    Next-gen COVID-19 vaccines generally fall into two categories: nasal vaccines that would provide better protection against infection, and pan-coronavirus vaccines that would provide better protection against new variants.

    Nasal vaccines basically deliver immunity with a spray into the nose, rather than a shot in the arm. This type of vaccine already exists for other common viruses, like the flu. They’re easier to receive for people wary of needles, but they also have a big advantage for the immune system: these vaccines boost immunity in the nose, mouth, and upper respiratory tract, which are the main places where the coronavirus typically infects people. With a nasal vaccine’s help, the immune system is better poised to fight off the virus at infection, rather than fighting off severe symptoms after someone is already infected.

    Pan-coronavirus vaccines, meanwhile, address the variant challenge. Our current COVID-19 vaccines are designed around the virus’ spike protein, a component on the outside of the virus that helps it break into human cells. But the spike protein is the primary area where the coronavirus mutates; the spike proteins of XBB.1.5.1 or XBB.1.16 are very different from that of the original virus. New pan-virus vaccine candidates are designed around different aspects of the virus that don’t mutate as much, and therefore would remain more protective against new variants.

    For more details on why these vaccine options are important and which candidates are now in the pipeline, I recommend reading this Substack post by Eric Topol, the prominent COVID-19 commentator and director of the Scripps Translational Research Institute. Topol has been calling on the Biden administration to support next-generation vaccines for a long time; he’s written extensively on this subject.

    Why is a federal program important to advance these vaccines?

    Operation Warp Speed was a monumental achievement, probably the most successful aspect of the U.S.’s response to COVID-19. The federal government provided significant funding to pharmaceutical companies, while also assisting with clinical trial development and facilitating collaboration between companies and the FDA. And the first mRNA vaccines were delivered within one year of the pandemic starting.

    Project Next Gen will provide a similar boost to the companies working on next-gen vaccines. It’s not going to operate at the same scale as Operation Warp Speed; it received $5 billion in funding, compared to Warp Speed’s $18 billion. Still, that’s a huge chunk of money for companies, and other types of federal support that will be crucial for quickly starting up large clinical trials.

    The White House is currently assessing pharmaceutical companies that it may partner with on this initiative, according to reporting by the Washington Post. There’s no clear timeline for Project Next Gen yet, as the government will need to work with specific companies and the FDA to plan trials, but it’ll certainly be much faster than these vaccines would get to people otherwise.

    What are the challenges facing Project Next Gen?

    While this initiative is great news, its implementation will face a lot of challenges—especially after the new vaccines become available. The federal government’s rhetoric around COVID-19, combined with our now-mostly-dismantled infrastructure for responding to the disease, will present major barriers to getting people vaccinated.

    For example, it’s obviously very ironic that the Project Next Gen announcement came in the same week as Biden signed a bill ending one of the federal COVID-19 emergencies. And the timing isn’t just coincidental: the White House and HHS are actually using the emergency’s end to fund this project, moving in money that was previously devoted to COVID-19 testing and other preventative measures.

    The administration is basically telling people: “COVID-19 is over, but uh, we might need you to get a new vaccine or two next year so that you don’t die from it.” It’s hard to blame people for not getting the second part of the message.

    We’re already seeing this with the Omicron boosters: only 17% of the U.S. population has received one, according to CDC data. Lack of awareness about those vaccines and the many barriers that now exist to get the shots contributed to that low number. Even if Project Next Gen delivers the most effective COVID-19 vaccines possible, a lot more investment would be necessary to actually get them to people.

    More on vaccines

  • National numbers, April 16

    National numbers, April 16

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

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

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

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

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

    Additionally, the U.S. reported:

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

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

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

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

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

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

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

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

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

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

  • COVID source callout: Iowa ends COVID-19 case reporting

    As of April 1, Iowa’s state health department is no longer requiring public health laboratories to report positive COVID-19 test results—and no longer reporting statewide data to the CDC. This decision, announced in late February, is part of a growing trend away from relying on case data as people use at-home tests instead of PCR tests.

    Iowa’s health department “will continue to review and analyze COVID-19 and other health data from several sources,” including hospitalization metrics and syndromic surveillance, according to the agency. It’s essentially treating COVID-19 similarly to the flu and other common respiratory viruses.

    As a result of this change, Iowa is now no longer reporting COVID-19 case data to the CDC, the national agency said in this week’s data update. National, regional, state, and county-level CDC data exclude the state of Iowa, starting on April 1.

    This move seems like a natural extension of the state health reporting changes that we’ve seen across the country since last spring. I wouldn’t be surprised if more state health departments similarly stop reporting every COVID-19 case when the federal health emergency ends in May. Unfortuantely, this will become another driver of increasingly-less-reliable COVID-19 data in the U.S.

  • Sources and updates, April 9

    • Second Omicron boosters for high-risk adults: The FDA and CDC are planning to authorize a second round of bivalent, Omicron-specific vaccines for high-risk adults, the Washington Post reported this week. This decision will apply to Americans over age 65 and those who have compromised immune systems, with these groups becoming eligible four months after their initial bivalent boosters. It’s unclear exactly when the decision will become official; the FDA and CDC will make authorizations sometime “in the next few weeks,” according to WaPo.
    • HHS announces (underwhelming) Long COVID progress: This week marks one year since Biden issued a presidential memo kicking off a “whole-of-government response” to Long COVID. The Department of Health and Human Services (HHS) commemorated the occasion with a fact sheet sharing the federal government’s progress so far. Unfortunately, that progress has been fairly minor, mostly consisting of reports and guidance that largely summarize existing government programs or build on existing systems (such as Veterans Affairs hospitals). Many of the Long COVID programs that Biden previously proposed have not received funding from Congress; meanwhile, the National Institutes of Health’s RECOVER initiative, the one program that has been funded, has faced a lot of criticism.
    • RECOVER PIs recommend action on treatment: Speaking of RECOVER: this week, a group of scientists leading research hubs within the national study called for federal funding that would support treatment. The principal investigators (PIs) of these hubs have developed expertise in Long COVID through recruiting and studying patients, leading them to identify gaps in available medical care for long-haulers. To respond, the PIs recommend that Congress allocate $37.5 million to support Long COVID medical care at the RECOVER research sites. Their proposed budget includes patient outreach, telehealth support, educating healthcare workers on Long COVID, and more.
    • Ventilation improvements in K-12 schools: The CDC released a new study this week in its Morbidity and Mortality Weekly Report, sharing results of a survey (conducted last fall) including about 8,400 school districts representing 62% of public school students in the U.S. Research company MCH Strategic Data asked the districts about how they’d improved ventilation in their school buildings, along with other COVID-19 safety measures. About half of the districts reported “maintaining continuous airflow in classrooms,” one-third reported HVAC improvements, 28% reported using HEPA filters, and 8% reported using UV disinfectants. The results indicate that many districts have a long way to go in upgrading their indoor air quality.
    • Flu vs. COVID-19 mortality risk: Ziyad Al-Aly and his colleagues at the VA healthcare system in St. Louis have published another paper analyzing COVID-19 through the VA’s electronic health records. This study, published in JAMA Network, describes the mortality risk of COVID-19 compared to seasonal flu for patients hospitalized during the 2022-2023 winter season. The researchers evaluated about 9,000 COVID-19 patients and 2,400 flu patients, finding that risk of death for COVID-19 patients in the 30 days following hospitalization was about 1.6 times as high as the risk of death for flu patients. Despite great advances in vaccines and treatments, COVID-19 remains more dangerous than other seasonal viruses, the study suggests.
    • Biobot launches mpox dashboard: This week, leading wastewater surveillance company Biobot Analytics launched a new dashboard displaying its mpox (formerly monkeypox) monitoring. Biobot tests for mpox at hundreds of sewage sites across the U.S., largely through its partnership with the CDC, and will continue this monitoring through at least summer 2023. The new dashboard shows mpox detections nationally over time and monitoring sites by state; it also includes some information on how mpox surveillance differs from COVID-19 surveillance.

  • National numbers, April 9

    National numbers, April 9

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

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

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

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

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

    Additionally, the U.S. reported:

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

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

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

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

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

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

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

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

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

  • COVID source callout: GISAID in danger of losing trust

    GISAID, the global database of virus sequences, has faced a lot of criticism recently from the virologists and bioinformaticians who rely on it—potentially hindering responses to future virus outbreaks.

    First, there was controversy around genetic information from environmental samples taken at the Huanan Seafood Wholesale Market in Wuhan, China, which Chinese researchers posted to GISAID. An outside group of scientists found the sequences and analyzed them, finding the samples supported the hypothesis that SARS-CoV-2 originated in animals and jumped to humans at the seafood market. And then, GISAID revoked those scientists’ access to the database. (The original Chinese research group eventually published their findings.)

    Last week, another controversy came to light: GISAID is claiming that the first SARS-CoV-2 sequence to be publicly shared was posted on its platform, back in January 2020. Even though plenty of evidence suggests the first sequence was shared days earlier at virological.org, a virology forum. Reporting in Science Magazine and evidence shared on Twitter shows the true story of these early days of info-sharing, as well as how GISAID has tried to retroactively revise the narrative.

    While these issues might seem inconsequential outside of a small circle of experts, the controversies could lead some of the world’s top virologists and epidemiologists to stop using a major source for outbreak information. It doesn’t really matter who posted a SARS-CoV-2 sequence first. But it does matter that experts have trusted places to share data and collaborate on vital research.

    Without open data-sharing platforms like GISAID, the world may be less prepared for coming novel disease outbreaks. These recent controversies (and the broader debate over COVID-19’s origins) also speak to larger gaps in trust that could hinder future collaborations.