COVID-19 Data Dispatch

Tag: flu

  • COVID source shout-out: CDC’s respiratory virus surveillance

    As fall begins, we’re approaching respiratory virus season—that time of year when viruses like the flu, RSV, common coronaviruses, and adenoviruses all spread readily throughout the Northern Hemisphere. Tracking systems for these viruses may also be helpful for following COVID-19 this fall and winter.

    While COVID-19 doesn’t yet follow a predictable, seasonal pattern, its activity has increased with these other viruses in the last couple of years. (Indoor gatherings and travel, particularly around the holidays, lead to outbreaks of all kinds.)

    This year, experts anticipate COVID-19 will spread with the colder weather again. But we have fewer systems tracking it than we did during earlier pandemic winters: no more case data, testing and hospitalization data aren’t as comprehensive or reliable, death data are significantly delayed (and more likely than ever to undercount true COVID-19 deaths), etc.

    So, people seeking to keep up with disease trends in their areas might find it helpful to look at surveillance sources that include COVID-19 along with other respiratory diseases. The CDC’s FluView dashboard is one major source, presenting data from clinical testing laboratories and healthcare settings that participate in the agency’s regular surveillance programs.

    Despite the name, FluView includes data on all viruses that cause cold and flu symptoms, including COVID-19. (In fact, the same lab network that informs this dashboard is also the current source of the CDC’s COVID-19 test positivity data.) FluView is a helpful place to see overall respiratory disease activity for the U.S. as a whole and for particular states and regions. I find the state-by-state map of influenza-like activity particularly useful.

    Tracking COVID-19 during fall and winter 2023 is going to be harder than it’s been during prior years. But we aren’t entirely in the dark. The CDC’s respiratory virus surveillance programs are one helpful source to look at, along with wastewater surveillance and the other COVID-specific programs that remain active.

    more source spotlights

  • Sources and updates, September 17

    • Public comments to the CDC about infection control measures: The People’s CDC, a public health communication and advocacy organization that seeks to fill gaps left by the federal CDC, has published a database of comments about the importance of infection control measures in healthcare settings. These comments were sent to the CDC’s Healthcare Infection Control Practices Advisory Committee (HICPAC), as the committee considers changing the agency’s guidance to be more lenient about preventing infections in healthcare settings. As the CDC has not published comments publicly itself, the People’s CDC “asked people to forward us their comments to HICPAC, and created the People’s Register.” For more details about HICPAC, see this post.
    • Recommendations for masks, nasal sprays, other tools: In response to last week’s post discussing how nasal sprays may be used to reduce COVID-19 risk, a reader shared this video from RTHM Health, a telehealth clinic focused on Long COVID and related complex chronic diseases. “This video has a section with a good overview of different sprays and the strength of evidence for each one,” the reader wrote. The video also includes recommendations for high-quality reusable masks and respirators, along with other COVID-19 safety tools.
    • Wastewater surveillance for flu, RSV: A new study, published this week in the CDC’s Morbidity and Mortality Weekly Report, discusses how wastewater surveillance can complement other methods of monitoring the flu and respiratory syncytial virus (RSV). Researchers at Wisconsin’s state health department, the CDC, and other collaborators tracked flu and RSV in three Wisconsin cities’ sewage during last winter’s respiratory virus season. They found that wastewater trends “often preceded a rise” in emergency department visits for these viruses. This study follows other research that has shown wastewater surveillance can be a predictive tool for many diseases, not just COVID-19.
    • Better understanding coronavirus interactions with human cells: Another recent study, published in the journal Viruses, discusses how SARS-CoV-2 interacts with the proteins in human cells as it replicates. The research team (based at the University of California Riverside) identified a specific cellular process that the virus’ N protein hijacks and uses to copy its genetic material, leading to more coronavirus in the body. These findings could be used to develop new antiviral treatments that target this cellular process, both for COVID-19 and other similar diseases, the researchers said in a press release.
    • Limitations of prior immunity to COVID-19: One more recent paper that caught my attention: researchers at the University of Geneva in Switzerland studied how prior infection and/or vaccination can impact COVID-19 risk, based on about 50,000 cases and associated contact tracing data from the city of Geneva. The researchers found that both a recent infection and vaccination reduced the risk of getting infected from a close contact sick with COVID-19. But both types of immunity faded within a few months, leading people to remain vulnerable in the long-term. This study suggests that vaccines alone are not sufficient to control the spread of COVID-19; masks, ventilation improvements, and other interventions are needed, the authors argue.
    • NIH tests universal flu vaccine: Speaking of vaccines: the National Institute of Allergy and Infectious Diseases (or NIAID, one of the National Institutes of Health) announced this week that it’s starting a new trial for a universal flu vaccine. This vaccine, developed by NIAID researchers, can prompt the body to make antibodies against a wide variety of flu strains rather than focusing on one variant. The vaccine has done well in animal studies and is now ready for a phase one clinical trial. NIAID plans to test the vaccine in 24 volunteers, and will follow them closely through immune system testing to see how the vaccine performs.

  • Answering reader questions: Incubation period, vaccines coming this fall, nasal sprays

    I received a couple of reader questions in recent weeks that I’d like to answer here, in the hopes that my responses will be more broadly helpful. As a reminder, if you ever have a COVID-19 question that you’d like to ask, you can email me at betsy@coviddatadispatch.com, or send it anonymously through this Google form.

    COVID-19’s incubation period

    One reader asked:

    I’d love to learn more about COVID’s incubation period. I have read that it’s 2 to 14 days … but the median time seems to be on the low end (and could be as low as 24 hours?) How likely is it that it’s more like 14 days? I’d love to better understand this so that I know how to better handle exposures… Should I avoid someone who has had an exposure for two full weeks?

    This is a tricky question for two reasons. First, the incubation period—or the time between exposure to COVID-19 and starting to show symptoms of infection—does indeed vary a lot. One review of studies on this topic, posted as a preprint in May, found a range from two to seven days, though it can be even longer. The CDC recommends precautions for up to ten days after exposure.

    Second, the incubation period has changed as the coronavirus has mutated. The virus is constantly evolving to keep infecting us even as people build up immunity; shortening the incubation period is one of its strategies. Omicron has a notably shorter period than past variants; Katherine Wu at The Atlantic wrote an article about this in December 2021 that I think is still informative.

    The preprint I cited above found that Omicron had an average incubation period of 3.6 days, shorter than other variants. I think it’s reasonable to assume that this period has continued to get shorter as Omicron has evolved into the many lineages we’re dealing with now. But the pace of research on this topic has slowed somewhat (with less contact-tracing data available for scientists to work with), so it’s hard to say for certain.

    So, with these complexities in mind, how should one handle exposures? My personal strategy for this (noting that I’m not a doctor or qualified to give medical advice, just sharing my own experience) is to rely on a combination of timing, testing, and symptom monitoring. For the first couple of days after exposure, you wouldn’t be likely to have a positive test result even if you are infected, as it takes time for enough virus to build up in the body for tests to catch it. So, for those days, I’d just avoid people as much as possible.

    After three to four days, PCR tests would start to be effective, and after five to six days, rapid tests would be. So at that point, I’d start testing: using a mix of PCR and rapid tests over the course of several days, up to two weeks after exposure. Studies have shown that the more tests you do, the more likely you are to catch an infection (and this applies to both PCRs and rapids). Daily is the best strategy, but less frequent regimens can still be useful if your access to tests is limited. At the same time, I’d keep track of any new symptoms, as that can be a sign of infection even if all tests are negative.

    I’d personally be comfortable hanging out with someone who has had an exposure but consistent negative test results and no symptoms. But others who are less risk-tolerant than I am might avoid any contact for two weeks. The type of contact matters, too: a short, outdoor meeting or one with masks on is safer than a prolonged indoor, no-mask meeting.

    Vaccine effectiveness

    Another reader asked:

    Is there any information on the effectiveness of the latest vaccines, including vaccines that combine Covid and RSV, and are there similarities between these viruses (related?)

    As we head into respiratory virus season in the U.S., there will be, for the first time, vaccines available for all three major diseases: COVID-19, the flu, and RSV. I’ll talk about effectiveness for each one separately, because they are all separate vaccines for separate viruses. There’s no combined COVID-RSV vaccine on the market.

    COVID-19: We know the fall boosters will target XBB.1.5, a variant that has dominated COVID-19 spread in the U.S. recently. There isn’t much data available on these vaccines yet, because the companies developing them (Pfizer, Moderna, Novavax) have yet to present about their boosters to the FDA and CDC, as is the typical process. The CDC’s vaccine advisory committee is meeting this coming Tuesday to talk fall vaccines, though, so it’s likely we will see some data from that meeting.

    Also worth noting: some early laboratory studies suggest that vaccines based on XBB.1.5 will provide good protection against BA.2.86, despite concerns about differences between these variants. (More on this later in today’s issue.)

    Flu: Every year, scientists and health officials work together to update flu vaccines based on the influenza strains that are circulating around the world. Effectiveness can vary from year to year, depending on how well the shots match circulating strains.

    This week, we got a promising update about the 2023 flu vaccines: CDC scientists and colleagues studied how well these shots worked in the Southern Hemisphere, which has its flu season before the Northern Hemisphere. The vaccine reduced patients’ risk of flu-related hospitalization by 52%, based on data from several South American countries that participate in flu surveillance. This is pretty good by flu vaccine standards; see more context about the study in this article from TIME.

    RSV: There are two new RSV vaccines that will be available this fall, both authorized by the FDA and CDC in recent months. These vaccines—one produced by Pfizer, one by GSK—both did well in clinical trials, reducing participants’ risks of severe RSV symptoms by about 90% (for the first year after infection, with effectiveness declining over time).

    Both vaccines were authorized specifically for older adults, and Pfizer’s was also authorized for pregnant people as a protective measure for their newborns. We’ll get more data about these vaccines as the respiratory virus season progresses, but for now, experts are recommending that eligible adults do get the shots. This article from Yale Medicine goes into more details.

    Nasal sprays as COVID-19 protection

    Another reader asked:

    I’m thinking of researching what foods and supplement are anti-viral anti-COVID. I’m wondering if anyone has done any research on that?

    I haven’t seen too much research on about foods and supplements, since dietary options are usually not considered medical products for study. Generally, having a healthy diet can be considered helpful for reducing risk from many health conditions, but it’s not something to rely on as a precaution in the same way as you might rely on masking or cleaning air.

    Another thing you might try, though, would be nasal sprays to boost the immune system. I have yet to try these myself, but have seen them recommended on COVID-19 Safety Twitter and by cautious friends. The basic idea of these nasal sprays is to kill viruses in one’s upper respiratory tract, essentially blocking any coronavirus that might be present from spreading further. People take these sprays as a preventative measure before potential exposures.

    A couple of references on nasal sprays:

    https://twitter.com/Clean_Air_Club_/status/1685790242681331713

  • National numbers, March 19

    National numbers, March 19

    New hospital admissions have fallen significantly from their recent peak in January, but are still much higher than at this time last year. Chart from the CDC.

    In the past week (March 9 through 15), the U.S. officially reported about 150,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 21,000 new cases each day
    • 46 total new cases for every 100,000 Americans
    • 20% fewer new cases than last week (March 2-8)

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

    • An average of 2,800 new admissions each day
    • 5.9 total admissions for every 100,000 Americans
    • 10% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 1,700 new COVID-19 deaths (240 per day)
    • 90% of new cases are caused by Omicron XBB.1.5; 2% by XBB.1.5.1; 0.5% by CH.1.1 (as of March 18)
    • An average of 40,000 vaccinations per day

    The trend continues: COVID-19 spread is still on the decline across the U.S., but it’s a slow decline. These updates are getting pretty repetitive to write, as we’ve been seeing this pattern since late January—which, honestly, I’m taking as a good sign.

    Last week, I noted that the drop in official COVID-19 cases (reported to the CDC) was exaggerated slightly because of data delays; three states didn’t report cases in the week ending March 8. This week, the same thing happened for three different states: Texas, Arkansas, and Indiana. We’ll likely continue to see reporting issues like this, as state and local health departments put fewer resources into tracking COVID-19.

    Even so, the official case data, hospital admissions, and wastewater surveillance all point to continued decreases in coronavirus transmission. National hospital admissions dropped by about 12% this week compared to the week prior. But there are still a lot of Americans getting severe COVID-19 symptoms, with more than 3,000 people newly hospitalized each week for the last month.

    Wastewater surveillance data from Biobot suggest that coronavirus spread is getting lower, but it’s still at much higher levels nationally than we saw at this time in 2021 and 2022. Regionally, the Midwest now has slightly more virus circulating than other parts of the country, but all four major regions are seeing slow declines or plateaus.

    In other good news: flu activity is still low nationally, according to the CDC’s flu surveillance. Experts had worried we might see a second flu surge, driven by a different strain of the influenza virus, after the initial surge died down in January. But so far, that hasn’t happened. Almost every state reported moderate or low levels of influenza-like activity in the week ending March 11.

    XBB.1.5 continues to be the dominant coronavirus lineage in the U.S., causing an estimated 90% of cases nationwide in the week ending March 18. XBB.1.5.1, a descendant of XBB.1.5, is growing slowly (it caused an estimated 2% of cases nationwide this week) and doesn’t seem to be very competitive yet. The CDC also has yet to break out XBB.1.9 or XBB.1.16, other subvariants that mutated from XBB.

    Yesterday, I spoke about wastewater surveillance at New York City School of Data, a civic conference that’s part of the city’s Open Data Week. While the conference wasn’t focused on health or science topics, the organizers required masks and checked attendees’ vaccinations. I also brought my CO2 monitor to the event, and found ventilation was generally good in the session rooms. This conference was a nice reminder that some organizations are still following the data and science on COVID-19 precautions.

    more national numbers

  • Sources and updates, March 5

    • FDA authorizes joint COVID/flu rapid test, but there’s a catch: Late last week, the FDA issued emergency use authorization to the U.S.’s first at-home, rapid test capable of detecting both COVID-19 and the flu. This could be a really useful tool for people experiencing respiratory symptoms, since COVID-19 and flu can appear so similar. But you might not be seeing this test on pharmacy shelves anytime soon: Lucira Health, the test’s manufacturer, just declared bankruptcy. And the company actually blamed FDA authorization delays for contributing to its financial situation, as it had produced supplies anticipating a fall/winter sale of tests. Brittany Trang at STAT News reported on the situation; read her story for more details.
    • COVID-19 surveillance stressed out essential workers: For a new report, the nonprofit Data & Society interviewed 50 essential workers from meatpacking and food processing, warehousing, manufacturing, and grocery retail industries about their experiences with COVID-19 surveillance efforts, like temperature checks and proximity monitoring. Overall, workers found that these surveillance measures added time and stress to the job but did not actually provide information about COVID-19 spread in their workplaces. (Companies often cited privacy concerns as a reason not to share when someone got sick, according to the report.) The report shows how health data often doesn’t make it back to the people most impacted by its collection.
    • Vaccinations vs. Long COVID meta-analysis: A new paper published this week in the BMJ examines how COVID-19 vaccination impacts Long COVID risk. The researchers (at Bond University in Australia) performed a meta-analysis, compiling results from 16 prior studies. While the studies overall showed that vaccination can decrease risk of getting Long COVID after an infection (and may reduce symptoms for patients already sick with Long COVID), the studies were too different in their methodologies to actually allow for “any meaningful meta-analysis,” the authors noted. To better study this question, more rigorous clinical trials are needed, the researchers wrote.
    • Tracking Long COVID with insurance data: Another notable Long COVID paper, published this week in JAMA Health Forum: researchers at the insurance company Elevance Health compared health outcomes for about 13,000 people with post-COVID symptoms compared to 27,000 who did not have symptoms. The researchers found that, in the one year following acute COVID-19, Long COVID patients had higher risks for several health outcomes, including strokes, heart failure, asthma, and COPD; people in the post-COVID cohort were also more likely to die in that year-long period. I expect insurance databases like the one used in this paper may become more common Long COVID data sources. Also, see Eric Topol’s Substack for commentary.
    • FDA committee recommends RSV vaccine applications: Finally, a bit of good news on the “other respiratory viruses” front: the FDA’s vaccine advisory committee has recommended the agency move forward with two applications for RSV vaccines. Major pharmaceutical companies Pfizer and GlaxoSmithKline (GSK) have been working on RSV vaccine options; while early data appear promising, clinical trials on both vaccines have found potentially concerning safety signals. The trial populations have been relatively small, making these signals difficult to interpret right now but worthy of additional study. As usual, Katelyn Jetelina at Your Local Epidemiologist has provided a great summary of the FDA advisory committee meeting.

    All featured sources
  • This winter’s COVID-19 surge wasn’t “mild”

    This winter’s COVID-19 surge wasn’t “mild”

    Wastewater surveillance data from Biobot suggests that COVID-19 spread this winter (2022-2023) was higher than all other surges prior to Omicron’s emergence.

    You might have seen some headlines like this in the last few weeks: COVID-19 was “mild” this winter. This winter was “better” than previous winters. COVID-19 is becoming “another seasonal virus” like flu and RSV. But is this true?

    While it’s accurate that the U.S. reported fewer COVID-19 cases this past winter compared to last year (when the country experienced our first, massive Omicron surge) or the prior year (our biggest surge pre-vaccines), this winter still saw an extraordinary amount of severe illness, death, and potential future disability due to COVID-19. Surges of other respiratory viruses also put enormous strain on the healthcare system.

    If we call this winter “mild,” we run the risk of believing this level of disease is acceptable. Such portrayals of COVID-19 seek to make us think future surges will be nothing to worry about, despite clear evidence to the contrary.

    Let’s go through some numbers. Since the beginning of November, the U.S. has reported:

    • More than 5 million new COVID-19 cases (reported). Note that cases are likely underreported by 10 to 20 times in our era of under-testing, so the true number may be closer to 100 million.
    • More than 400,000 new COVID-19 hospitalizations, piling on top of hospitalizations for the flu, RSV, and other diseases, and coming as hospitals deal with staff shortages and worker burnout.
    • More than 40,000 new COVID-19 deaths, amounting to more than 400 new deaths per day. This number is also likely an undercount, as death certificates can take a long time to be processed.
    • The majority of COVID-19 deaths were among vaccinated people. A report from the Kaiser Family Foundation found that breakthrough deaths started to outnumber those among unvaccinated people in summer 2022, a trend that has continued with low booster uptake.
    • Coronavirus levels in wastewater were higher than all surges prior to Omicron, including the winter surge in 2020-2021 and the Delta surge in summer 2021, according to data from Biobot.
    • XBB.1.5, the latest and most contagious Omicron subvariant, evolved in the U.S. this winter, likely in New York State. Unchecked COVID-19 spread makes it easier for the virus to keep mutating.
    • More than 5% of American adults are currently experiencing Long COVID. This number has ranged from 5.5% to 7% since September 2022, according to the CDC and Census’ Household Pulse Survey.
    • Almost 80% of adults with Long COVID report activity limitations due to the condition, including about 25% who report “significant” activity limitations, per the Household Pulse Survey.

    In an average week this winter, the U.S. reported more deaths from COVID-19 than the number of casualties on September 11, 2001. The latter event was a horrific tragedy that inspired lasting changes to national security, while the former has been written off as “mild.”

    Past surveys from many sources—including the CDC itself—have suggested that, when people know COVID-19 is spreading widely in their communities, they’re willing to take basic safety precautions. But when government leaders and mainstream media outlets downplay the risks, people don’t have the information they need to make informed choices. We’ve seen this pattern at a large scale this winter, and I worry that the trend will only continue.

    And here’s what concerns me even more: in previous winters, cases went up over the holidays, then declined through January and February. This year, however, the decline isn’t really happening. Transmission has gone down a bit from its peak, but it’s now plateaued at a level higher than the peaks of previous surges, per Biobot’s data.

    So, not only did we have a bad surge this winter, we’re now stuck at a high-COVID baseline that seems very difficult to shake, in the era of many new variants and few public health precautions. The situation reminds me of a Twitter thread from the evolutionary biologist T. Ryan Gregory, which I shared when writing about XBB.1.5 in early January:

    That “area under the curve” is what the U.S. is seeing now, as COVID-19 spread stays at high levels. Thousands of cases a day, thousands of hospitalizations a day, hundreds of deaths a day.

    As a journalist and as an individual capable of taking precautions, I resist the narrative that any of this is acceptable. If you’re reading this, I hope you can, too.

    More federal data

  • Sources and updates, February 5

    • CDC warns of risk to immunocompromised people: As of January 2023, there are no longer any monoclonal antibody treatments available for COVID-19, as these treatments do not provide protection against recent versions of Omicron. The no-longer-effective treatments include Evusheld, a drug used as a protective measure (to reduce risk of symptomatic COVID-19 for immunocompromised people. With Evusheld now unavailable, the CDC issued recommendations last week for people who have severely compromised immune systems. Of course, the CDC’s recommendations are largely targeted to individual action; to actually protet this vulnerable group, all Americans would need to follow collective public health measures.
    • Modeling COVID-19 as a persistent “endemic“: A recent preprint, from researchers at the drug company Fractal Therapeutics and collaborators, estimates just how challenging it is for people to avoid COVID-19 when the disease is not managed at a societal level. The researchers estimated Americans’ long-term COVID-19 risk based on an epidemiological model incorporating frequent reinfections, and limited individual-level protections. People who are vaccinated but don’t take other measures to reduce their risk of getting COVID-19 “can expect to spend an average of 6 days a year acutely sick with COVID-19 and also incur a 12% risk of long COVID (symptoms lasting more than 3 months),” the researchers write.
    • Global COVID-19 vaccination rate: Another new study, published in the CDC’s Morbidity and Mortality Weekly Report, provides an update on global vaccination rates, calculated by researchers at the World Health Organization. According to the WHO team, about 76% of older adults (ages 60 and older) have received a primary series of COVID-19 vaccines. (The study doesn’t report on booster rates, which are likely much lower worldwide.) As the vast majority of COVID-19 deaths worldwide have occurred among this age group, it should be a priority for vaccination, including the primary series and booster doses.
    • COVID-19 litigation database: I recently learned about this database of COVID-related legal documents, run by researchers at the University of Trento in Italy. The database aims to publish case documents from around the world reflecting challenges to COVID-19 policies. As of February 4, it includes documents from 1,978 cases, which can be searched by country, year, type of human rights issue, vulnerable group involved, and more.
    • Flu vaccine works well this year: A bit of non-COVID good news: this season’s flu vaccine is well-matched to the flu strain currently circulating in North America, according to a recent study from Canadian researchers and public health officials. Receiving a flu shot halved an individual’s risk of a severe flu case that needed medical care, the study found. Flu shots often have an effectiveness below 40%, explained STAT’s Helen Branswell on Twitter, as the vaccines do not always perfectly match up to circulating viral strains. But this year, the shot appears to be working well.
    • NYC declares end of mpox epidemic: And one more bit of good news: New York City officials have declared that the city’s epidemic of mpox (formerly called monkeypox) is now over. The city was a hub for mpox transmission last summer and became a center of the U.S. outbreak; but NYC has reported low case numbers since early fall. The federal public health emergency for mpox also recently ended.

    All featured sources
  • 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
  • National numbers, December 11

    National numbers, December 11

    The CDC’s influenza-like illness map shows that the vast majority of the country is facing either high or very high levels of respiratory disease.

    In the past week (December 1 through 7), the U.S. reported about 460,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 66,000 new cases each day
    • 140 total new cases for every 100,000 Americans
    • 50% more new cases than last week (November 24-30)

    In the past week, the U.S. also reported about 34,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 4,800 new admissions each day
    • 10.3 total admissions for every 100,000 Americans
    • 14% more new admissions than last week

    Additionally, the U.S. reported:

    • 3,000 new COVID-19 deaths (430 per day)
    • 68% of new cases are caused by Omicron BQ.1 and BQ.1.1; 6% by BF.7; 4% by BN.1;  5% by XBB (as of December 10)
    • An average of 300,000 vaccinations per day

    It’s now undeniable that Thanksgiving led to a jump in COVID-19 spread: officially-reported cases went up 50% this past week compared to the week of the holiday, following the trend that we first saw in wastewater data. Hospital admissions for COVID-19 also continue to go up.

    As always, it’s important to remember that official case counts are significantly underreported, due to dwindling access to (and interest in) PCR testing. So, the CDC’s estimate of 66,000 new COVID-19 cases each day likely amounts to over a million actual new infections each day. And that’s adding to the surges of flu, RSV, and other respiratory viruses already going strong.

    “Levels of flu-like illness, which includes people going to the doctor with a fever and a cough or sore throat, are at either high or very high levels in 47 jurisdictions,” CDC Director Dr. Rochelle Walensky said at a media briefing last Monday. That “flu-like illness” metric, shown on the CDC’s flu dashboard, is primarily used as an estimate of flu cases, but in our era of under-testing it likely includes COVID-19 and other viruses with similar symptoms.

    Dr. Walensky said that current hospitalizations for flu are the highest they’ve been in a decade for this time of year, indicating that the U.S. is having a bad flu season earlier in the winter than usual. According to Inside Medicine, flu hospitalizations actually overtook COVID-19 hospitalizations for the first time in the pandemic recently; though this trend could reverse as COVID-19 spreads more.

    The flu surge could peak and give us a milder January, or it could continue to go up from here—it’s currently hard to say. Flu vaccination rates have been low this year, which doesn’t help. CDC officials highlighted the benefits of both the flu vaccine and the updated COVID-19 booster shots at their briefing on Monday.

    Those updated COVID-19 boosters offer better protection against Omicron infection than prior vaccines, as real-world data has demonstrated. That should include protection against BQ.1 and BQ.1.1, the descendants of Omicron BA.5 that are currently causing the majority of cases in the U.S.—about 68% of new cases in the week ending December 10, per the CDC. XBB, the BA.2 subvariant that led to surges in Asian countries, is on the rise.

    Last week, wastewater data from Biobot showed a steep increase in COVID-19 spread. This week, the company’s dashboard suggests that this surge may have already peaked in some parts of the country. Was Thanksgiving the start of a major winter wave, or was it more of a holiday blip? Future weeks of data will help answer this.

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  • National numbers, November 20

    National numbers, November 20

    Data from the CDC indicate that much of the country is seeing high flu levels. Chart as of November 12.

    In the past week (November 10 through 16), the U.S. reported about 280,000 new COVID-19 cases, according to the CDC. This amounts to:

    • An average of 40,000 new cases each day
    • 86 total new cases for every 100,000 Americans
    • 3% fewer new cases than last week (November 3-9)

    In the past week, the U.S. also reported about 24,000 new COVID-19 patients admitted to hospitals. This amounts to:

    • An average of 3,400 new admissions each day
    • 7.3 total admissions for every 100,000 Americans
    • 1% fewer new admissions than last week

    Additionally, the U.S. reported:

    • 2,200 new COVID-19 deaths (320 per day)
    • 50% of new cases are caused by Omicron BQ.1 and BQ.1.1; 8% by BF.7; 5% by BN.1;  2% by BA.2.75 and BA.2.75.2 (as of November 19)
    • An average of 400,000 vaccinations per day

    Nationwide, reported COVID-19 cases and new hospital admissions are still in a plateau; both metrics declined very slightly this week after rising slightly last week (declining by 3% and 1%, respectively).

    While we have yet to see as clear of a fall/winter surge as we did in the last two years, infection levels are still quite high. Evidence for this comes from wastewater data, which doesn’t rely on people getting PCR tests; trends from Biobot suggest that viral transmission is at a similar level to late October/early November of last year, when Delta was still the dominant variant.

    Biobot’s data also indicate that the West coast region is now seeing a notable uptick in COVID-19 spread, taking over from the Northeast (which has been a regional hotspot since September). Wastewater testing sites in cities like Los Angeles is reporting significant transmission spikes in the last couple of weeks.

    The West coast, like the Northeast, has been a hotspot for newer Omicron subvariants BQ.1 and BQ.1.1, according to CDC estimates. Nationwide, the BQ lineage caused about half of new cases in the last week—solidly outcompeting its parent lineage, BA.5. And there are several other Omicron subvariants spreading, including two lineages from BA.2, BF.7 and BN.1.

    With all these new variants circulating and colder weather throughout the country, why haven’t we seen a significant jump in COVID-19 spread? It’s possible that the U.S. has enough prior immunity from vaccinations and past infections to prevent a big surge, White House COVID-19 coordinator Ashish Jha said at the STAT Summit last week.

    I hope Jha is right, but I personally remain skeptical. Way too few people have received the new booster shots that protect against Omicron variants, while we’re heading into several weeks of holiday travel and gatherings—with fewer COVID-19 protections than in the last two years.

    At the same time, the U.S. is dealing with flu and RSV surges. About a dozen states, plus New York City and Washington, D.C., reported “very high” levels of influenza-like activity in the week ending November 12, according to the CDC. And the country’s RSV wave continues at high intensity, though it might be reaching its peak.

    These two respiratory diseases may be less severe than COVID-19 at an individual level (especially accounting for the burden of Long COVID), but they can still put intense pressure on healthcare systems—especially those focused on treating children. Wearing a mask, avoiding indoor crowds, improving ventilation, and other measures can protect against all three diseases.

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