COVID-19 Data Dispatch

Tag: RSV

  • 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

  • Sources and updates, July 23

    • Grants to help with global pandemic preparedness: This week, the World Bank’s Pandemic Fund announced the recipients of its first round of grants. The fund is a finance initiative to “strengthen pandemic prevention, preparedness, and response capacities,” particularly for low- and middle-income countries. Its first round of grants will go to 37 countries across 6 global regions, distributing $338 million in funding. The full list of awards is available on the World Bank’s website.
    • Genetic marker of asymptomatic COVID-19: A new paper published in Nature this week reports on a common genetic marker that may lead people to have symptom-free COVID-19 cases. The researchers (a team from the University of California San Francisco and other institutions) searched for genetic patterns among 30,000 people who shared their COVID-19 symptom information through a smartphone app. They found a correlation between asymptomatic infection and a specific version of a gene related to T cells. As Eric Topol notes in his newsletter, this study follows two others that examined genetic markers of Long COVID.
    • Quantifying cognitive symptoms of Long COVID: Speaking of Long COVID: researchers at Kings College London studied the condition’s cognitive symptoms (also called brain fog) by measuring patients’ performance in different mental tasks. The study included over 3,000 participants, more than half of whom completed two rounds of testing over two years. Overall, the researchers found that cognitive symptoms persisted for nearly two years after patients’ initial infections, and most severe for patients with the longest-lasting Long COVID impacts. For these patients, “the effect of COVID-19 on test accuracy was comparable in size to the effect of a 10-year increase in age,” per a press release by Kings College London.
    • Long COVID is common in children: Another Long COVID study published this week: researchers at a hospital in Toronto compiled a review paper examining the condition’s prevalence among children. Their review included 30 studies including about 15,000 total pediatric patients. Across all the studies, researchers reported that about 16% of children experienced at least one Long COVID symptom three or more months after their COVID-19 infections. However, compiling these data was a challenging task because different studies used different definitions of Long COVID, different methods of following up with patients over time, and other inconsistencies, the authors wrote.
    • Dogs detecting COVID-19 through scent: One more paper that stuck out to me this week: a pair of researchers (one at the University of California, Santa Barbara and one at a biotech company focused on sniffing for COVID-19) examined how well dogs can detect the coronavirus. This was also a review paper, including 29 studies and 31,000 COVID-19 test samples. Overall, the dogs performed with similar accuracy to PCR tests, researchers found. “We believe that scent dogs deserve their place as a serious diagnostic methodology that could be particularly useful during pandemics,” one of the authors said in a statement.
    • Monoclonal antibody to protect babies from RSV: Finally, a bit of good news for combatting another common respiratory virus: the FDA has approved a new monoclonal antibody treatment to protect infants and young children against RSV. The therapy is likely to be recommended by the CDC and manufactured in time for respiratory virus season this fall. In clinical trials, it lowered the risk of an RSV infection requiring medical care by about 76%—which is a big deal for a disease that leads to more babies in hospitals than any other in the U.S., reports Helen Branswell at STAT.

  • Sources & updates, June 25

    • Commonwealth Fund releases 2023 state health scorecard: This week, health research organization the Commonwealth Fund published its 2023 rankings of state health systems. These rankings are an extensive data source for anyone seeking to better understand the decentralized health system in the U.S., and may be particularly useful for local reporters looking for data on how their state compares to others. In the 2023 rankings, the researchers have added new metrics related to care and health outcomes for women, mothers, and infants. This year’s data also highlight preventable deaths from COVID-19 and other causes, and state efforts to take people off of Medicaid following the pandemic emergency’s end.
    • New advisory about Long COVID and mental health: The U.S. Substance Abuse and Mental Health Services Administration (SAMHSA), a federal health agency under the overall Department of Health and Human Services (HHS), published a detailed advisory explaining the mental health implications of Long COVID. This advisory is directed at primary care doctors who may be seeing Long COVID among their patients, as well as others in the medical community who may benefit from the information. SAMHSA highlights that mental health symptoms may result from a coronavirus infection itself as well as from the stress and social isolation that long-haulers experience. For more on this topic, check out this article I wrote last year.
    • Rapid test accuracy can vary widely: A common question that I’ve received from readers in the last few months has been, “How accurate are rapid tests with newer variants?” A new study, published last week in the journal Microbiology Spectrum, offers some insight. The researchers (a team at CalTech) found that rapid tests still work to detect the coronavirus, but their accuracy varies based on viral load and specimen type. Tests that involved swabbing the patient’s throat (along with their nose) were significantly more accurate than nose swabs alone. Tests conducted later in the course of a patients’ infection, when they had higher viral loads, were also more accurate, though some patients never tested positive on rapid tests despite testing positive on PCR. My takeaway here: swabbing your throat and testing multiple times help improve accuracy, but the best option is always to get a PCR if you can.
    • CDC and state agencies track reinfections: Another new study, published this week in the CDC’s Morbidity and Mortality Weekly Report, examines coronavirus reinfections in the era of Omicron. Researchers at the CDC and 18 state and local health departments collaborated to track reinfections from September 2021 through December 2022, finding that these infections went up significantly when Omicron arrived in late 2021. The median time between infections ranged from 269 to 411 days, the researchers found, suggesting that Americans may expect to be sick with COVID-19 once or twice a year while our Omicron baseline persists. 
    • COVID-19 risk and air pollution exposure: One more study I wanted to highlight this week: researchers at Hasselt University in Belgium tracked the air pollution exposures of about 330 COVID-19 patients at hospitals in Belgium. Patients who were exposed to worse air pollution prior to their admission experienced more severe COVID-19 outcomes, including longer hospitalization and admission to the ICU. This paper provides further confirmation that poor air quality and COVID-19 can be compounding health problems for many people.
    • Data problems persist with non-COVID vaccines: The CDC’s vaccine advisory committee met this week to discuss two new RSV vaccine candidates, recently approved by the FDA for seniors. While the CDC committee did vote to recommend these vaccines, I was struck by discussion (in Helen Branswell’s coverage for STAT) that the experts said they did not have sufficient data to make a truly informed decision. I’ve written a lot about data issues for COVID-19 vaccines; the same decentralized health system problems that make it hard to track COVID-19 vaccine effectiveness also apply to products for other diseases.

  • Sources and updates, May 21

    • New funding from CDC’s forecasting center: The CDC’s Center for Forecasting and Analytics (CFA) announced a new funding opportunity for state and local health agencies to develop new disease modeling tools. CFA is a relatively new center itself; it launched last year with the goal of modernizing the U.S.’s disease forecasting capacities (see my FiveThirtyEight article about the center for more details). This funding opportunity will, I expect, enable the CFA’s growing staff to work directly with health agencies on advancing analytical methods. I look forward to seeing the results of those projects.
    • Experts argue to keep masks in healthcare: A new commentary article, published this week in the Annals of Internal Medicine, argues in favor of keeping mask requirements in healthcare settings. The experts (from the National Institutes of Health and George Washington University) point to real-world experience, suggesting transmission between patients and healthcare workers is less likely when everyone is wearing a mask, preferably one of high quality. This article coincides with an advocacy campaign to keep masks in healthcare, including virtual and in-person actions across the U.S.
    • CDC releases provisional drug overdose data for 2022: The CDC’s National Center for Health Statistics has released overdose data for 2022, reporting that nearly 110,000 Americans died of overdoses for the second year in a row. Overdoses have leveled off from 2021, but the 2022 data still represent a sharp increase from pre-pandemic trends. Some states in the South and West Coast (such as Texas, Oklahoma, Wyoming, Washington) saw the sharpest increases from 2021 to 2022, according to the CDC. These data are all preliminary and will be updated later in the year.
    • Pediatric COVID-19 boosters could save school days: A new modeling study, published this week in JAMA Network Open, suggests that the U.S. could have seen about 10,000 fewer kids hospitalized with COVID-19 and 5.5 million fewer school days lost during the 2022-2023 respiratory virus season, if kids received booster shots in large numbers. The researchers arrived at these estimates through a model that simulated COVID-19 booster vaccination rates at similar levels to annual flu vaccination in kids. Future booster campaigns should focus on children in addition to older adults, the authors argue.
    • RSV vaccine for infants moves ahead: Speaking of pediatric vaccinations: the FDA’s vaccine advisory committee met last week to discuss a new vaccine candidate from Pfizer, which would protect infants from RSV. Unlike most pediatric vaccines, this shot would be delivered to pregnant parents in order to protect their babies at birth. While the FDA’s advisors endorsed the vaccine for its effectiveness, some committee members expressed concerns over safety. Helen Branswell at STAT has more details.

    All featured sources

  • Sources and updates, May 7

    • KFF Medicaid Unwinding tracker: The Kaiser Family Foundation just published a new tracker detailing Medicaid enrollment by state. Enrollment rose to record levels during the pandemic, as a federal measure tied to the public health emergency forbid states from taking people off the insurance program. Now, states are going through the slow process of evaluating people’s eligibility and taking some off the program, in a process called “unwinding.” The KFF tracker is following this process, presenting both Medicaid enrollment data by state and information on each state’s timeline for evaluation.
    • Biden administration ends vaccine mandates: In time with the federal public health emergency’s end, the Biden administration has announced that it will lift its COVID-19 vaccine rules for federal workers and contractors. International travelers to the U.S. also will no longer need to provide proof of their vaccination status, and the administration is working to end requirements for other groups of workers and travelers. This change is, essentially, another signal of the administration giving up on mass vaccination campaigns; after all, most of the people who got their shots under these rules haven’t received an Omicron booster.
    • Vaccine protection wanes over time: A new review paper from researchers in Trento, Italy, published this week in JAMA, shows the importance of booster shots for maintaining protection from COVID-19. The researchers compiled and analyzed findings from 40 studies that evaluated vaccine effectiveness. Overall, they found, the protection that both primary series and booster shots provide against an Omicron infection drops significantly by six months and nine months after vaccination. Remember: Americans over 65 and/or immunocompromised, you’re now eligible for another bivalent/Omicron-specific booster.
    • Disparities in COVID-19 deaths persist: Two new studies this week examine COVID-19 deaths by race and ethnicity. The first study, from the CDC’s National Center for Health Statistics, examined deaths of all causes during the pandemic, finding that Black and Native Ameircans had higher death rates than other racial/ethnic groups. COVID-19 was the fourth highest cause of death in 2022, after heart disease, cancer, and unintentional injury. The second study, from Andrew Stokes and collaborators, examined COVID-19 deaths during the U.S.’s first Omicron wave compared to earlier surges, finding that disparities decreased—but only because white deaths went up during the second year of the pandemic.
    • Characterizing Long COVID neurological symptoms: Another new study from this week: researchers at the NIH performed detailed examinations of 12 Long COVID patients to better understand their neurological symptoms. The researchers used an approach called “deep phenotyping,” which involves a variety of tests that aren’t typically used in clinical settings. They found that the patients had a number of abnormalities in their immune systems and autonomic nervous systems compared to healthy controls, pointing to different potential drivers of symptoms.
    • FDA approves RSV vaccine: Finally, a bit of non-COVID good news: for the first time, the FDA has approved a vaccine for RSV, the seasonal respiratory virus that can cause severe symptoms in older adults and young children. This vaccine, made by GSK, was approved for adults ages 60 and up and will likely get distributed during the next cold/flu season. Scientists have been working on RSV vaccines for decades, making this a major milestone for reducing the disease’s impact. Helen Branswell at STAT has more details.

    All featured sources

  • 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 â€śmild”

    This winter’s COVID-19 surge wasn’t â€śmild”

    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

  • 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, 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.

    more national numbers
  • COVID source shout-out: HealthWeather dashboard

    COVID source shout-out: HealthWeather dashboard

    Data from Kinsa suggest that diseases causing fever are rising sharply among children ages five to 12, compared to past fall/winter seasons.

    I recently learned about the Kinsa HealthWeather dashboard, a resource providing COVID-19 risk estimates by state and county based on data from smart thermometers.

    Kinsa is a health tech company based in San Francisco that offers a health app paired with a smart thermometer. Users can submit their temperature data and symptoms to receive guidance on how to manage their illness. And at the population level, epidemiologists and data scientists can predict disease prevalence based on information from 2.5 million households using the app.

    Danielle Bloch, epidemiology lead at Kinsa (and a former COVID Tracking Project volunteer, like myself), explained the process this way:

    The data come from a network of 2.5 million households (of which about 600,000 users have taken a temperature in the past year) that have opted in to share information about their body temperature and symptoms, which are recorded through an app and smart thermometer. We’re currently in the process of updating our site to better incorporate other circulating infectious illnesses beyond COVID (Flu, GI symptoms, other respiratory infections) given the current landscape of diseases.

    Right now, Bloch said, Kinsa’s data are showing an increase in fevers across the U.S.—with the biggest uptick in children ages five to 12. This trend likely reflects increasing COVID-19, flu, and RSV spread all at once.

    As official case data from public health agencies become less reliable, new sources like Kinsa’s dashboard are a helpful way to continue tracking disease spread at the local level. I hope to see more sources like these in the future, along with more environmental monitoring (wastewater, air quality, etc.)

    more source spotlights