Tag: Delta variant

  • Answering your COVID-19 questions

    Answering your COVID-19 questions

    The Delta surge is waning. Will this be the last big surge in the U.S., or will we see more? This question and more, answered below; chart from the CDC.

    Last week, I asked readers to fill out a survey designed to help me reflect on the COVID-19 Data Dispatch’s future. Though the Delta surge—and the pandemic as a whole—is far from over, I’m considering how this publication may evolve in a “post-COVID” era. Specifically, I’m thinking about how to continue serving readers and other journalists as we prepare for future public health crises.

    Thank you to everyone who’s filled out the survey so far! I really appreciate all of your feedback. If you haven’t filled it out yet, you can do so here

    Besides some broader questions about the CDD’s format and topics we may explore in the future, the survey asked readers to submit questions that they have about COVID-19 in the U.S. right now. In the absence of other major headlines this week, I’m devoting this week’s issue to answering a few of those questions.

    Should I get a booster shot? If so, should it be a different one from the first vaccine I got? When will my kids (5-11) likely be eligible?

    I am not a doctor, and I’m definitely not qualified to give medical advice. So, the main thing I will say here is: identify a doctor that you trust, and talk to them about booster shots. I understand that a lot of Americans don’t have a primary care provider or other ways to easily access medical advice, though, so I will offer some more thoughts here.

    As I wrote last week, we do not have a lot of data on who’s most vulnerable to breakthrough COVID-19 cases. We do know that seniors are more vulnerable—this is one point where most experts agree. We know that adults with the same health conditions that make them more likely to have a severe COVID-19 case without a vaccine (autoimmune conditions, diabetes, kidney disease, etc.) are also more vulnerable to breakthrough cases, though we don’t have as much data here. And we know that vaccinated adults working in higher-risk locations like hospitals, nursing homes, and prisons are more likely to encounter the coronavirus, even if they may not necessarily be more likely to have a severe breakthrough case.

    The FDA and CDC’s booster shot guidance is intentionally broad, allowing many Americans to receive a booster even if it is not necessarily needed. So, consider: what benefits would a booster shot bring you? Are you a senior or someone with a health condition that makes you more likely to have a severe COVID-19 case? Do you want to protect the people you work or live with from potentially encountering the coronavirus?

    If you answered “yes” to one of those questions, a booster shot may make sense for you. And, while you may be angry about global vaccine inequity, one individual refusal of a booster shot would not have a significant impact on the situation. Rather, many vaccine doses in the U.S. may go to waste if not used for boosters. But again: talk to your doctor, if you’re able to, about this decision.

    Currently, Pfizer booster shots are available for people who previously got vaccinated with Pfizer. The FDA’s vaccine advisory committee is meeting soon to discuss Moderna and Johnson & Johnson boosters: they’ll discuss Moderna on October 14 and J&J on October 15. Vaccine approval in the U.S. depends upon data submission from vaccine manufacturers—and vaccine manufacturers have not been studying mix-and-match booster regimens—so coming approvals will likely require Americans to get a booster of the same vaccine that they received initially. We will likely see more discussion of mix-and-match vaccinations in the future, though, as more outside studies are completed.

    As for when your kids will likely be eligible: FDA’s advisory committee is meeting to discuss Pfizer shots for kids ages 5 through 11 on October 26. If that meeting—and a subsequent CDC meeting—goes well, kids may be able to get vaccinated within a week of that meeting. (Potentially even on Halloween!)

    Why don’t people get vaccinated and how can we make them?

    I got a couple of questions along these lines, asking about vaccination motivations. To answer, I’m turning to KFF’s COVID-19 Vaccine Monitor, a source of survey data on vaccination that I (and many other journalists) have relied on since early 2021.

    KFF released the latest round of data from its vaccine monitor this week. Here are a few key takeaways:

    • The racial gap in vaccinations appears to be closing. KFF found that 71% of white adults have been vaccinated, compared to 70% of Black adults and 73% of Hispanic adults. Data from the CDC and Bloomberg (compiling data from states) similarly show this gap closing, though some parts of the country are more equitably vaccinated than others.
    • A massive partisan gap in vaccinations remains. According to KFF, 90% of Democrats are vaccinated compared to just 58% of Republicans. This demonstrates the pervasiveness of anti-vaccine misinformation and political rhetoric among conservatives.
    • Rural and younger uninsured Americans also have low vaccination rates (62% and 54%, respectively). Both rural and uninsured people have been neglected by the U.S. healthcare system and face access barriers; for more on this topic, I recommend this Undark article by Timothy Delizza.
    • Delta was a big vaccination motivator. KFF specifically asked people who had gotten their shots after June 1 why they chose to get vaccinated. The most popular reasons were, in order: the increase in cases due to Delta (39%), concern about reports of local hospitals and ICUs filling with COVID-19 patients (38%), and knowing someone who got seriously ill or died from COVID-19 (36%).
    • Mandates and social pressures were also vaccination motivators. 35% of KFF’s recently vaccinated survey respondents said that a big reason for their choice was a desire to participate in activities that require vaccination, like going to the gym, a big event, or traveling. 19% cited an employer requirement and 19% cited social pressure from family and friends.

    The second part of this question, “how can we make them?”, reflects a dangerous attitude that has permeated vaccine conversations in recent months. Yes, it’s understandable to be frustrated with the Americans who have refused vaccination. But we can’t “make” the unvaccinated do anything, and such a forceful attitude may put off people who still have questions about the vaccines or who have faced discrimination in the healthcare system. To increase vaccinations among people who are still hesitant, it’s important to remain open-minded, not condescending. For more: read Ed Yong’s interview with Dr. Rhea Boyd.

    That said, we’re now getting a sense of which strategies can increase vaccination: employer mandates, vaccination requirements for public life, and personal experience with the coronavirus. As the Delta surge wanes, it will take more vaccination requirements and careful, open-minded conversations to continue motivating people to get their shots.

    What are some things I might say to convince people of Delta’s severity and the need to not relax on masking, distancing, etc?

    To answer this, I’ll refer you to the article I wrote about Delta on August 1, as the findings that I discuss there have been backed up by further research.

    Personally, there are two statistics that I use to express Delta’s dangers to people:

    • Delta causes a viral load 1,000 times higher than the original coronavirus strain. This number comes from a study in Guangzhou, China, posted as a preprint in late July. While viral load does not correspond precisely to infectiousness (there are other viral and immune system factors at play), I find that this “1,000 times higher” statistic is a good way to convey just how contagious Delta is, compared to past variants.
    • An interaction of one second is enough time for Delta to spread from one person to another. Remember the 15-minute rule? In spring 2020, being indoors with someone, unmasked, for 15 minutes or more was considered “close contact.” Delta’s increased transmissibility means that an interaction of one second is now enough to be a “close contact.” The risk is lower if you’re vaccinated, but still—Delta is capable of spreading very quickly in enclosed spaces.

    You may also find it helpful to discuss rising numbers of breakthrough cases in the U.S. While vaccinated people continue to be incredibly well protected against severe disease and death caused by Delta, the vaccines are not as protective against coronavirus infection and transmission. (They are protective to some degree, though! Notably, coronavirus infections in vaccinated people tend to be significantly shorter than they are in the unvaccinated, since immune systems can quickly respond to the threat.)

    It’s true that rising breakthrough case numbers are, in a way, expected—as more people get vaccinated, breakthrough cases will naturally become more common, because the virus has fewer and fewer unvaccinated people to infect. But considering the risks of spreading the coronavirus to others, plus the risks of Long COVID from a breakthrough case… I personally don’t want a breakthrough case, and so I continue masking up and following other safety protocols.

    What monitoring do we have in place for COVID “longhaulers” and their symptoms/health implications?

    This is a great question, and one I wish I could answer in more detail. Unlike COVID-19 cases, hospitalizations, and other major metrics, we do not have a comprehensive national monitoring system to tell us how many people are facing long-term symptoms from a coronavirus infection, much less how they’re faring. I consider this one of the country’s biggest COVID-19 data gaps, leaving us relatively unprepared to help the thousands, if not millions, of people left newly disabled by the pandemic.

    In February, the National Institutes of Health (NIH) announced a major research initiative to study Long COVID. Congress has provided over $1 billion in funding for the research. This initiative will likely be our best source for Long COVID information in the future, but it’s still in early stages right now. Just two weeks ago, the NIH awarded a large share of its funding to New York University’s Langone Medical Center; NYU is now setting up long-term studies and distributing funding to other research institutions.

    As I wrote in the September 19 issue, the NIH’s RECOVER website currently reports that between 10% and 30% of people infected with the coronavirus will go on to develop Long COVID; hopefully research at NYU and elsewhere will lead to some more precise numbers.

    While we wait for the NIH research to progress, I personally find the Patient-Led Research Collaborative (PLRC) to be a great source for Long COVID research and data. The PLRC consists of Long COVID patients who research their own condition; it was founded out of Body Politic’s Long COVID support group. This group produced one of the most comprehensive papers on Long COVID to date, based on an international survey including thousands of patients, and has more research currently ongoing.

    If you have the means to support Long COVID patients—many of whom are unable to work and facing homelessness—please see the responses to this tweet by PLRC researcher Hannah Davis:

    Why is the CDC not doing comprehensive high volumes of sequencing on all breakthrough cases at the very least?

    I wish I knew! As I wrote last week (and in several other past issues), the lack of comprehensive breakthrough case data in the U.S. has contributed to a lack of clarity on booster shots, as well as a lack of preparedness for the next variants that may become threats after Delta. The CDC’s inability to track and sequence all breakthrough cases—not just the severe ones—is dangerous.

    That said, it is very difficult to track breakthrough cases in a country like the U.S. Consider: the U.S. does not have a comprehensive, national electronic records system for patients admitted to hospitals, much less those who receive COVID-19 tests and other care at outpatient clinics. This lack of comprehensive records makes it difficult to match people who’ve been vaccinated with those who have received a positive COVID-19 test. Thousands, if not millions of Americans are now relying on rapid tests for their personal COVID-19 information—and most rapid tests don’t get entered into the public health records system at all. 

    Plus, local public health departments are chronically underfunded, understaffed, and burned out after almost two years of working in a pandemic; they have little bandwidth to track breakthrough cases. Many Americans refuse to participate in contact tracing, which hinders the public health system’s ability to collect key information about their cases. And there are other logistical challenges around genomic sequencing; despite new investments in this area, many parts of the country don’t have sequencing capacity, or the information infrastructure needed to send sequencing results to the CDC.

    So, if the CDC were tracking non-severe breakthrough cases, they’d likely miss a lot of the cases. But that doesn’t mean they shouldn’t be trying, in my opinion.

    How safe is it to visit my family for the holidays?

    This is another place where I don’t feel qualified to give advice, but I can offer some thoughts. If I were you, I would think about the different ways in which holiday travel might pose risk to me and to the people at the other end of my trip. I would consider:

    • Quarantining beforehand. Do your occupation and living circumstances allow you to quarantine for a week, or at least limit your exposure to settings where you might be at risk of catching the coronavirus, before you travel? Can you get a test before traveling?
    • Types of travel. Can you make the trip in a car or on public transportation, or do you need to fly? If you need to fly, can you select an airline that has stricter COVID-19 safety requirements? (United recently reported that over 96% of its employees are now vaccinated, for example.) Can you wear a high-quality mask for the flight?
    • Quarantining and/or testing upon arrival. Can you spend a couple of days in quarantine once you get to your destination? Would you have access to testing (with results in under 24 hours) upon your arrival, or would you be able to bring rapid tests with you?
    • Who you’re spending time with. Among the family you’d be visiting, is everyone vaccinated (besides young children)? If anyone is not vaccinated, could your potential travel be a motivator to help convince them to get vaccinated? Does the group include seniors or people with health conditions that put them at high risk for COVID-19, and if so, can they get booster shots?
    • Activities that you do at your destination. Would you be able to have large gatherings outside, or in a well-ventilated space? What else can you do to reduce the risk of these activities?

    Like other activities, travel can be relatively safe or fairly dangerous depending on the precautions that you’re able to take, and depending on COVID-19 case rates where you live and at your destination. And, like other activities, your choice to travel or not travel depends a lot on your personal risk tolerance. Nothing is zero-risk right now; each person has a threshold that determines what level of COVID-19 risk they are and are not comfortable taking. Through some self-reflection, you can determine if travel is above or below your risk threshold.

    Why are policies so different now than they were at this time last year?

    Public health tends to go through cycles of “panic” and “neglect.” Ed Yong’s latest feature goes into the history of this phenomenon:

    Almost 20 years ago, the historians of medicine Elizabeth Fee and Theodore Brown lamented that the U.S. had “failed to sustain progress in any coherent manner” in its capacity to handle infectious diseases. With every new pathogen—cholera in the 1830s, HIV in the 1980s—Americans rediscover the weaknesses in the country’s health system, briefly attempt to address the problem, and then “let our interest lapse when the immediate crisis seems to be over,” Fee and Brown wrote. The result is a Sisyphean cycle of panic and neglect that is now spinning in its third century. Progress is always undone; promise, always unfulfilled. Fee died in 2018, two years before SARS-CoV-2 arose. But in documenting America’s past, she foresaw its pandemic present—and its likely future.

    During the COVID-19 pandemic, the U.S. took a nosedive into the “neglect” cycle before we were even finished with the “panic” cycle. Congress has already slashed its funding for future pandemic preparedness, while state and local governments across the country restrict the powers of public health officials. As a result, we’re seeing an “everyone for themselves” attitude at a time when we should be seeing new mask mandates, restrictions on public activities, and other safety measures.

    Basically, America decided the pandemic was over and acted accordingly—and if you get COVID-19 now, it’s “your fault for not being vaccinated.” This phenomenon has been especially pronounced in rural areas, which struggled a lot (but saw few cases) during spring 2020 lockdowns and are extremely hesitant to do anything approaching a “lockdown” again.

    We need an attitude shift—and more investment in public health—to actually end this pandemic and prepare for the next health crisis. Yong’s feature goes into this in more detail; definitely give that a read if you haven’t yet.

    When is this going to be over?!?

    Unfortunately, this is very hard to predict—even for the expert epidemiologists and computational biologists who make the models. Check out the CDC’s compilation of COVID-19 case models: most of them agree that cases will keep going down in the coming weeks, but they’re kind of all over the place.

    Last week, I summarized two stories—from The Atlantic and STAT News—that discuss the coming winter, and kind of get at this question. It’s possible that cases keep declining from their present numbers, and that the Delta surge we just faced is the last major surge in the U.S. It’s also possible that a new variant arises out of Delta and sends us into yet another new surge. If that happens, more people will be protected by vaccination and prior infection, but healthcare systems could come under strain once again.

    As long as the coronavirus continues spreading somewhere in the world, it will continue to pose risk to everyone—able to cause new outbreaks and mutate into new variants. This will continue until the vast majority of the world is vaccinated. And then, at some point, the coronavirus will probably become endemic, meaning it persists in the population at some kind of “acceptable” threshold. Just like the flu.

    Dr. Ellie Murray, epidemiologist at Boston University’s School of Public Health, explained how a pandemic becomes endemic in a recent Twitter thread:

    Dr. Murray points out that, even when a disease reaches endemic status, tons of scientists and public health workers will still continue to monitor it. This is the case for the flu—think about all of the effort that goes into a given year’s flu shot!—and it will likely be the case for COVID-19.

    In short, public health leaders need to figure out what level of COVID-19 transmission is “acceptable” and how we will continue to monitor it. This needs to happen at both U.S. and global levels. And, thanks to our vaccine-rich status, it’ll likely happen in the U.S. long before it happens globally.


    Again, if you haven’t filled out the survey yet, you can do so here. I may answer more questions next week!

  • National numbers, October 3

    National numbers, October 3

    Delta dominates throughout the U.S. The CDC’s variant map has looked like this for a few weeks now.

    In the past week (September 25 through October 1), the U.S. reported about 750,000 new cases, according to the CDC. This amounts to:

    • An average of 106,000 new cases each day
    • 227 total new cases for every 100,000 Americans
    • 13% fewer new cases than last week (September 18-24)

    Last week, America also saw:

    • 58,000 new COVID-19 patients admitted to hospitals (18 for every 100,000 people)
    • 10,000 new COVID-19 deaths (3.2 for every 100,000 people)
    • 99% of new cases are Delta-caused (as of September 25)
    • An average of 800,000 vaccinations per day (including booster shots; per Bloomberg)

    COVID-19 cases continue to go down in the U.S.; by next week, the country will likely be back under 100,000 new cases a day. Hospitalizations are also dropping: this week, the number of COVID-19 patients currently hospitalized across the U.S. dropped about 12%, to 72,000.

    But over 10,000 COVID-19 deaths were reported this week, for the third week in a row. Many of these deaths likely occurred earlier in the Delta surge, but showed up in the numbers more recently due to reporting lags.

    The U.S. passed 700,000 COVID-19 deaths this week, many of them unvaccinated. To quote Ed Yong’s latest feature: “Every adult in the U.S. has been eligible for vaccines since mid-April; in that time, more Americans have died of COVID-19 per capita than people in Germany, Canada, Rwanda, Vietnam, or more than 130 other countries did in the pre-vaccine era.”

    Alaska is now the number one COVID-19 hotspot in the country. According to Friday’s Community Profile Report, the state saw almost 1,200 new COVID-19 cases for every 100,000 residents in the week ending September 29. That’s twelve times higher than the CDC’s threshold for “high transmission,” 100 new cases for every 100,000 people in a week.

    Hospitals in Alaska are completely overwhelmed. The state currently has about 40% more COVID-19 patients in hospitals than it did at the peak of the winter surge. In a recent video posted to Facebook and shared with local leaders, a nurse at Fairbanks Medical Hospital describes the dire process of dying from COVID-19—something that has become incredibly common in her workplace. About 50% of Alaska’s population is fully vaccinated.

    On the other side of the spectrum, Connecticut has joined California in the “substantial transmission” range. Connecticut saw 98 new cases for every 100,000 people in the past week, while California saw 73 new cases for every 100,000.

    Over 99% of new cases in the U.S. are caused by Delta, as has been the case for over a month. Delta has solidly outcompeted the Mu variant, and remains dominant across the country. Will this variant peter out as the surge slowly wanes, or will Delta evolve into another more-dangerous variant? The CDC’s current data makes it hard to look for signals.

  • Featured sources, September 26

    • CDC updates its variant classifications: This one is more of an update than a new source. On Thursday, the CDC updated the list of coronavirus variants that the agency’s scientists are watching. This list now includes three categories: Variants of Concern (or VOCs, which pose a significant threat to the U.S.), Variants of Interest (which may be concerning, but aren’t yet enough of a threat to be VOCs), and Variants Being Monitored (which were previously concerning, but now are circulating at very low levels in the U.S.). Notably, Delta is now the CDC’s only VOC; all other variants are Variants Being Monitored.
    • COVID-19 School Data Hub: Emily Oster, one of the leading (and most controversial) researchers on COVID-19 cases in K-12 schools, has a new schools dashboard. The dashboard currently provides data from the 2020-2021 school year, including schools’ learning modes (in-person, hybrid, virtual) and case counts. Of course, data are only available for about half of states. You can read more about the dashboard in this Substack post from Oster.
    • Influenza Encyclopedia, 1918-1919: In today’s National Numbers section, I noted that the U.S. has now reported more deaths from COVID-19 than it did from the Spanish flu. If you’d like to dig more into that past pandemic, you can find statistics, historical documents, photographs, and more from 50 U.S. cities at this online encyclopedia, produced by the University of Michigan Center for the History of Medicine.

  • Our pandemic winter: Stories on what to expect

    This week, two of the outlets that I consider to be among the most reliable COVID-19 news sources published stories on our coming pandemic winter. Obviously, you should read both pieces in full, but here are my takeaways.

    The first story comes from The Atlantic’s science desk, with a triple-star byline including Katherine J. Wu, Ed Yong, and Sarah Zhang.

    This piece focuses on the changing role of vaccination in protecting the U.S. from COVID-19. After a few months of encouraging data, suggesting that vaccines could protect us against coronavirus infection and transmission, we are now back to using COVID-19 vaccines for their initial purpose: preventing severe disease and death. As we see higher numbers of breakthrough cases, we can take comfort in the fact that those cases will rarely lead to hospitalization or death. (Though the risk of Long COVID after vaccination is less known.)

    The Atlantic’s article also explains who is now most at risk of COVID-19, and how that risk may shift in the coming months. Right now, unvaccinated children face high risk, especially if they live in communities where most of the adults aren’t vaccinated. But that won’t always be the case:

    Relative risk will keep shifting, even if the virus somehow stops mutating and becomes a static threat. (It won’t.) Our immune systems’ memories of the coronavirus, for instance, could wane—possibly over the course of years, if immunization against similar viruses is a guide. People who are currently fully vaccinated may eventually need boosters. Infants who have never encountered the coronavirus will be born into the population, while people with immunity die. Even the vaccinated won’t all look the same: Some, including people who are moderately or severely immunocompromised, might never respond to the shots as well as others.

    At the end of the article, the writers touch on variants. Delta is now the world’s major concern, but future variants might develop new mutations and pose new dangers. Yet the writers say that any variant “can be stopped through the combined measures of vaccines, masks, distancing, and other measures that cut the conduits they need to travel.”

    The second “pandemic winter” story comes from ace STAT News reporter Helen Branswell. Branswell goes into more detail about potential variant scenarios, outlining what Delta may do and how other mutations may arise as the weather gets colder.

    Some modeling efforts suggest that COVID-19 case numbers may stay low once the Delta wave ends, Branswell reports, because the majority of Americans are now fully vaccinated or have some immunity from a prior infection. But if another dangerous variant comes along, we could be in trouble. Still, if cases go up again, we won’t see as many hospitalizations or deaths as we did last winter, thanks to the vaccines.

    I personally take comfort in this quotation from computational biologist Trevor Bedford:

    “It is likely that we’ll see some wave,” Bedford said. “I would like to think it’s very unlikely to be as big as it was last year.”

    Because Delta is causing the vast majority of the world’s COVID-19 cases right now, Branswell reports, future variants would likely arise from Delta. That could mean even more transmissibility or challenges to the human immune system. There’s a lot of uncertainty involved in trying to predict mutations, though. Branswell points out:

    Early in the pandemic, coronavirus experts confidently opined that this family of viruses mutates far more slowly than, say, influenza, and major changes weren’t likely to undermine efforts to control SARS-2. But no one alive had watched a new coronavirus cycle its way through hundreds of millions of people before.

    Branswell’s story also spends time explaining the potential pressures that COVID-19 could put on the healthcare system if combined with flu or other respiratory viruses. Healthcare workers may need to distinguish COVID-19 cases from flu cases, then treat both with similar equipment.

    The story makes a pretty good argument for getting your flu shot now, if it’s available to you. I got mine last week.

  • Boosters for the vulnerable: FAQs following the FDA advisory meeting

    Boosters for the vulnerable: FAQs following the FDA advisory meeting

    This past Friday, the Food and Drug Administration (FDA)’s vaccine advisory committee voted to recommend booster shots of the Pfizer-BioNTech vaccine for all Americans over age 65 and those who are particularly vulnerable to the virus, due to their health conditions and/or work environments. This was a notable recommendation because it went against the FDA’s ask: booster shots for everyone over the age of 16.

    Let’s walk through the data behind this decision.

    How is the current two-dose vaccine regimen faring against severe COVID-19 disease?

    Before we get into any numbers, it’s important to remember the initial goal of the COVID-19 vaccines: protect people against severe disease, hospitalization, and death, basically reducing the coronavirus’ power to cause deadly harm.

    On this front, all of the vaccines are performing well. Numerous papers cited during the advisory meeting, as well as the U.S.’s breakthrough case data, suggest that vaccination protects against severe COVID-19 disease for the vast majority of recipients. Among over 178 million people who had been fully vaccinated in the U.S. by mid-September, just 3,000 have died following a positive COVID-19 test. Those 3,000 deaths account for just about 1% of all COVID-19 deaths in the U.S. since January 2021.

    The numbers get a bit more complex, however, when you look at older adults and other vulnerable populations. Those who were more vulnerable to a severe COVID-19 case in the first place are also more vulnerable to having a severe breakthrough case, if they encounter the virus after vaccination. One chart, presented at the FDA meeting, provides a picture of this trend. From late January to mid-July, 2021, the hospitalization rate among younger adults (ages 18-49) was 23 times higher for the unvaccinated than for the vaccinated. For seniors (over age 65), however, the rate was 13 times higher for the unvaccinated.

    Seniors are more likely to experience a severe breakthrough case than younger adults, CDC data suggest.

    How is that current regimen faring against coronavirus infection?

    This is where we see a bigger drop in efficacy. Multiple studies point to the Pfizer and Moderna vaccines becoming less capable of protecting recipients against infection, over time; in other words, if you got your two shots in April 2021, you’re more likely to get a positive test result now, in September, than you were in May. (Though your case will likely be mild or asymptomatic!)

    While the vaccines are still highly effective against severe disease, their effectiveness against coronavirus infection appears to be waning.

    We can also see this in breakthrough case numbers when we look at all infections, as opposed to only those cases that lead to severe disease or death. This type of analysis is difficult to do in the U.S., as the CDC is only systematically tracking those severe cases, but we can see patterns in the data from local jurisdictions that are reporting their breakthrough cases more comprehensively.

    For example, let’s look at Washington, DC, which reports breakthrough cases in extensive detail:

    Washington, D.C. is seeing many more breakthrough cases now than it was earlier in 2021.

    During the week of March 8, DC reported 14 breakthrough cases. The district reported about 800 cases overall that week, meaning that breakthroughs accounted for 2% of all cases. 

    During the week of August 23, however, the district reported almost 500 breakthrough cases. In that week, the district reported about 1,400 cases overall—meaning that breakthrough cases have jumped from 2% of all weekly DC cases to 35% of all weekly DC cases.

    DC also reports a breakdown of breakthrough cases according to the time it’s been since residents were fully vaccinated. This reveals that most breakthroughs occur at least two months after an individual completed their dose series, with the highest number of breakthroughs in people who’d been vaccinated three to four months ago. We can assume that similar patterns are occurring elsewhere in the country.

    It’s also worth noting that we don’t have a great sense of how well the vaccines protect against Long COVID—though data thus far suggest that post-vaccination Long COVID cases are much rarer than non-breakthrough cases.

    Why are the vaccines appearing to lose their effectiveness?

    This was a big point of discussion for the FDA advisory committee. Are the Pfizer and Moderna vaccines appearing to lose their ability to protect us against coronavirus infection because Delta has a special ability to evade the vaccines or because the vaccines become less effective over time?

    One early-morning presenter at the FDA meeting, medical statistician Jonathan Sterne from the University of Bristol, dove into this issue. His presentation focused on confounders, a statistical term for an outside force that influences the question a researcher is trying to study. In the case of vaccine effectiveness, Sterne said, there are a lot of confounders; these include vaccine recipients’ ages, how long ago they were vaccinated, and when they were vaccinated (i.e. in which phase of the pandemic?).

    Sterne’s presentation focused on the confounders that make it difficult to estimate vaccine effectiveness.

    Sterne and other British researchers have taken advantage of the U.K.’s extensive electronic health records to analyze how well the vaccines are working, attempting to take these confounders into consideration. Overall, he said, it’s very challenging to get trustworthy effectiveness numbers—though the U.K. has approved boosters for residents over age 50, so it’s clear that the country’s public health agency does see some need for the additional shots.

    Sterne’s presentation, as did a presentation from Israeli public health officials, also underscored the need for the U.S. to collect more standardized data on breakthrough cases, among other things.

    Why did the FDA advisory committee vote against booster shots for everyone, ages 16 and over?

    When this advisory committee votes on a question regarding vaccines or another biological product, the committee is specifically asked to consider whether the benefits of the product outweigh the risks. In this case, do the benefits of widespread boosters outweigh the risks of potential side effects from those additional doses?

    When it comes to those risks of potential side effects, the committee had strikingly little data to evaluate. Pfizer did conduct a clinical trial of booster shots, but it only included 306 participants—an incredibly small number, when compared to the massive trials of the vaccine’s original two-dose regimen. The trial didn’t include any participants under age 18 or over age 55, which some advisory committee members found problematic, as they were being asked to consider approval for all Americans over age 16.

    Israel—which has now administered booster shots to over 2.8 million residents—provided some data on side effects, but their utility is limited. The country started giving boosters to older adults before moving to younger adults, limiting Israeli health officials’ ability to identify potential risk for myocarditis or other severe side effects that might be more common in the younger population.

    Israel has only identified 19 serious vaccine side effects from its booster shot rollout thus far, but the majority of the country’s young adults have yet to be vaccinated.

    While data from Israel do suggest that booster shots can bring down infection numbers in an overall population, the FDA advisory committee did not find that a sufficient argument to recommend boosters for all Americans. Not at this time, anyway.

    Why did the committee vote to support boosters for seniors and other vulnerable populations?

    The risks of booster shots may not be clear for younger adults, but the risks of a breakthrough COVID-19 case are clear for older adults and others with health conditions that make them more vulnerable to severe COVID-19 case. The committee’s vote to recommend boosters for vulnerable groups aligns with a growing scientific consensus: that the U.S. should protect seniors, nursing home residents, and others who are at higher risk for serious COVID-19 cases.

    What happens next?

    It’s important to underscore here that this booster shot recommendation came from a committee that advises the FDA, not from the FDA itself. The agency typically follows its committee’s recommendations, but it doesn’t have to. We can expect the FDA’s decision—approval of booster shots for vulnerable groups, for everyone over age 16, or something else—within a couple of days.

    Next week, on Wednesday and Thursday, a CDC advisory committee is set to meet to further discuss booster shots. If both the FDA and CDC approve boosters, health departments across the country are prepared to begin administering them to eligible Americans; this will likely include seniors and other vulnerable adults who previously got two shots of the Pfizer vaccine. 

    What about everyone who got the Moderna or Johnson & Johnson vaccines?

    Again, this decision focused on the Pfizer vaccine, so Moderna and J&J recipients will need to wait for more data and more deliberation. Moderna has formally applied to the FDA for authorization of its booster shot, so we may see a similar series of meetings about that vaccine in the coming weeks.

    J&J vaccine recipients will likely experience a longer wait as researchers collect data on the effectiveness of this one-shot vaccine. CNET has a good explainer of the situation.

    Also: If you’d like to read a more detailed breakdown of everything that happened at Friday’s advisory committee meeting, I highly recommend the STAT News liveblog by Helen Branswell and Matthew Herper, which I drew upon heavily in writing this post.

    More vaccines reporting

  • National numbers, September 19

    National numbers, September 19

    Some previous Delta hotspots are seeing case numbers decrease, while others are now seeing their highest cases yet. Charts from the September 16 Community Profile Report.

    In the past week (September 11 through 17), the U.S. reported about one million new cases, according to the CDC. This amounts to:

    • An average of 146,000 new cases each day
    • 312 total new cases for every 100,000 Americans
    • 6% more new cases than last week (September 4-10)

    Last week, America also saw:

    • 78,000 new COVID-19 patients admitted to hospitals (24 for every 100,000 people)
    • 10,000 new COVID-19 deaths (3.1 for every 100,000 people)
    • 100% of new cases now Delta-caused (as of September 11)
    • An average of 800,000 vaccinations per day (per Bloomberg)

    Last week, national case numbers appeared to be in a decline, with a 13% decrease from the prior week. This week, cases bumped back up slightly—most likely due to delayed reporting driven by the Labor Day weekend, as I predicted in last week’s issue.

    Still, this week’s daily new case average is lower than it was a couple of weeks ago. And the number of COVID-19 patients newly admitted to hospitals, a crucial metric that’s less susceptible to holiday reporting interruptions, has continued to drop: from about 12,000 new patients a day last week to 11,000 new patients a day this week.

    But we can’t say the same thing for death numbers, unfortunately. Over 10,000 COVID-19 deaths were reported in the U.S. last week, the highest number since March 2021 (at the tail end of the winter surge.)

    The country reached a sad milestone this week: one in 500 Americans have died of COVID-19, according to a Washington Post analysis. For Black, Hispanic, and Native Americans, as well as states that have been harder-hit by the pandemic, that number is lower. In Brooklyn, where I live, COVID-19 has killed one in every 240 residents.

    In some parts of the country, the Delta surge appears to be letting up. Florida saw an 18% decrease in cases from last week to this week, according to the September 16 Community Profile Report, while Texas saw an 8% decrease. California—where residents just voted to keep harsh-on-COVID-19 Governor Gavin Newsom in power—saw a whopping 23% decrease in cases, week over week.

    Meanwhile, other parts of the South and West are seeing their highest case numbers yet. Both Tennessee and West Virginia have recorded over 700 new cases for every 100,000 residents in the past week. (For context: the CDC says that over 100 new cases per 100,000 constitutes high transmission.) In West Virginia, hospitals are “overwhelmingly inundated” with COVID-19 patients. And in Alabama, though case numbers are coming down, a whopping 50% of hospital ICU patients have COVID-19.

    According to the latest CDC variant estimates, 99.7% of new cases in the country are now caused by Delta. Delta has been causing over 99% of cases for a few weeks now. Has the variant run its course here? Could it mutate into something even more transmissible, or more deadly? Or is the CDC even collecting data comprehensively enough for us to tell? Many different scenarios seem plausible as we head into the colder months.

  • National numbers, September 12

    National numbers, September 12

    COVID-19 cases appear to be going down in the U.S., though some of that drop may be due to Labor Day reporting delays. Chart from the CDC, retrieved September 12.

    In the past week (September 4 through 10), the U.S. reported about 960,000 new cases, according to the CDC. This amounts to:

    • An average of 137,000 new cases each day
    • 291 total new cases for every 100,000 Americans
    • 13% fewer new cases than last week (August 29-September 3)

    Last week, America also saw:

    • 82,000 new COVID-19 patients admitted to hospitals (25 for every 100,000 people)
    • 7,500 new COVID-19 deaths (2.3 for every 100,000 people)
    • 99% of new cases now Delta-caused (as of September 4)
    • An average of 700,000 vaccinations per day (per Bloomberg)

    Last week, I wrote that national U.S. COVID-19 cases were in a plateau. The pattern has continued this week: cases are down 13% from last week, new hospitalized patients are down 4%, and deaths are down 11%.

    It’s important to note here, though, that Labor Day likely skewed these numbers. As is typical of COVID-19 reporting on holidays, many local public health agencies—the initial source of case counts and other metrics—took the weekend off, leading those counts to get delayed. We may see higher numbers next week as reports catch up.

    Even as the national numbers drop, though, some states are seeing record case counts and overwhelmed hospitals. South Carolina is one example: this state is now seeing the highest case rate in the U.S., with 680 new cases for every 100,000 residents in the past week, per Community Profile Report data. Kentucky and West Virginia are ranking highly too, with 625 and 586 new cases for every 100,000 people in the past week, respectively.

    Both South Carolina and Kentucky have record numbers of COVID-19 patients in hospitals right now, while West Virginia is approaching its winter 2020 numbers. In Idaho, another state seeing record hospitalizations, state public health leadership placed several northern hospitals under “crisis standards of care,” meaning that clinicians could ration limited resources and prioritize those patients who are deemed most likely to survive.

    All of these states, of course, have low vaccination rates—under 50% of their populations are fully vaccinated. While vaccination rates rose nationally in August, dose counts now seem to be going down again: from a daily average of one million last week to 700,000 now.

    The Delta variant continues to dominate America’s COVID-19 surge. For several weeks now, this variant has been causing over 99% of new cases. And, while the Mu (or B.1.621) variant has made headlines, this variant appears not transmissible enough to compete with Delta. The CDC COVID Data Tracker Weekly Review noted this week that the Mu variant “reached its [U.S.] peak in late June,” causing under 5% of cases, and “has steadily decreased since.” It’s currently causing just 0.1% of cases, the CDC estimates.

    Also, we still aren’t doing enough testing. The overall national PCR test positivity rate is 9.1%, while rapid tests—increasingly popular during the Delta surge—are difficult to find in many settings. A lack of testing makes it difficult to identify all breakthrough cases and look out for future variants that may arise.

  • Delta updates: Disease severity, kids, boosters

    Delta updates: Disease severity, kids, boosters

    The states with the highest numbers of children in the hospital are also the states with the lowest vaccination rates, per CDC analysis.

    It’s been a minute since I last did a Delta variant update, and this seemed like a good week to check in. Here are a couple of major news items that I’ve seen, along with sources where you can read more.

    The Delta variant continues to be highly transmissible. On August 1, I wrote that an interaction of a few seconds is enough for Delta to spread from one person to another, when both people are unvaccinated and unmasked.

    All the new evidence that we have on Delta outbreaks backs up its incredible ability to spread. For example, in a California elementary school, an unvaccinated teacher spread the coronavirus to 12 out of the 24 students in her class, with students sitting closer to the teacher more likely to be infected. The classroom outbreak led to 27 cases in total, including the teacher—who worked for two days after first reporting her symptoms. All the cases were identified as Delta.

    Growing evidence points to Delta being more severe. A recent study in The Lancet from epidemiologists in the U.K. suggests that Delta causes severe disease more frequently than the Alpha variant (B.1.1.7). The researchers looked at hospitalization rates for British COVID-19 patients, finding that patients with Delta were twice as likely to require hospital care compared to those with Alpha. Delta patients were also younger, on average—though this could be conflated by high vaccination rates among British seniors.

    Commenting on this study in Your Local Epidemiologist, Dr. Katelyn Jetelina writes:

    This adds to the growing evidence that Delta is more severe. An early Scotland study found that the risk of hospitalization was nearly double than previous variants. An early Public Health of England technical report found this too. We also saw this in Singapore where Delta infection was associated with higher risk of oxygen requirement, ICU admission, or death.

    For kids, higher hospitalization rates are tied to community vaccination, not Delta severity. This Friday, the CDC released two reports on COVID-19 hospitalization in children.

    One major finding: out of all children with COVID-19 cases, the proportion of kids who have a severe case has not increased from previous surges to this current Delta surge. Prior to June 2021, about 27% of hospitalized COVID-19 patients under age 18 required ICU admission; in late June and July (during the Delta surge), that number was 23%. Also, the average hospital stay was shorter during the Delta surge than previously (1-4 days compared to 2-5 days). These statistics indicate that Delta isn’t more severe for kids—rather, we’re seeing cases in such high numbers that it drives up hospitalizations.

    According to the CDC’s other Friday report, hospitalizations among children (under age 18) were four times higher in states with low vaccination levels compared to states with high vaccination levels. In other words: vaccination is crucial not just to protect yourself from severe COVID-19, but to lower community transmission and protect young children who can’t yet be vaccinated.

    Evidence for boosters continues to be questionable. After the Biden administration announced that the U.S. plans to provide third vaccine doses to everyone who received Pfizer or Moderna’s vaccines, I wrote that evidence and transparency on this decision were lacking. The situation hasn’t changed much; while studies show that COVID-19 antibody levels decline several months after vaccination, many experts are not convinced that boosters are necessary for everyone at this point.

    If immunity is “waning,” why don’t we need extra shots? As usual, Katherine Wu at The Atlantic has a great article explaining the complexities here. Here’s a key paragraph from her piece:

    Defensive cells study decoy pathogens even as they purge them; the recollections that they form can last for years or decades after an injection. The learned response becomes a reflex, ingrained and automatic, a “robust immune memory” that far outlives the shot itself, Ali Ellebedy, an immunologist at Washington University in St. Louis, told me. That’s what happens with the COVID-19 vaccines, and Ellebedy and others told me they expect the memory to remain with us for a while yet, staving off severe disease and death from the virus at extraordinary rates.

    In short, though antibody levels may drop, that represents just one measurement of the immune system’s ability to fight COVID-19. Other parts of the immune system will remain ready to address the coronavirus for long after an individual is vaccinated—you just might be more likely to have an asymptomatic or mild case, rather than avoiding infection entirely. (One big caveat here: We don’t know much about the risk of Long COVID after vaccination.)

    In fact, both Rochelle Walensky (CDC director) and Janet Woodcock (interim head of the FDA) are reportedly “pushing back on the White House’s plan” for booster shots, saying they need more time to collect and review data. I, for one, hope all of their data — and discussions — are made public in the coming weeks.

    More variant news

    • National numbers, August 29

      National numbers, August 29

      Delta is causing 99% or a higher share of new cases in every region of the U.S., according to CDC estimates.

      In the past week (August 21 through 27), the U.S. reported about one million new cases, according to the CDC. This amounts to:

      • An average of 142,000 new cases each day
      • 303 total new cases for every 100,000 Americans
      • 3% more new cases than last week (August 14-20)

      Last week, America also saw:

      • 86,000 new COVID-19 patients admitted to hospitals (26 for every 100,000 people)
      • 6,000 new COVID-19 deaths (1.8 for every 100,000 people)
      • 99% of new cases now Delta-caused (as of August 21)
      • An average of 900,000 vaccinations per day (per Bloomberg)

      COVID-19 cases in the U.S. just keep rising, approaching 150,000 new cases a day. Case numbers have not been this high since January, during the winter surge. The case rise does seem to be decelerating, however: cases are only up 3% this week compared to last week, after much higher jumps in late July and early August.

      It’s worth emphasizing here that, per the CDC’s latest estimates, a full 99% of new COVID-19 cases in the U.S. are driven by Delta. Alpha, the variant we were all so worried about back in the spring, is down to just 0.2% of cases. On a practical level, that means anywhere you may encounter the coronavirus—at a restaurant, on the train, at an elementary school—this virus is highly transmissible, capable of spreading between unvaccinated people in just a few seconds.

      Florida and Louisiana continue to be major COVID-19 hotspots, but Mississippi is now seeing the country’s highest case numbers—753 cases per 100,000 residents in the past week, per Friday’s Community Profile Report. Kentucky, South Carolina, Georgia, Alabama, and Arkansas all recorded over 500 cases per 100,000 last week as well. Hurricane Ida, now on track to hit New Orleans, is sure to complicate COVID-19 prevention efforts in Louisiana and other coastal states.

      While the South lights up with record cases and hospitalizations, every single state is currently seeing high coronavirus transmission, according to the CDC’s categories (over 100 new cases per 100,000 in the past week and/or test positivity over 10%). Almost every county is in the red as well.

      Almost 90,000 Americans are in the hospital with COVID-19 right now, about three-quarters of the way to last winter’s peak. While vaccinations continue to increase, we’ll need more mitigation than just shots in arms to control this current surge.

    • Featured sources, August 15

      • CDC Variant Proportions: The CDC has adjusted the update schedule of its variant proportions estimates, from every two weeks to once a week. Variant numbers are still somewhat delayed (the most recent estimates are now from August 7, about a week ago), but this is a big improvement. The agency has also expanded its estimates to include Delta sub-lineages, called AY.1, AY.2, and AY.3.
      • COVID-19 Vaccination among People with Disabilities: Another recent change to the CDC’s COVID Data Tracker is this new page, reflecting vaccination coverage among Americans with disabilities. Data come from the Census’ Household Pulse Survey, which began asking respondents about their disability and vaccine status in April 2021.
      • Breakthrough cases by state, NYT: The New York Times has compiled and analyzed state data from on breakthrough (post-full-vaccination) COVID-19 cases, hospitalizations, and deaths. This information is available for 40 states and Washington, D.C.; the remaining 10 states failed to share their data with the NYT. Raw data underlying this analysis have yet to be made public on the NYT GitHub repository.
      • Education Stabilization Fund: The U.S. Department of Education has distributed a lot of money to school districts in the past year and a half—funding technology for remote learning, ventilation updates to buildings, COVID-19 tests, and more. This DOE database provides detailed records on which schools received funding and how much of the money has been spent.