COVID-19 Data Dispatch

Category: Vaccines

  • Omicron variant: What we know, what we don’t, and why not to panic (yet)

    Omicron variant: What we know, what we don’t, and why not to panic (yet)

    On Thanksgiving, my Twitter feed was dominated not by food photos, but by news of a novel coronavirus variant identified in South Africa earlier this week. While the variant—now called Omicron, or B.1.1.529—likely didn’t originate in South Africa, data from the country’s comprehensive surveillance system provided enough evidence to suggest that this variant could be more contagious than Delta, as well as potentially more able to evade human immune systems.

    Note that the words suggest and could be are doing a lot of work here. There’s plenty we don’t know yet about this variant, and scientists are already working hard to understand it.

    But the early evidence is substantial enough that the World Health Organization (WHO) designated Omicron as a Variant of Concern on Friday. And, that same day, the Biden administration announced new travel restrictions on South Africa and several neighboring countries. (More on that later.)

    In today’s issue, I’ll explain what we know about the Omicron variant so far, as well as the many questions that scientists around the world are already investigating. Along the way, I’ll link to plenty of articles and Twitter threads where you can learn more. As always, if you have more questions: comment below, email me, (betsy@coviddatadispatch.com), or hit me up on Twitter.

    Where did the Omicron variant come from?

    This is one major unknown at the moment. South Africa was the first country to detect Omicron this past Monday, according to STAT News. But the variant likely didn’t originate in South Africa; rather, this country was more likely to pick up its worrying signal because it has a comprehensive variant surveillance system.

    Per The Conversation, this system includes: “a central repository of public sector laboratory results at the National Health Laboratory Service, good linkages to private laboratories, the Provincial Health Data Centre of the Western Cape Province, and state-of-the-art modeling expertise.”

    Researchers from South Africa and the other countries that have detected Omicron this week are already sharing genetic sequences on public platforms, driving much of the scientific discussion about this variant. So far, one interesting aspect of this variant is that, even though Delta has dominated the coronavirus landscape globally for months, Omicron did not evolve out of Delta.

    Instead, it may have evolved over the course of a long infection in a single, immunocompromised individual. It also may have flown under the radar in a country or region with poor genomic surveillance—which, as computational biologist Trevor Bedford pointed out on Twitter, is “certainly not South Africa”—and then was detected once it landed in that country.

    Why are scientists worried about Omicron?

    Omicron seems to be spreading very quickly in South Africa—potentially faster than the Delta variant. Based on publicly available sequence data, Bedford estimated that it’s doubling exponentially every 4.8 days.

    An important caveat here, however, is that South Africa had incredibly low case numbers before Omicron was detected—its lowest case numbers since spring 2020, in fact. So, we cannot currently say that Omicron is “outcompeting” Delta, since there wasn’t much Delta present for Omicron to compete with. The current rise in cases may be caused by Omicron, or it may be the product of a few superspreading events that happen to include Omicron; we need more data to say for sure.

    Still, as Financial Times data reporter John Burn-Murdoch pointed out: “There’s a clear upward trend. This may be a blip, but this is how waves start.”

    Another major cause for concern is that Omicron has over 30 mutations on its spike protein, an important piece of the coronavirus that our immune systems learn to recognize through vaccination. Some of these mutations may correlate to increased transmission—meaning, they help the virus spread more quickly—while other mutations may correlate to evading the immune system.

    Notably, a lot of the mutations on Omicron are mutations that we simply haven’t seen yet in other variants. On this diagram from genomics expert Jeffrey Barrett, the purple, yellow, and blue mutations are all those we haven’t seen on previous variants of concern, while the red mutations (there are nine) have been seen in previous variants of concern and are known to be bad. 

    Some of these new mutations could be terrible news, or they could be harmless. We need more study to figure that out. This recent article in Science provides more information on why scientists are worried about Omicron’s mutations, as well as what they’re doing to investigate.

    How many Omicron cases have been detected so far?

    As of Sunday morning, genetic sequences from 127 confirmed Omicron cases have been shared to GISAID, the international genome sharing platform. The majority of these cases (99) were identified in South Africa, while 19 were identified in nearby Botswana, two in Hong Kong, two in Australia, two in the U.K., one in Israel, one in Belgium, and one in Italy.

    According to BNO News, over 1,000 probable cases of the variant have already been identified in these countries. Cases have also been identified in the Netherlands, Germany, Denmark, the Czech Republic, and Austria. Many of the cases in the Netherlands are connected to a single flight from South Africa; the travelers on this flight were all tested upon their arrival, and 61 tested positive—though authorities are still working to determine how many of those cases are Omicron. 

    The U.K. Health Security Agency announced on Saturday that it had confirmed two Omicron cases in the country. Both of these cases, like those in Israel and Belgium, have been linked to travel—though the Belgium case had no travel history in South Africa. “This means that the virus is already circulating in communities,” Dr. Katelyn Jetelina writes in a Your Local Epidemiologist post about Omicron. 

    After South African scientists sounded the alarm about Omicron, cases were detected in Botswana, Australia, Hong Kong, Israel, the U.K., and other countries. Chart via GISAID, screenshot taken about 11:30 AM NYC time on November 28.

    Omicron hasn’t been detected in the U.S. yet. But the CDC is closely monitoring this variant, the agency announced in a rather sparse Friday press release.

    Luckily, Omicron is easy to identify because one of its spike protein mutations enables detection on a PCR test—no genomic sequencing necessary. Alpha, the variant that originated in the U.K. last winter, has a similar quality.

    How does Omicron compare to Delta?

    This is another major unknown right now. As I mentioned earlier, Omicron is spreading quickly in South Africa, at a rate faster than Delta spread when it arrived in the country a few months ago. But South Africa was seeing a very low COVID-19 case rate before Omicron arrived, making it difficult to evaluate whether this new variant is directly outcompeting Delta—or whether something else is going on.

    (Note that a couple of the tweets below refer to this variant as “Nu,” as they were posted prior to the WHO designating it Omicron.)

    We also don’t know if Omicron could potentially evade the human immune system, whether that means bypassing immunity from a past coronavirus infection or from vaccination. However, vaccine experts say that a variant that would entirely evade vaccines is pretty improbable.

    Every single coronavirus variant of concern that we’ve encountered so far has responded to the vaccines in some capacity. And the variants that have posed more of a danger to vaccine-induced immunity (Beta, Gamma) have not become dominant on a global scale, since they’ve been less transmissible than Delta. Our vaccines are very good—not only do they drive production of anti-COVID antibodies, they also push the immune system to remember the coronavirus for a long time.

    It’s also worth noting here that, so far, Omicron does not appear to be more likely to cause severe COVID-19 symptoms. Angelique Coetzee, chairwoman of the South African Medical Association, announced on Saturday that cases of the variant have been mild overall. Hospitals in South Africa are not (yet) facing a major burden from Omicron patients.

    What can scientists do to better understand Omicron?

    One thing I cannot overstate here is that scientists are learning about Omicron in real time, just as the rest of us are. Look at all the “We don’t know yet.”s in this thread from NYU epidemiologist Céline Gounder:

    Gounder wrote that we may have answers to some pressing questions within two weeks, while others may take months of investigation. To examine the vaccines’ ability to protect against Omicron, scientists are doing antibody studies: essentially testing antibodies that were produced from past vaccination or infection to see how well they can fight off the variant.

    At the same time, scientists are closely watching to see how fast the variant spreads in South Africa and in other countries. The variant’s performance in the U.K., where it was first identified on Saturday, may be a particularly useful source of information. This country is currently facing a Delta-induced COVID-19 wave (so we can see how well Omicron competes); and the U.K. has the world’s best genomic surveillance system, enabling epidemiologists to track the variant in detail.

    How does Omicron impact vaccine effectiveness?

    We don’t know this yet, as scientists are just starting to evaluate how well human antibodies from vaccination and past infection size up against the new variant. The scientists doing these antibody studies include those working at Pfizer, Moderna, and other major vaccine manufacturers. Pfizer’s partner BioNTech has said it expects to share lab data within two weeks, according to CNBC reporter Meg Tirrell:

    If BioNTech finds that Omicron is able to escape immunity from a Pfizer vaccination, the company will be able to update that vaccine within weeks. Moderna is similarly able to adjust its vaccine quickly, if lab studies show that an Omicron-specific vaccine is necessary.

    Even if we need an updated vaccine for this variant, though, people who are already vaccinated are not going back to zero protection. As microbiologist Florian Krammer put it in a Twitter thread: “And even if a variant vaccine becomes necessary, we would not start from scratch… since it is likely that one ‘variant-booster’ would do the job. Our B-cells can be retrained to recognize both, the old version and the variant, and it doesn’t take much to do that.”

    What can the U.S. do about Omicron?

    On Friday, the Biden administration announced travel restrictions from South Africa and neighboring countries. The restrictions take effect on Monday, but virus and public health experts alike are already criticizing the move—suggesting that banning travel from Africa is unlikely to significantly slow Omicron’s spread, as the variant is very likely already spreading in the U.S. and plenty of other countries.

    At the same time, travel restrictions stigmatize South Africa instead of thanking the country’s scientists for alerting the world to this variant. Such stigma may make other countries less likely to share similar variant news in the future, ultimately hurting the world’s ability to fight the pandemic.

    So what should the U.S. actually be doing? First of all, we need to step up our testing and genomic surveillance. As I mentioned above, Omicron can be identified from a PCR test; an uptick in PCR testing, especially as people return home from Thanksgiving travel, could help identify potential cases that are already here.

    We also need to increase genomic surveillance, which could help identify Omicron as well as other variants that may emerge from Delta. In a post about the Delta AY.4.2 variant last month, I wrote that the U.S. is really not prepared to face surges driven by coronavirus mutation:

    We’re doing more genomic sequencing than we were at the start of 2021, which helps with identifying potentially concerning variants, but sequencing still tends to be clustered in particular areas with high research budgets (NYC, Seattle, etc.). And even when our sequencing system picks up signals of a new variant, we do not have a clear playbook—or easily utilized resources—to act on the warning.

    We also need to get more people vaccinated, in the U.S. and—more importantly—in the low-income nations where the majority of people remain unprotected. In South Africa, under one-quarter of the population is fully vaccinated, according to Our World in Data.

    What can I do to protect myself, my family, and my community?

    In general, do all of the same things that you’ve already been doing. Most importantly, get vaccinated (including a booster shot, if you’re eligible).

    Also: Wear a mask in indoor spaces, ideally a good quality mask (N95, KN95, or double up on surgical and cloth masks). Avoid crowds if you’re able to do so. Monitor yourself for COVID-19 symptoms, including those that are less common. Utilize tests, including PCR and rapid tests—especially if you’re traveling, or if you work in a crowded in-person setting. 

    I’ve seen some questions on social media about whether people should consider canceling holiday plans, or other travel plans, because of Omicron. This is a very personal choice, I think, and I’m no medical expert, but I will offer a few thoughts.

    As I said in the title of this post, we don’t yet know enough about this variant for it to be worth seriously panicking over. All of the evidence—based on every single other variant of concern that has emerged—suggests that the vaccines will continue to work well against this variant, at least protecting against severe disease. And all of the other precautions that work well against other variants will work against this one, too.

    So, if you are vaccinated and capable of taking all the other standard COVID-19 precautions, Omicron is most likely not a huge risk to your personal safety right now. But keep an eye on the case numbers in your community, and on what we learn about this variant in the weeks to come. 

    What does Omicron mean for the pandemic’s trajectory?

    This variant could potentially lead to an adjustment in our vaccines, as well as to new surges in the U.S. and other parts of the world. It’s too early to say how likely either scenario may be; we’ll learn a lot more in the next couple of weeks.

    But one thing we can say right now, for sure, is that this variant provides a tangible argument for global vaccine equity. If the country where Omicron originated had a vaccination rate as high as that of the U.S. and other high-income nations, it may not have gained enough purchase to spread—into South Africa, and on the global path that it’s now taking. 

    As physician, virologist, and global health expert Boghuma Kabisen Titanji put it in a recent interview with The Atlantic:

    If we had ensured that everyone had equal access to vaccination and really pushed the agenda on getting global vaccination to a high level, then maybe we could have possibly delayed the emergence of new variants, such as the ones that we’re witnessing.

    I will end the post with this tweet from Amy Maxmen, global health reporter at Nature. The Omicron variant was a choice.

    More variant reporting

  • COVID source callout: CDC’s breakthrough case data

    The CDC has not updated its breakthrough case data since September. A full two months ago.

    Earlier in 2021, the agency reported a total count of breakthrough infections, hospitalizations, and deaths—then switched to reporting only those breakthrough cases leading to hospitalization or death in May.

    The page that used to house this data now no longer includes total case counts; instead, the CDC redirects users to a couple of other pages:

    The CDC and FDA expanded booster shot eligibility to all adults in part because of increasing COVID-19 cases across the country.  But without comprehensive breakthrough case data, as I’ve said numerous times, it’s hard to pinpoint exactly how well the vaccines are working—and who’s most at risk of a breakthrough case.

    MedPage Today, which published a detailed article on this topic, received a statement from the CDC claiming that the breakthrough case and death data will be updated “in mid-November, to reflect data through October 2.” This long lag is due to the time it takes for the CDC to link case surveillance records to vaccination records, the agency said.

    Almost a year into the U.S.’s COVID-19 vaccination campaign, you’d really think our national public health system would have a better way of monitoring breakthrough cases by now.

    more source spotlights
  • Boosters for all adults: Why eligibility expanded, and what it means for you

    Boosters for all adults: Why eligibility expanded, and what it means for you

    As of November 20, almost 35 million Americans have received a booster shot. That number is likely to shoot up in the coming weeks with expanded eligibility. Chart via the CDC.

    On Friday morning, the FDA authorized booster shots of Pfizer’s and Moderna’s COVID-19 vaccines for all adults in the U.S., six months after their first two doses. The CDC’s vaccine advisory committee voted to support this expanded booster eligibility that afternoon, and CDC leadership signed off on it a few hours later.

    Although the Biden administration has supported boosters for all adults since August, this specific federal eligibility expansion was preceded by several state and local leaders. Prior to Friday, the governors of Colorado, New Mexico, California, and other states said that any adult living in their jurisdictions could go get a booster, even if they didn’t fit the current national criteria. New York City leaders made a similar announcement this past Monday.

    Perhaps spurred on by these state decisions, the FDA and CDC moved quite quickly to authorize booster shots for a larger group of Americans. The FDA was originally just considering the move for Pfizer’s vaccine, then added Moderna to the mix just this week (when Moderna sent in a formal application).

    And the CDC’s vaccine advisory committee meeting had somewhat less time for deliberation than this committee typically tends to take. As Helen Branswell wrote in STAT News:

    The meeting was called on such short notice — it was announced Tuesday — that only 13 of the committee’s members were able to attend. When the meeting went longer than scheduled, two members had to leave without voting.

    I discussed expanded booster shot eligibility this week in a FiveThirtyEight Chat with editor Chadwick Matlin and science writer Maggie Koerth. Today at the COVID-19 Data Dispatch, I’d like to expand on the ideas in that chat piece, and attempt to answer a couple of other questions.

    Why expand booster eligibility to all adults?

    The short answer here is 1) more compelling evidence that boosters provide additional protection against coronavirus infection and 2) cases are rising in the U.S., and boosters might help make the surge less severe. Also, so far, very few cases of severe side effects have been reported following booster shots.

    Since the last FDA and CDC booster shot deliberations, more evidence has rolled in showing their efficacy. One notable study, from the Imperial College of London, was published this past Wednesday; the report suggests that people who’ve received two COVID-19 vaccine doses are more than twice as likely to test positive than those who’ve received three doses.

    While the study hasn’t yet been peer-reviewed, it’s part of a long-running surveillance project in the U.K. that examines COVID-19 prevalence in the entire population—including all age groups and comparing those who received Pfizer and AstraZeneca vaccines. “What they found is very, very strong data showing that as soon as 7 days after a third COVID-19 vaccine dose, the risk of infection is cut in half when you look at the entire population,” wrote Dr. Jorge Caballero in a Twitter thread summarizing the study. 

    https://twitter.com/DataDrivenMD/status/1461167298102784001

    At the same time, cases are going up in the U.S.—appearing to indicate a new winter surge. It’s no coincidence that Colorado and New Mexico, two of the states that were among the first to expand booster eligibility to all adults, are also among the states with the highest COVID-19 case rates.

    When Delta hit Israel this past summer, the country started administering booster shots: first to seniors at the end of July, then for younger and younger age groups until all adults were able to get the shots. Data from the country’s national health agency suggest that these booster shots played a key role in driving down case numbers among both vaccinated and unvaccinated Israelis.

    Personally, I am still a bit skeptical that Israel’s drop in cases was thanks to booster shots alone, as the data don’t necessarily show causation. But for a lot of U.S. leaders, the Israeli data provide a compelling model: it seems like booster shots can potentially drive down a case surge. This fits nicely into the national strategy that the Biden administration has already been preaching for months, which I call “vaccinate out of the pandemic.”

    Here’s how I explained it in the FiveThirtyEight chat piece:

    Listening to the advisory-committee meetings, I noticed that there seems to be this tension between the scientific experts who want to make robust evidence-based decisions — and the sense that, here in the U.S., our overall pandemic strategy is basically “vaccinate our way out of the pandemic.” If we had better masking, distancing, contact tracing, ventilation, rapid tests and everything else, we would not need boosters to stop people’s mild cases. But we’re not doing a great job at any of those other things, so … we kinda need boosters.

    Maggie Koerth also pointed out that booster shots are also politically easier for a lot of leaders than some of the other COVID-19 strategies I mentioned. We already have the shots stockpiled, so it’s just a matter of telling people to go get them—unlike, say, expanding contact tracing, which would take a huge investment in hiring and training people.

    In addition, the eligibility expansion solves communication and logistics challenges: now, every adult in the U.S. can just go get a booster shot, once enough time has passed from their first two doses. Almost 90% of vaccinated Americans were eligible already, but a lot of people were confused about whether they fit the criteria; the situation became much simpler after Friday.

    Should you get a booster shot?

    If you’re over 65 or you have a health condition that makes you particularly vulnerable to severe COVID-19 symptoms, answering this question is easy: YES. Go get a booster shot, as soon as you’re able to do so.

    If you live or work in a setting that puts you at risk of contracting the coronavirus—or if you live or work in a setting with other people who are more vulnerable than you—then you also have a pretty solid argument towards getting a booster shot.

    Even if you’re very unlikely to have a severe case of COVID-19 thanks to your initial vaccination, a mild case could still disrupt your work, your household, and others in your community. A teacher with breakthrough COVID-19 might cause their classroom to shut down for a week, for example, while a parent with breakthrough COVID-19 may interrupt their kids’ lives if those kids are too young to be vaccinated themselves.

    For those who don’t fall into these categories (like me!), the situation is a bit more complicated. But after following all of the news this week, I’ve decided that it does make sense for me to get my booster shot.

    Here’s why: much as I wish that national leadership and my own local leaders in NYC were investing in other measures to control COVID-19 cases, I don’t foresee widespread mask mandates, rapid tests, contact tracing, or any other safety overhauls anytime soon. Instead, my public health leaders are asking me (and those around me) to get booster shots in order to potentially lower case rates. So, I’ll do my part to contribute to that “vaccinate out of the pandemic” strategy, though I don’t necessarily agree with it.

    It’s also important to note here that vaccinating the people who are still unvaccinated is much more important for lowering overall case counts—and for keeping people out of the hospital—than boosters. That includes kids in the 5 to 11 age group. As Maggie Koerth said in our chat:

    If you’re under 65 and you’re not immune compromised, it almost certainly matters more to get your kiddos vaxxed the first time than to get yourself a booster. That’s my parent-centric takeaway from all this reading.

    And, of course, to end the pandemic on a global scale, we need to get first and second doses to everyone in the world. Right now, booster shots are hindering global vaccination: according to the WHO, there are about six times more boosters administered daily in wealthy nations right now than there are first and second doses administered in low-income nations.

    The U.S. has already chosen to stockpile millions of doses for boosters, so refusing a booster shot on an individual level doesn’t have any impact on the global situation. But there are other options for people who want to take action about vaccine inequality: for example, you can contact your congressional representatives about the issue.

    What happens after a lot of Americans get booster shots?

    Someone asked me this question on Twitter earlier this week. Do booster shots lead to other loosening COVID-19 restrictions, or something else?

    It’s difficult to answer that right now, because the U.S. is still close to the beginning of our booster shot rollout. Within a couple of months—and millions more doses—we’ll have some data on whether booster shots here lead to a drop in cases, like what we saw in Israel. At the same time, many European countries are similarly offering booster shots to wide swaths of their populations; we can also watch what happens in those nations.

    The U.S. is still likely to face a case surge this holiday season, I think, simply due to cold weather combined with travel and gatherings. But perhaps booster shots will mean that hospitalizations don’t rise as much as cases do, or that a higher share of the cases are mild. We’ll have to see.

    Looking beyond this winter, we could see three shots become standard for COVID-19 vaccines. (Several other vaccines, such as HPV, are three-shot series.) We could also see annual boosters for COVID-19, similar to flu shots. More study of the booster shots’ effectiveness and of long-term COVID-19 immunity in general will help scientists figure this out.

    Finally, I couldn’t end this post without pointing out the continued data gaps here. The U.S. is still not tracking breakthrough cases in any kind of comprehensive manner, and a lot of information is missing on who’s getting booster shots—the CDC and most states are not reporting demographic data on booster recipients.

    To quote Dr. Katelyn Jetelina from her recap of Friday’s CDC advisory committee meeting:

    And this is it. This [three small studies] is all the data the CDC presented today. Which is insane— the United States does not have a real-time, comprehensive picture of our vaccines, nor the number of breakthrough cases, nor who’s more likely to have a breakthrough case or not. I cannot emphasize enough of how detrimental this is to our public health response. Bad data produces (potentially) bad policy. We are flying blind.

    More vaccine reporting

  • Public health data in the US is “incredibly fragmented”: Zoe McLaren on booster shots and more

    Public health data in the US is “incredibly fragmented”: Zoe McLaren on booster shots and more

    This week, I had a new story published at the data journalism site FiveThirtyEight. The story explores the U.S.’s failure to comprehensively track breakthrough cases, and how that failure has led officials to look towards data from other countries with better tracking systems (eg. Israel and the U.K.) as they make decisions about booster shots.

    In the piece, I argue that a lack of data on which Americans are most at risk of breakthrough cases—and therefore most in need of booster shots—has contributed to the confusion surrounding these additional doses. Frequent COVID-19 Data Dispatch readers might recognize that argument from this CDD post, published at the end of September.

    Of course, an article for FiveThirtyEight is able to go further than a blog post. For this article, I expanded upon my own understanding of the U.S.’s public health data disadvantages by talking to experts from different parts of the COVID-19 data ecosystem.

    At the CDD today, I’d like to share one of those interviews. I spoke to Zoe McLaren, a health economist at the University of Maryland Baltimore County, about how the U.S. public health data system compares to other countries, as well as how data (or the lack of data) contribute to health policies. If you have been confused about your booster shot eligibility, I highly recommend giving the whole interview a read. The interview has been lightly edited and condensed for clarity.

    Betsy Ladyzhets: I’m writing about this question of vaccine effectiveness data and breakthrough case data in the U.S., and how our data systems and sort-of by extension public health systems compare to other countries. So, I wanted to start by asking you, what is your view of the state of this data topic in the U.S.? Do you think we can answer key questions? Or what information might we be missing?

    Zoe McLaren: It’s the age-old problem of data sources. A lot of cases are not going to be reported at all. And then even the ones that are reported may not be connected to demographic data, for example, or even whether the people are vaccinated or not. Whereas other countries like Israel, and the U.K., your positive COVID test goes into your electronic health record that also has all the other information. 

    And Medicare patients, they have that whole [records] system. There will be information [in the system] about whether they got vaccinated, as well as whether they have a positive test. So that data will be in there. But for other people, it may or may not be in an electronic health record. And then of course, there’s multiple different electronic health record systems that can’t be integrated easily. So you don’t get the full picture.

    But it’s all about sample selection. Not everyone [who actually has COVID] is ending up in the data, which messes up both your numerator and denominator when you’re looking at rates.

    BL: Could you say more about how our system in the U.S. is different from places like Israel and the U.K., where they have that kind of national health record system?

    ZM: When the government is providing health insurance, then all of your records and the [medical] payments that happen, there’s a record of them… And then, because it’s a national system, it’s already harmonized, and everyone’s in the same system. So it’s really easy to pull a dataset out of that and analyze it.

    Whereas in the US, everything is incredibly fragmented. The data, and the systems and everything is very fragmented. The electronic health systems don’t merge together easily at all. And so you get a very fragmented view of what’s going on in the country.

    BL: Right, that makes sense. Yesterday, I was talking to a researcher at the New York State Health Department who did a study where they matched up the New York State vaccination records with testing records and hospitalization records, and were able to do an analysis of vaccine effectiveness. And he said, basically, the more specific, you tried to go with an analysis, the harder it is to match up the records correctly, and that kind of thing.

    ZM: Exactly. It’s easy to match on things like age, sex, race, since everybody has them. But then, the different data fields are gonna have different formats and be much harder to merge together.

    BL: So what can we do to improve this? I know Medicare for All is one option— 

    ZM: Medicare for All, end of story, end of article. It would solve so many problems.

    It’s tricky, though, because there isn’t a simple fix. All of these health systems have their own electronic health records, and integrating them is really costly and hard to do, and who is going to pay for that? There’s also additional privacy concerns about integrating things, in terms of protecting privacy and confidentiality. So, that’s really tricky.

    The way that we get around that, in general, is to have reporting requirements. Like with COVID tests, [providers are] required to report to the CDC or the HHS… Still, that’s also costly and time consuming. But that is kind-of the best thing that we can do right now, is have the different [public health] entities produce reports on a regular basis and send that to a centralized location. And the reports are supposed to be produced in a way that they are harmonized, they’re easy to put together from all the different systems.

    The problem with the different systems not integrating is, it requires everyone to basically fill out the equivalent of a form and send it in—listing individual patient information, or at the state level, individual county information. An example of that is the COVID data. All of the COVID data gets reported up to the national level [by state and county health departments]… 

    But the reporting often gives you the numerators, when you need to figure out the denominators. Because you would want to know, for example, we want to know what proportion of breakthrough cases end up hospitalized. But if only the hospitalized people end up in the data, and a lot of breakthrough cases go either undetected or never tested, or they do an at-home test and there’s no record of that positive case in the system, then your denominator is—there’s a problem with your denominator. That’s a problem with sample selection, you get people that are self-selecting into the numerator [by testing positive], but also self-selecting into the denominator [by getting a test to begin with].

    BL: Yeah, that makes sense. I know you said it would be pretty complicated to basically force different public health departments—to standardize them so that they’re all reporting in the same way. Is there more that researchers in the US could be doing in the short-term to either improve data collection or use what we have to answer questions like, what occupations might confer higher risk of a breakthrough case? 

    ZM: This is a coordination problem. Because in general, we all have an incentive to contribute to having a better understanding of breakthrough cases. But the trick is that, unless the national government or the CDC takes the role of saying what the [data] format’s gonna look like…

    Part of the problem is that there’s an effort involved [in collecting these data] and people don’t want to put in the effort. But if they do want to put in the effort, then you still have a coordination problem, because who gonna to be deciding what format we’re using?

    BL: Or like, what the data definitions are.

    ZM: Exactly. Like, do you report the month and the day of the vaccination dose, or just the month of the dose? Things like that where it doesn’t seem like a big deal, but it does matter for research purposes. If you look, for example, at the Census, or any of the national surveys, like the Current Population Survey or the National Labor Force Survey where we get unemployment numbers, there are big committees that figure out which questions we’re asking and how we ask them. So, if the CDC just says, like, “This is the dataset we’re building,” then everyone [local agencies] will be like, “Okay, we’re gonna send our reports in that way.” 

    Part of [the challenge] is that it takes effort to produce the data, and part of it is somebody needs to coordinate. And usually that would be something the CDC would do, saying, “This is the data that needs to be reported to us,” and everybody reports to them. But they could be doing more, they could be asking for more detailed information—for example, data based on vaccination status, because that information will be important for understanding the progression of the pandemic.

    BL: Yeah. I volunteered for the COVID Tracking Project for a while, and one of the most tedious things that we had to do there was figuring out different definitions for like, what states were considering a case or a test, or whatever else. So that definitely makes sense to me.

    ZM: Exactly. And the COVID Tracking Project filled a gap. Nobody was doing that [collecting data from the states], so the COVID Tracking Project did that… But it’s tricky, because a lot of the stuff that seems like splitting hairs [on definitions] really does make a difference when you’re doing your analysis.

    BL: I also wanted to ask you about what the implications are of this lack of standardized data in the U.S., and the lack of information that we have—largely around vaccinations, but I think there are other areas as well where we’re missing information. So I’m trying to figure out, for this story, how data gaps might contribute to the confusion that people feel when they watch health agencies make decisions. Like watching all the back and forth on booster shots, or thinking about Long COVID, other things like that.

    ZM: Well, we talk about evidence-based medicine, and we also care about evidence-based policy. And so it means that when the quality of data is poor, the quality of our policy is going to be worse. So it really is in everybody’s best interest to have high-quality data, because that is the bedrock of producing high quality policy.

    BL: Right. So if we don’t know, for example, if people who live and work in certain situations are more likely to have a breakthrough case, then we can’t necessarily tell them—we can’t necessarily say, “These specific occupations should go get booster shots.” And then we just say, “Everyone can go get a booster shot.”

    ZM: It means that we’re flying blind. And the problem of flying blind is twofold. One is that you can end up making poor decisions, the wrong decisions, because you don’t have the data. And then the other problem is that you end up making decisions that, in economics, we call it “inefficient.” I think about [these decisions] as, you end up with “one size fits all.” 

    If we have really high quality data, then we’re able to create different policies for different types of people, and that helps minimize any of the downsides. But the less data we have, the more we have to rely on “one size fits all.” And of course, if “one size fits all,” it’s going to be too much for some people and too little for others. Data would help improve that.

    BL: How do you think that this kind of “one size fits all” contributes to how individual people might be confused or might not be sure how to kind of interpret the policies for their own situations?

    ZM: I think in a “one size fits all,” people get very frustrated because they see in their own lives, both the uncertainty and how that can be stressful—and also the waste. The situations where they fall under one policy, but they have enough information to know that that policy doesn’t necessarily apply to them. It does undermine confidence in policymaking. People get frustrated with “one size fits all,” because it seems wasteful.

    Though sometimes the “one size fits all” is still optimal, it’s better than the alternative. For example, the recommendation of “one size fits all” wearing masks tends to trump the “one size fits all” of not wearing masks. But there’s waste. There are situations where we end up wearing masks where they wouldn’t necessarily be needed. And vice versa.

    BL: Yeah. That makes me think of friends I have who are eligible to get booster shots because of medical conditions, but they’re sort-of thinking, “I wish the shots could go to another country where they need vaccinations more.” And that’s not something individuals have any control over, but it’s frustrating.

    ZM: Part of it is, with the booster shots, is the guidelines that say people who have higher occupational exposure to risk [are eligible] without specifying exactly who that is. That is one way that we allow some leeway. So it’s not a “one size fits all” where nobody gets it, because there’s actually people who qualify under higher occupational exposure. But we also don’t want to have a “one size fits all” where we tell everyone they need it, because we do want to be sending doses abroad as well.

    So that’s a situation where we know that a “one size fits all” is not perfect. And so we create a, like, “use your judgement, talk to your doctor” kind-of thing that tries to help people self-select into the right groups… There are likely a lot of people who do have higher exposure and should be getting it, but don’t think the benefit applies to them.

    Editor’s note: According to one analysis, about 89% of U.S. adults will qualify for a booster shot after enough time has passed from their primary vaccine series. And, according to the October COVID-19 Vaccine Monitor report, four in ten vaccinated adults were unsure whether they qualified.

    BL: I also wanted to ask, you mentioned rapid tests—those don’t necessarily get reported. Are there other other things that you think pose data gaps in the U.S. public health system?

    ZM: With rapid tests, the actual tests are not getting reported. But the important thing is, people are getting tested. I mean, the reason we want good data quality is to reduce cases, and we wouldn’t want to limit access to rapid tests in order to collect data, because it’s much easier to prevent the cases by allowing people to get tested in their homes.

    But yeah, just the fact that there’s no centralized database for analysis [is a gap]. I mean, if you look at the U.K., and Israel, they have these great studies, because they’re able to just download, like, the entire population into a dataset. And it has all the information they need, like demographic factors. The fact that the U.S. has made so much of its national policy based on Israeli data, this shows how far behind we are with having our own data to answer these questions.

    BL: Yeah. I know, it’s something like half or a third of cases in the U.S., the CDC doesn’t have race and ethnicity information for [editor’s note: it’s 35%], and other stuff like that. It’s wild.

    ZM: Yeah… And one of the things about reporting is that every additional piece of data you want is very costly. And so you have to be very judicious about [collecting new values].

    BL: Well, those were all my questions. Is there anything I didn’t ask you that you think would be important for me to know for this story?

    ZM: Just that data is helpful for planning now, and helpful for the future. If we can improve our data systems now—it’s part of being prepared for the next pandemic.

    More vaccine reporting

  • Booster shot data slowly makes it onto state dashboards, but demographic information is lacking

    Booster shot data slowly makes it onto state dashboards, but demographic information is lacking

    Ohio is one of just eight states reporting demographic data for booster shots administered in the state. Screenshot taken on November 7.

    It’s now been over a month since the FDA and the CDC authorized third doses of Pfizer’s COVID-19 vaccine for a large swath of the U.S. population, and a couple of weeks since the agencies did the same thing for additional doses of Moderna and Johnson & Johnson’s vaccines. In that time, over 20 million Americans have received their boosters.

    This weekend, I set out to see what data are now available on these booster shots. I updated my vaccination data in the U.S. resource page, which includes detailed annotations on every state’s vaccine reporting along with several national and international sources.

    The majority of states (and national dashboards) are now including booster shots in their vaccine reporting, I found. But in most cases, the reporting stops at just one statistic: the total number of residents who have received an additional dose. A few states are reporting time series information—i.e. booster shots administered by day—and a few are reporting demographics—i.e. booster shot recipients by age, gender, race, and ethnicity—but these metrics are lacking across most dashboards.

    Demographic information, particularly race and ethnicity, should be a priority for booster shot data, as it should be for numerous other COVID-19 metrics. At the beginning of the U.S.’s vaccine rollout, Black and Hispanic/Latino Americans lagged behind white Americans in getting their shots, but limited data hindered the public health system’s ability to respond to this trend. (Now, the trends have evened out somewhat, though Black vaccination rates still lag white rates in some states.)

    Will we see the same pattern with booster shots? Considering the immense confusion that has surrounded America’s booster shot rollout in the last couple of months, it would not be surprising if disadvantaged communities are less likely to know about their potential need for a booster, or where and how to get those shots.

    But so far, we don’t have enough data to tell us whether this pattern is playing out. The CDC has yet to report booster shot data by race or ethnicity, though the agency is now reporting some figures by age and by state. Note: the CDC still has yet to report detailed vaccination data by race and ethnicity, period; the agency just reports national figures, nothing by state or other smaller geographies.

    At the state level, just eight states are reporting booster shots by race and ethnicity. 13 states are reporting some kind of time series (boosters administered by day or week), and three are reporting doses administered by vaccine manufacturer.

    Here are all the states that I found reporting booster shot data, with links to their dashboards:

    • Arkansas: Reporting total boosters only.
    • California: Total boosters only.
    • Colorado: Reporting demographics; age, race/ethnicity, and sex.
    • DC: Total boosters for DC and non-DC residents.
    • Delaware: Reporting demographics; age, race/ethnicity, and sex.
    • Florida: Total boosters only.
    • Indiana: Total boosters and doses administered by day.
    • Kansas: Total boosters and doses administered by day.
    • Louisiana: Total boosters only.
    • Massachusetts: Total boosters and doses administered by day.
    • Maryland: Reporting demographics; age, race/ethnicity, and sex.
    • Michigan: Reporting demographics (age, race/ethnicity, and sex) as well as doses administered by week and by manufacturer.
    • Minnesota: Total boosters only.
    • Missouri: Total boosters and doses administered by day.
    • Mississippi: Reporting demographics (age and race/ethnicity) as well as doses administered by facility type (total and for the prior week).
    • North Dakota: Total boosters and doses administered by day.
    • New Jersey: Reporting demographics (age, race/ethnicity, and sex) as well as doses administered by day and by manufacturer.
    • New Mexico: Total boosters only.
    • Ohio: Reporting demographics (age, race/ethnicity, and sex) as well as doses administered by day and by county.
    • Oklahoma: Total boosters only.
    • Oregon: Total boosters, doses administered by day and by county.
    • Pennsylvania: Total boosters and doses administered by day.
    • Rhode Island: Boosters administered by day only.
    • South Carolina: Boosters administered by day only.
    • South Dakota: Total boosters, doses administered by week and by county.
    • Texas: Total boosters only.
    • Virginia: Reporting demographics; age, race/ethnicity, and sex.
    • Vermont: Total boosters only.
    • Wyoming: Total boosters and doses administered by manufacturer.

    Local reporters: If your state is reporting demographic data, I recommend taking a look at those numbers. How does the population receiving booster shots compare to the overall population of your state, or to the population that’s received one or two doses? And if your state is not reporting demographic data (or any booster data at all), ask your public health department for these numbers!

    You can see my vaccine annotations page for more information on all of these state dashboards. And if there are any states or metrics I missed, please let me know! Comment here or email me at betsy@coviddatadispatch.com.

    More vaccine reporting

  • FDA authorizes Pfizer vaccine for younger children

    FDA authorizes Pfizer vaccine for younger children

    The Pfizer vaccine will likely be available to children ages 5 to 11 next week, but many parents are hesitant about getting their kids vaccinated. Chart via the KFF COVID-19 Vaccine Monitor.

    Last week, the Food and Drug Administration (FDA) recommended Pfizer’s COVID-19 vaccine for children ages 5 to 11, under an Emergency Use Authorization. The agency’s vaccine advisory committee met on Tuesday to discuss Pfizer’s application and voted overwhelmingly in favor; the FDA followed this up with an EUA announcement on Friday.

    This coming week, the process continues: CDC’s own vaccine advisory committee will discuss and vote on vaccinating kids in the 5-11 age group, and then the agency will make an official decision. If all goes well—and all is expected to go well—younger kids will be able to get their vaccines in time for Thanksgiving.

    Many of the parents I know have been eagerly awaiting this authorization, but the sentiment is far from universal. COVID-19 vaccinations for kids are incredibly controversial, more so than vaccinations for adults. The public comment section of the FDA advisory committee meeting—in which basically anyone can apply to share their thoughts—was full of anti-vaxxers, many of them sharing misinformation. Even some experts on the FDA advisory committee were not fully convinced that vaccines are needed for all young kids, though all but one eventually voted in favor.

    Now, let me be clear: there are definite benefits to vaccinating younger children. While kids are less likely to have severe COVID-19 cases than adults, the disease has still been devastating for many children. Almost 100 kids in the 5 to 11 age range have died of COVID-19, making this disease one of the top 10 causes of death for this group over the past year and a half.

    Plus, children who get infected with the coronavirus are at risk for Long COVID and MIS-C, two conditions with long-lasting ramifications. There have been about 5,200 MIS-C cases thus far—and the majority of these cases have occurred in Black and Hispanic/Latino children. Minority children are also at much higher risk for COVID-19 hospitalization. 

    Vaccination can prevent children from severe ramifications of a potential COVID-19 case, as well as from the mild infections that lead to missed school and other disruptions. But the FDA committee had to carefully weigh this benefit against potential side effects from vaccination, namely myocarditis—a type of heart inflammation.

    The U.S. system for tracking vaccine side effects has identified a small number of myocarditis cases in children ages 12 to 15 after their second shots of Pfizer or Moderna vaccines. For the meeting this past Tuesday, the FDA presented some models weighing potential myocarditis cases in young kids against vaccination benefits; the models showed that, in almost every scenario, the number of severe COVID-19 cases prevented by vaccination is higher than the myocarditis cases.

    It’s worth noting: in Pfizer’s clinical trial for the 5 to 11 age group, no child had a severe adverse reaction to the vaccine. But the Pfizer researchers did observe five medical events that were unrelated to vaccination—including one kid who swallowed a penny.

    https://twitter.com/ENirenberg/status/1453218125520982019

    Some of the FDA advisory committee members suggested that perhaps vaccines would be most beneficial for children with underlying medical conditions, who are more susceptible to severe COVID-19. But the committee ultimately voted in favor of vaccines for all kids in the 5 to 11 age group, allowing parents to consult their pediatricians and pursue vaccination if they deem it necessary.

    Polling data suggest that many parents don’t currently deem it necessary, though. The latest survey from the Kaiser Family Foundation found that just 27% of parents with kids in the 5 to 11 age range plan to get their kids vaccinated immediately, once shots are available. 33% intend to “wait and see,” 5% will only pursue vaccination if it’s required by the child’s school, and 30% say “definitely not.”

    Public health experts, pediatricians, and others in the science communication world have a lot of work ahead of us to convey the importance of vaccinating kids—and dispel misinformation.

    Note: this post relies heavily on STAT News’s liveblog of the FDA committee meeting.

    More vaccine coverage

  • Booster shots exacerbate global vaccine inequity

    At the end of last week’s post on booster shots, I wrote that these additional doses take up airtime in expert discussions and in the media, distracting from discussions of what it will take to vaccinate the world.

    But these shots do more harm than just taking over the media cycle. When the U.S. and other wealthy nations decide to give many residents third doses, they jump the vaccine supply line again—leaving low-income nations to wait even longer for first doses.

    I explained how this process works in a new article for Popular Science. Essentially, the big vaccine manufacturers (Pfizer, Moderna, Johnson & Johnson, etc.) have created artificial scarcity of vaccine doses, by insisting on controlling every single dose of their products—rather than sharing the vaccine technology with other manufacturers around the world.

    Then, out of this limited supply of doses, the big companies sell to wealthy nations first. The wealthy nations are “easier markets to service,” WHO spokesperson Margaret Harris told me, since they can pay more money and have logistical systems in place already to deliver the vaccine doses.

    If a wealthy nation wants boosters, it’s in the vaccine companies’ best interests to sell them boosters—before sending primary series doses to other parts of the world. Or, as South Africa-based vaccine advocate Fatima Hassan put it: “Supplies that are currently available are diverted” for boosters. “Just to serve preferred customers in the richer North.”

    The FDA and CDC authorized booster shots for Moderna, Johnson & Johnson, and mix-and-match regimens this week. Advisory committee discussions did not mention that, worldwide, three in five healthcare workers are not fully vaccinated.

    More international data

    • Another COVID-19 endgame take

      Trevor Bedford, computational virologist at the Fred Hutchinson Cancer Research Center—and widely regarded expert on coronavirus variants—wrote a useful Twitter thread this week. In the thread, Bedford provides his take on the “COVID-19 endgame.” In other words, what will happen once the virus reaches endemic levels? (Endemic here meaning, the virus is still circulating but it’s not infecting enough people to cause major concern.)

      First of all, COVID-19 will become endemic in different places at different times, Bedford says. In the U.S., where over half the population is vaccinated, we’re closer to endemicity than other nations. 

      Then, endemicity itself will be a push-and-pull between two things: vaccination levels and the virus’ ability to spread through the population. The Delta variant—which is much more contagious than the original coronavirus—will need to be countered by a lot of vaccination. Bedford also suggests that immunity (from vaccination and prior infection) will likely drop at least somewhat from one year to the next, like what we see now for the flu.

      The U.S. will likely still see a lot of COVID-19 infections each year, Bedford says. They’ll likely be more common during a specific “season,” like how our flu season takes place in the fall and winter. Most infections will be “relatively mild,” he says, but with enough virus transmission, some people will get seriously ill.

      Overall, Bedford suggests that COVID-19 will become similar to the flu—not comparable to cancer or heart disease, he says, but “still a substantial public health burden.” And his estimates of annual deaths do not mention Long COVID, another dimension of the potential health burden that yearly COVID-19 outbreaks may cause.

      (We know that vaccination reduces Long COVID risk, but a lot of other information about this condition remains unknown.)

      more vaccine coverage
    • Unreliable population numbers hinder vaccination rate analysis

      Unreliable population numbers hinder vaccination rate analysis

      An excellent article in the Financial Times, published this past Monday, illuminates one major challenge of estimating a vaccine campaign’s success: population data are not always reliable. Health reporter Oliver Barnes and data reporter John Burn-Murdoch explain that, in several countries and smaller regions, inaccurate counts of how many people live in the region have led to vaccination rate estimates that make the area’s vaccine campaign look more successful—or less successful—than it really is.

      Why does this happen? It’s actually pretty challenging to get a precise count of how many people live somewhere. Think about the U.S. Census, for example: this program attempts to count every person living in the country, once every ten years. But it may miss people who don’t have a straightforward living situation (like college students, the incarcerated, and people living in shelters); it may have confusing messaging that discourages some people (like undocumented residents) from filling out the necessary form; and some people may simply choose not to give information to the government.

      When the Census is inaccurate, the inaccuracies ripple out to different government analyses—including analyses of how many people have been vaccinated. Here’s a quote from the Financial Times article:

      “The average person would be surprised that governments don’t know how many people are actually in the country,” said Stian Westlake, chief executive of the UK’s Royal Statistical Society. “But this great unknown can cause a whole host of data glitches, especially when responding to a health emergency.”

      The Financial Times provides several examples of these data glitches leading to incorrect vaccination estimates.

      • In England: Overestimates of the unvaccinated population, based on data from the U.K.’s Health Security Agency, suggest that case rates are lower among unvaccinated Brits than they actually are.
      • In several EU countries: Underestimates of the senior population lead to vaccination rates inaccurately suggesting that over 100% of certain age groups in Ireland, Portugal, and other countries have received at least one dose of a vaccine.
      • In Miami, Florida: A number of ZIP codes have senior vaccination rates that appear to be over 100% of seniors, due to retirees (who do not have permanent residence in Florida, and therefore aren’t counted in the state’s population) getting vaccinated in Miami during their winter vacations.
      Image
      Miami, Florida is a particularly egregious example of inaccurate vaccination rates. Chart shared on Twitter by John Burn-Murdoch.

      Incorrect vaccination rates can cause issues for public health agencies leading vaccine campaigns, the Financial Times reports. If you think you have vaccinated 100% of seniors in your county due to population underestimates, you likely aren’t looking out for the seniors who in fact remain unvaccinated—leaving those seniors still vulnerable to COVID-19.

      At the same time, data glitches can provide fodder for anti-vax groups. “Worst of all, anti-vaxxers and Covid deniers feed on the daylight between reality and the incomplete data we currently have as evidence of a grand conspiracy or bureaucratic incompetence,” Jennifer Nuzzo, epidemiologist Jennifer Nuzzo told the Financial Times.

      I recommend reading the Financial Times article in full. But you can also check out this Twitter thread from John Burn-Murdoch for more highlights:

      more vaccine coverage
    • Booster shots: What we’ve learned—and what we still don’t know

      Booster shots: What we’ve learned—and what we still don’t know

      This week, the FDA’s vaccine advisory committee had a two-day meeting to discuss booster shots for Moderna’s and Johnson & Johnson’s COVID-19 vaccines. From the outside, these meetings may have appeared fairly straightforward: the committee voted unanimously to recommend booster shots for both vaccines.

      But in fact, the discussions on both days were wide-reaching and full of questions, touching on the many continued gaps in our knowledge about the need for additional vaccine doses. The FDA committee continues to make decisions based on rather limited data, as do other top U.S. officials. Case in point: on Thursday, the committee was asked to consider data from Israel’s booster shot campaign—which is utilizing Pfizer vaccines—as evidence for Moderna boosters in the U.S.

      In the Moderna vote on Thursday afternoon, committee member Dr. Patrick Moore, a virologist at the University of Pittsburgh, said that he voted “on gut feeling rather than really truly serious data.” The comment exemplified how much we still don’t know regarding the need for boosters, thanks in large part to the CDC’s failure to comprehensively track breakthrough cases in the U.S.

      Still, there are a few major facts that we have learned since the FDA and CDC discussions on Pfizer boosters that took place a couple of weeks ago. Here’s my summary of what we’ve learned—and what we still don’t know.

      What we’ve learned since the Pfizer discussion:

      Israel’s booster rollout continues to align with falling case numbers. On Thursday, representatives from the Israeli national health agency presented data on their booster shot rollout—which, again, is using Pfizer vaccines. The vast majority of seniors in Israel have now received a third dose, and over 50% of other age groups have as well. According to the Israeli scientists, this booster rollout both decreased the risk of severe COVID-19 disease for older adults and helped to curb the country’s Delta-induced case wave, causing even unvaccinated adults to have a decreased risk of COVID-19.

      In Israel, severe cases among both vaccinated and unvaccinated adults decreased after the country provided third Pfizer doses to its residents. Screenshot taken from Thursday’s VRBPAC meeting.

      You can read more about Israel’s booster campaign in this paper, published in the New England Journal of Medicine in early October. It’s worth noting, however, that Delta is known to spur both case increases and decreases in cycles that can be somewhat unpredictable—and may not be exactly linked to vaccination. So, I personally take the Israeli claims that boosters stopped their case wave with a grain of salt.

      Decreased vaccine effectiveness against infection may be tied more to Delta and behavioral factors than “waning antibodies.” This week, the New York State Department of Health (DOH) announced results from a large study of vaccine effectiveness which is, from what I’ve seen, the first of its kind in the U.S. The New York DOH used state databases on COVID-19 vaccinations, tests, and hospitalizations to examine vaccine effectiveness against both infection and hospitalization in summer 2021, when Delta spread rapidly through the state.

      They found that vaccine effectiveness against infection did decline over the summer. But the declines occurred similarly for all age groups, vaccine types, and vaccine timing (i.e. which month the New Yorkers in the study received their vaccines)—suggesting that the decline in effectiveness was not tied to waning immune system protection. Rather, the effectiveness decline correlated well with Delta’s rise in the state. It also correlated with reduced safety behaviors, like the lifting of New York’s indoor mask mandate and the reopening of various businesses.

      Vaccine effectiveness against hospitalization declined for older adults, but remained at very high levels for New Yorkers under age 65, the study found. Here’s what lead author Dr. Eli Rosenberg said in a statement:

      The findings of our study support the need for boosters in older people in particular, and we encourage them to seek out a booster shot from their health care provider, pharmacy or mass vaccination site. We saw limited evidence of decline in effectiveness against severe disease for people ages 18 to 64 years old. While we did observe early declines in effectiveness against infections for this age group, this appears to have leveled off when the Delta variant became the predominant strain in New York. Together, this suggests that ongoing waning protection may be less of a current concern for adults younger than 65 years.

      I was surprised that this study didn’t come up in the FDA advisory committee meetings this week, and will be curious to see if it’s cited in future booster shot discussions. The study does align, however, with the committee’s decision against recommending booster shots for all adults over age 18 who received Moderna vaccines.

      Johnson & Johnson vaccine recipients appear to need boosters more than mRNA vaccine recipients. On Friday, presentations from both J&J representatives and FDA scientists made a clear case for giving J&J vaccine recipients a second dose of this adenovirus vaccine. In one 30,000-patient study, patients who received a second J&J shot two months after their first shot saw their vaccine efficacy (against symptomatic infection) rise from 74% to 94%.

      Interestingly, unlike the Pfizer and Moderna vaccines, a J&J shot’s ability to protect against coronavirus infection appears relatively stable over time. However, a booster shot can make this vaccine more effective—especially against variants. Despite arguments from J&J representatives that their vaccine’s second dose should come six months after the first dose, the FDA advisory committee voted to recommend second J&J shots just two months after the first dose, for all adults over age 18.

      It’s worth noting that this vaccine regimen might effectively change J&J’s product from a one-shot vaccine to a two-shot vaccine. STAT’s Helen Branswell and Matthew Herper go into the situation more in their liveblog.

      Mixing and matching vaccines is a strong strategy for boosting immunity, especially if one of the vaccines involved uses mRNA technology. This week, the National Institutes of Health (NIH) released a highly anticipated study (posted as a preprint) on mix-and-match vaccine regimens. The NIH researchers essentially tested every possible booster combination among the three vaccines that have been authorized in the U.S. Before and after vaccination, the researchers took blood samples and tested for antibodies that would protect against the coronavirus.

      In short, the NIH study found that all three vaccines—Pfizer, Moderna, and J&J—will provide a clear antibody boost to people who have received any other vaccine. But the mRNA vaccines (Pfizer and Moderna) provide bigger benefits, both in the form of higher baseline antibody levels (after two shots) and a higher boost. The best combination was a J&J vaccine initially, followed by a Moderna booster, Dr. Katelyn Jetelina notes in a Your Local Epidemiologist summary of the study.

      Every vaccine provided a “boost” of protective antibodies to recipients of every other vaccine. Figure from the NIH preprint. mrna-1273 refers to the Moderna vaccine, Ad26.COV2.S refers to the J&J vaccine, and BNT162b2 refers to the Pfizer vaccine.

      The booster regimens also appeared to be safe, with limited side effects. But this was a relatively small study, including about 450 people. In their discussion on Friday afternoon, the FDA advisory committee members said that they would be very likely to authorize mix-and-match vaccine regimens after seeing more safety data.

      Moderna and J&J boosters appear to be safe, with similar side effects to second shots. Safety data from Moderna’s and J&J’s clinical trials of their booster shots, along with data from the NIH mix-and-match study, indicate that the additional doses cause similar side effects to first and second doses. After a booster, most recipients had a sore arm, fatigue, and other relatively minor side effects.

      And here’s what we still don’t know:

      Which medical conditions, occupations, and other settings confer higher breakthrough case risk? I wrote about this issue in detail in September. The U.S. continues to have little-to-no data on breakthrough case risk by specific population group, whether that’s groups of people with a specific medical condition or occupation. This data gap persists, even though U.S. researchers have some avenues for breakthrough risk analysis at their disposal (see: this post from last week).

      This lack of data came up in FDA advisory committee discussions on Thursday. An FDA representative was unable to cite any evidence that people in specific occupational settings are at a higher risk for breakthrough cases.

      Are there any rare vaccine side effects that may occur after breakthrough doses? When I covered the FDA advisory committee meeting on Pfizer boosters, I noted that Pfizer’s clinical trial of these shots included just 306 participants—providing the committee members with very limited data on rare adverse events, like myocarditis. Well, Moderna’s clinical trial of its booster shots was even smaller: just 171 people. J&J had a larger clinical trial, including over 9,000 people.

      These trials and the NIH mix-and-match study indicated that booster shots cause similar side effects to first and second shots, as I noted above. But few clinical trials are large enough to catch very rare (yet more serious) side effects like myocarditis and blood clots. (In J&J’s case, blood clots occur roughly twice for every million doses administered.) Federal officials will carefully watch for any side effects that show up when the U.S.’s booster rollout begins for Moderna and J&J.

      How do antibody levels correlate to protection against COVID-19, and what other aspects of the immune system are involved? The NIH mix-and-match study focused on measuring antibody levels in vaccine recipients’ blood, as did other booster shot trials. While it may sound impressive to say, for example, “J&J recipients had a 76-fold increase in neutralizing antibodies after receiving a Moderna booster,” we don’t actually know how this corresponds to protection against COVID-19 infection, severe disease, and death.

      Some experts—including a couple of those on the FDA advisory committee—have said that discussions focusing on antibodies distract from other types of immunity, like the memory cells that retain information about a virus long after antibody levels have fallen. More research is needed to tie various immune system measurements to real-world protection against the coronavirus.

      What needs to happen at the FDA for mix-and-match vaccination to be authorized? One challenge now facing the FDA is, the federal agency has clear evidence that mix-and-match vaccine regimens are effective—but it does not have a traditional regulatory pathway to follow in authorizing these regimens. Typically, a company applies for FDA authorization of its specific product. And right now, no vaccine company wants to apply for authorization of a regimen that would involve people getting a different product from the one that brings this company profit.

      So, how will the FDA move forward? There are a couple of options, like the CDC approving mix-and-match boosters directly. See this article for more info.

      Finally: I can’t end this post without acknowledging that, as we discuss booster shots in the U.S., millions of people in low-income countries have yet to even receive their first doses. Many countries in Africa have under 1% of their populations vaccinated, according to the Bloomberg tracker. While the Biden administration has pledged to donate doses abroad, boosters take up airtime in expert discussions and in the media—including in this publication. Boosters distract from discussions of what it will take to vaccinate the world, which is our true way out of the pandemic.

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