A couple of data sources, and a few data-related news items:
COVID-19 vaccine data annotations: Yesterday, I updated my annotations page on U.S. vaccination data sources for the first time in a few weeks. The page lists both national dashboards and vaccine data pages from all 50 state public health agencies, including notes on what each source offers. Going through the dashboards yesterday, I was struck by how many states are now offering data on booster shots (43, by my count), as well as how counts of doses distributed in a state, once a major feature of these dashboards, have become less useful now that the U.S. has ample vaccine supplies.
Order more free rapid tests from the federal government: The COVIDtests.gov site is now open for additional orders of free rapid at-home tests, as part of the federal program that launched in mid-January. Each household can now order two sets of four tests. I ordered a set of tests last Monday, and received them on Thursday—much faster than the initial round of this program!
Scientists are investigating combinations of Delta and Omicron: You might have seen some recent headlines about “Deltacron,” a portmanteau of the two variants of concern. When a very unlucky person gets infected with both Delta and Omicron at the same time, the variants can combine and form a new strain with genetic elements of both lineages. Scientists have recently identified a small number of “Deltacron” cases in France, Denmark, the Netherlands, and the U.S.; it’s not cause for major concern at this time, but is under study to determine if this combined strain might have any transmission or severity advantages. The Guardian has a good explainer on the subject.
New studies on masks, vaccines for kids: This week, the CDC MMWR published a new study on masking in K-12 schools; the researchers found that Arkansas school districts with a universal mask requirement in the fall 2021 semester had 23% lower cases than schools that did not have a requirement. The journal also published a new study on vaccinations in children ages 5 to 11; this study found that, within three months of COVID-19 vaccines becoming available for this age group, 92% of kids ages 5 to 11 lived within 5 miles of a vaccine provider. However, vaccination coverage in this age group is low, suggesting the need for more targeted communication to families with young kids.
NIH starts new trial on allergic reactions to vaccines: The National Institutes of Health (NIH) recently announced a new clinical trial to understand “rare but potentially serious systemic allergic reactions” to the COVID-19 vaccines. The trial will include up to 100 people between the ages of 16 and 69 who had allergic reactions to their first vaccine doses; the NIH will provide second doses under heavily monitored conditions and study how these patients respond.
How to better recruit for COVID-19 trials: Speaking of clinical trials, a new preprint posted this week to medRxiv outlines a potential strategy for better studying effectiveness and potential rare side effects of COVID-19 treatments. The preprint authors propose targeting recruitment to people who are high-risk for coronavirus infection, so that studies may collect data on a statistically significant number of cases more quickly.
COVID-19 at the Tokyo Olympics: Another study that caught my eye this week: researchers from Tokyo described the results of intensive surveillance testing for athletes who competed in the 2021 Tokyo Olympics and Paralympics. In total, among over one million PCR tests conducted before and during the Olympic games, just 299 returned positive results—a positivity rate of 0.03%.
COVID-19 on Capitol Hill: Reporters at The Hill analyzed data on COVID-19 test results among House and Senate lawmakers, finding that more than one-quarter have tested positive since the pandemic began. The highest case numbers occurred in January 2022 during the Omicron wave, aligning with the U.S. overall. (Though I imagine many legislators travel and socialize indoors more than the average American.)
COVID-19 cases are rising rapidly in countries where Omicron is spreading, including South Africa, the U.K., and Denmark. Chart from Our World in Data, retrieved September 12.
We continue to learn more about this new variant as it spreads rapidly across the world, though much of the data are still preliminary. Here are a few major updates:
Omicron is still spreading very quickly in South Africa, as well as in the U.K. and Denmark—two other countries with great genetic surveillance. Preliminary estimatesbased on data from these countries suggest that the variant’s R-value is between 3 and 4, indicating that the average person infected with Omicron infects three or four others. As Sarah Zhang put it in The Atlantic: “Omicron is spreading in highly immune populations as quickly as the original virus did in populations with no immunity at all.”
Early vaccine studies show a drop in antibody levels against Omicron, but that doesn’t necessarily correspond to overall protection. This week, we saw the first results from early studies evaluating how well vaccines work against Omicron. Here’s a summary, drawing from Katherine Wu’s coverage of these studies in The Atlantic: vaccinated people confronted with Omicron appear to produce a lot fewer antibodies that can fight the virus, compared with older variants. Numbers range from a five-fold drop in antibodies to a 41-fold drop. But remember, antibodies are just one part of the immune system—specifically, they’re the part that’s easiest to measure. Vaccinated people also have memory immune cells that provide protection over a long time period, which isn’t captured in antibody studies. We’ll need more time and more data to actually evaluate how vaccines fare against Omicron in the real world, rather than in the lab.
The vaccines seem to protect against severe disease and death from Omicron. So far, the data suggest that our existing COVID-19 vaccines still work quite well at protecting people from severe symptoms—even when those severe symptoms are caused by an Omicron case. “When the shots’ protection ebbs, it tends to do so stepwise: first, against infection, then transmission and symptoms, and finally against severe disease,” Wu writes. For vaccinated people to lose protection against severe disease, the virus would have to change much more than Omicron has. At the same time, however, some experts are concerned that non-mRNA vaccines may not fare as well against Omicron as Moderna and Pfizer, conferring a disadvantage to the low- and middle-income countries that have had less access to the mRNA vaccines.
Booster shots increase protection against Omicron. While vaccinated people are less protected against infection with Omicron than previous variants, booster shots appear to help close that gap—even though currently-available booster shots are not designed specifically for Omicron. One U.K. study suggests that boosters can increase vaccine effectiveness against infection from 30% to 75%, for people who received the Pfizer vaccines. In other words: Omicron is a good reason to go get your booster shot, if you’re eligible and you live in a place where the shots are available.
Experts continue to be skeptical about Omicron being “more mild.” Reports out of South Africa continue to suggest that cases caused by Omicron are more mild than cases caused by Delta, with doctors saying that fewer patients are requiring hospitalization and those hospital stays are shorter than previous outbreaks. But many of the South Africans getting sick with Omicron may have some protection from vaccination or past infection; this means they’re more likely to have mild cases, as biostatistician Natalie Dean explains in an excellent Twitter thread. Plus, even if Omicron is more mild, it appears to be more transmissible—and a smaller share of severe cases out of a larger pool of cases overall can still lead to a pretty big number of people going to the hospital. In addition, we have zero data at this point on how Omicron may impact Long COVID cases, or how well vaccines protect against Long COVID from an Omicron infection.
Early U.K. data confirm Omicron’s high contagiousness and its capacity for evading protection from vaccines and prior cases. After the U.K.’s best-in-the-world genetic surveillance agency first identified Omicron in late November, I wrote that the country would likely provide invaluable data on this variant. Less than two weeks later, the U.K. Health Security Agency has released its first Omicron report. The country’s real-world data confirm that Omicron can spread quite fast: for example, “19% of Omicron cases resulted in household outbreaks vs 8.5% of Delta cases,” wrote epidemiologist Meaghan Kall in a summary of the report. The report also “paints a very consistent picture for Omicron being immune evading,” Kall said, though booster shots help a lot.
Anime NYC was a likely Omicron superspreader event. More and more reports have emerged of Omicron cases connected to Anime NYC, a convention held in Manhattan in mid-November. The CDC is currently investigating the convention: officials are working with the NYC health department to contact all 53,000 convention attendees for testing and contact tracing. “Data from this investigation will likely provide some of the earliest looks in this country on the transmissibility of the variant,” CDC Director Dr. Rochelle Walensky said at a press briefing on Tuesday.
The CDC formally named Omicron a Variant of Concern. On Friday, the CDC officially designated Omicron as a Variant of Concern and added it to the variant tracking page of the agency’s COVID-19 dashboard. As of December 4, Omicron is causing 0.0% of new COVID-19 cases in the U.S., the CDC estimates. The variant has yet to be added to the CDC’s state-by-state data. Given the continued geographic disparities of the U.S.’s genomic surveillance system, however, we may expect that the variant is already spreading in states where it has yet to be formally identified.
Omicron can likely compete with Delta, but we need more data to get a better sense of how well. “Omicron is picking up speed in Europe, which has often served as a preview of what was headed the U.S.’s way. It’s an early sign that the already bleak situation here may get worse,” writes Andrew Joseph in a recent STAT News story. U.K. data suggest that Omicron could cause a majority of cases there within two to four weeks, Joseph reports, and the U.S. may not be far behind. Still, more real-world data from countries and regions with clear Omicron outbreaks will give us a better idea of just how worried we need to be about a potential Omicron-fueled surge.
In summary:
There's been a lot of new data for Omicron in the last day, much still preliminary, but here's my summary of the good and bad pic.twitter.com/pL8uiD7hfV
All major COVID-19 metrics shot up in the U.S. this week. Chart from the December 9 HHS Community Profile Report.
In the past week (December 4 through 10), the U.S. reported about 830,000 new cases, according to the CDC. This amounts to:
An average of 119,000 new cases each day
253 total new cases for every 100,000 Americans
37%more new cases than last week (November 27-December 3)
Last week, America also saw:
52,000 new COVID-19 patients admitted to hospitals (16 for every 100,000 people)
7,600 new COVID-19 deaths (2.3 for every 100,000 people)
99.9% of new cases are Delta-caused (as of December 4)
An average of 2.3 million vaccinations per day (including booster shots; per Bloomberg)
Remember how, last week, I said that the dip in the CDC’s case counts was a vestige of Thanksgiving data delays—and we’d see more cases in the next week? Well, we’re seeing those cases now. Cases have increased by 37% from last week to this week, and they’ve increased by 55% in the last month.
Hospitalizations are also going up: the number of new COVID-19 patients admitted to hospitals each day has risen 16%, to over 7,000. About 56,000 people are currently hospitalized with COVID-19 in the U.S., as of Thursday. And, tragically, death counts are rising as well: once again, over 1,000 Americans are dying from COVID-19 every day.
Current hotspots include states in the Northeast and Midwest. New Hampshire reported the most cases per capita last week, at 659 new cases for every 100,000 people, per the latest Community Profile Report. Michigan, Minnesota, Rhode Island, and New Mexico also all reported over 500 new cases for every 100,000 people.
In many parts of the country, COVID-19 patients have once again pushed hospitals to their breaking points, as the pandemic intersects with staff shortages and burnout as well as flu and other conditions. “We’re at capacity on a daily basis,” the president of a hospital system in Detroit told a local reporter.
Seeing more and more reports like this around the country, where local waves of Covid patients have swamped hospitals: https://t.co/F4liGxxaqw
Despite growing Omicron concerns (more on that later), the Delta variant is clearly driving this surge. According to the CDC’s estimates, the Delta variant has caused more than 99% of cases in the week ending December 4, while Omicron has yet to cause even 0.1%. If Omicron is able to outcompete Delta in the U.S., the situation could become even more dire.
It’s now been two years since a COVID-19 patient first sought medical attention, at a hospital in Wuhan, China. Though most Americans didn’t become aware of the pandemic until March 2020, the coronavirus was already spreading in December 2019—meaning that now, in December 2021, we’re entering Year Three of this global crisis. I hope this can be the year that we get vaccines to every country in the world, and truly get the virus under control.
This past Monday, President Biden gave a speech about the Omicron variant. He told America that Omicron is “cause for concern, not a cause for panic,” and thanked the South African scientists who alerted the world to this variant. (Though a travel ban is not a great way to thank those scientists!)
Towards the end of the speech, he said: “We’re throwing everything we can at this virus, tracking it from every angle.” Which I, personally, found laughable. As I’ve pointed out in a previous post about booster shots, the U.S.’s anti-COVID strategy basically revolves around vaccines, and has for most of 2021.
wild to hear Biden say "we are throwing everything we can at this virus" … like, sir, no we aren't. we are throwing ONE THING (vaccines) at this virus.
My Tweet about Biden’s vaccine-only strategy got more attention than I’m used to receiving on the platform, so I thought it was a worthwhile topic to expand upon in the COVID-19 Data Dispatch. Why aren’t vaccines enough to address Omicron—or our current surge, for that matter—and what else could the Biden administration be doing to slow the coronavirus’ spread?
Why aren’t vaccines enough?
Prior to Delta’s spread, there was some talk of reaching herd immunity: perhaps if 70% or 80% of Americans got fully vaccinated, it would be sufficient to tamp down on the coronavirus. But Delta’s increased capacity to spread quickly, combined with the vaccines’ decreased capacity to protect against infection and transmission, have shown that vaccines are not enough to eradicate the virus.
Here, then, is the current pandemic dilemma: Vaccines remain the best way for individuals to protect themselves, but societies cannot treat vaccines as their only defense. And for now, unvaccinated pockets are still large enough to sustain Delta surges, which can overwhelm hospitals, shut down schools, and create more chances for even worse variants to emerge. To prevent those outcomes, “we need to take advantage of every single tool we have at our disposal,” [Shweta Bansal of Georgetown University] said. These should include better ventilation to reduce the spread of the virus, rapid tests to catch early infections, and forms of social support such as paid sick leave, eviction moratoriums, and free isolation sites that allow infected people to stay away from others.
Remember that Swiss cheese model of pandemic interventions? Vaccines may be the best protection we have against the coronavirus, but they’re still just one layer of protection. All the other layers—masks, testing, ventilation, etc.—are still necessary, too. Especially when we’re dealing with a new variant that might not respond as well to our vaccines.
Re-upping this brilliant image from last year as a reminder on how mitigation measures work together to prevent the spread of coronavirus. pic.twitter.com/p7Z8u7fS2w
One strategy that we could employ against Omicron, as well as against the current Delta surge, is better masks. While cloth masks certainly make it less likely for the coronavirus to spread from one person to another, their efficacy varies greatly depending on the type of material, the number of layers, and the mask’s fit.
N95 masks do the best job at stopping the coronavirus from spreading, followed by KN95 masks. Surgical masks do a better job than cloth masks, but making sure these masks fit properly can be a challenge for some people (including yours truly, who has a very narrow face!). Layering a surgical mask and cloth mask may be a safer option to get both good fit and protection, though two layers of mask can be challenging to wear for long periods of time.
Some experts have recommended that the U.S. mail N95 or KN95 masks to all Americans, or at least require these masks in high-risk areas, such as on flights. Germany and other European countries established similar requirements last summer.
Given how transmissible Delta is—and the likelihood that Omicron is also highly transmissible—consider upgrading to an N95/KN95 mask or equivalent when indoors and around others, especially if you're elderly or immunocompromised.
In many countries—including the U.K., Germany, India, and others—rapid tests are freely available. Here in the U.S., on the other hand, the tests are quite expensive (often upwards of $10 for one test) and difficult to find, with pharmacies often limiting the number of packages that people can buy at once.
Biden has attempted to increase rapid testing access as part of his latest COVID-19 plan: in January, private insurance companies will be required to cover the cost of rapid tests. But this doesn’t solve the supply issue, and it doesn’t really make the tests more accessible, either. The measure would still require people to buy tests out of pocket, then fill out insurance reimbursement forms to maybe get their money back. Can you imagine anyone actually doing this?
In addition, as some experts have pointed out, the people most likely to need rapid tests—essential workers and others in high-risk environments—are also those less likely to have insurance. Biden is also distributing some rapid tests to community health centers, but that’s not enough to meet the need here.
This part of Biden’s omicron plan is also short-sighted.
Sure reimbursement by private health insurance of rapid test costs is a nice thing to have, but the people who MOST need rapid tests are the same people who DONT have private health care. What’s the plan for helping them? pic.twitter.com/tnlC8T0PDk
Ideally, the Biden administration would mail every American a pack of, like, 20 rapid tests, along with that pack of N95 or KN95 masks I mentioned above. Free of charge.
And at the same time, of course, we need more readily available PCR testing. Even in New York City, which has a better testing infrastructure than most other parts of the country, the lines at free testing sites are getting long again as cases go up. Any American who wants to get tested should be able to easily make an appointment within a day or two, and get their results within another day after that.
Increased testing is not only important for identifying Omicron cases (and cases of any other new variant); it’s also key for the Merck and Pfizer antiviral treatments due to be approved in the U.S. soon. Without efficient testing, patients won’t be able to start these treatments within days of their symptoms starting.
What we could do: improve genetic surveillance
The U.S. is doing a lot more coronavirus sequencing than we were in early 2021: we’ve gone from under 5,000 cases sequenced a week to over 80,000. The CDC worked with state and local health agencies, as well as research organizations and private companies, to increase sequencing capacity across the country.
Urban centers close to large academic centers tend to be well covered, while rural areas are less so. That means public health departments in large parts of the country are still flying blind, even as they are figuring out ways to prioritize Omicron-suspicious samples.
A lack of testing compounds this problem. If someone doesn’t confirm their COVID-19 case with a PCR test, their genetic information will never make it to a testing lab, much less a sequencing lab. While rapid tests are very useful for quickly finding out if you’re infected with the coronavirus, you need a PCR test for your information to actually be entered into the public health system.
In addition, even where the U.S. is sequencing a lot of samples, the process can take weeks. Vox’s Umair Irfan writes:
Still, it takes the US a median time of 28 days to sequence these genomes and upload the results to international databases. Contrast that with the United Kingdom, which sequences 112 genomes per 1,000 cases, taking a median of 10 days to deposit their results. A delay of only a few days in detection can give variants time to silently spread within communities and across borders.
Despite sequencing shortfalls in the U.S., we’re still doing much more surveillance than the majority of countries. Many nations in Africa, Asia, South America, and other parts of the world are sequencing fewer than 10 cases per 1,000, Irfan reports. As the U.S. should be doing more to get the world vaccinated, the U.S. should also do more to help other countries increase their sequencing capacity—monitoring for the variants that will inevitably follow Omicron.
What we could do: stricter domestic travel requirements
Starting on Monday, all international travelers coming into the U.S. by air will need to show a negative COVID-19 test, taken no more than one day before their flight. This includes all travelers regardless of nationality or vaccination status. At the same time, any non-U.S. citizens traveling into the country must provide proof of their vaccination against COVID-19.
But travelers flying domestically don’t face any such requirements. There are mask mandates on airplanes, true, but people can wear cloth masks, often pulled down below their noses, and airports tend to have limited enforcement of any mask rules.
Both experts and polls have supported requiring vaccination for domestic air travel, though the Biden administration seems very hesitant to put this requirement in place. Speaking for myself, I felt very unsafe the last time I flew domestically. A vaccine mandate for air travel would make me much more likely to fly again.
What we could do: more social support
In the U.S., a positive COVID-19 test usually means that you’re in isolation for 10 to 14 days, along with everyone else in your household. This can pull kids out of school, and pull income from families. As has been the case throughout the pandemic, support is needed for people who test positive, whether that’s a safe place to isolate for two weeks, grocery delivery, or rapid tests for the rest of the household.
This type of support could make people actually want to get tested when they have symptoms or an exposure risk, rather than avoiding the public health system entirely.
Within days of its first identification, the Omicron variant has been found on every continent except Antarctica. Chart via GISAID, retrieved December 5.
There is still a lot we don’t know about the Omicron variant, first identified in Botswana and South Africa in late November. For the most part, what I wrote last Sunday remains true: this variant is spreading quickly in South Africa and has a number of mutations—some of which may correspond to increased capacity for transmission or evading prior immunity—but we don’t yet have enough information to determine how it may shape the next phase of the pandemic.
Still, we’ve learned a few new things in the last week. Here’s a quick roundup:
More than 30 cases have been detected in the U.S., with the earliest detection in states with robust genetic surveillance. The first U.S. case was identified in California, in a San Francisco resident who had recently traveled to South Africa. As I pointed out on Twitter, California is one state that’s sequencing a lot of coronavirus genomes; combine that with San Francisco’s large international airport, and it may be unsurprising that the variant was first picked up there. The second U.S. case was identified in Minnesota; this state, too, has sequenced a lot of cases, with a lab at the University of Minnesota providing sequencing services for other Midwest states.
Omicron is spreading rapidly in South Africa. On Friday, South African scientists said that the variant may be spreading “more than twice as quickly as Delta,” according to the New York Times, though it may also be less contagious than Delta. This announcement aligns with modeling by computational biologist Trevor Bedford, who wrote on Saturday that Omicron appears to have a transmission advantage over Delta. “These are still very early estimates and all this will become more clear as we get comparable estimates from different geographies and with different methods,” Bedford wrote. “But ballpark current Rt of Omicron in South Africa of between 3 and 3.5 seems pretty reasonable.” Rt refers to how fast the virus is spreading; for context, Delta’s Rt when it first hit the U.S. was about 1.5.
Anime NYC may have been a superspreading event. The Minnesota resident who became the second Omicron case identified in the U.S. had attended Anime NYC, an anime convention held at the Javits Center between November 19 and 21. City and state officials urged other attendants of the convention to get tested; and a number of the Minnesota resident’s friends have tested positive, according to The Washington Post,though sequencing results are not yet available for these cases. Anime NYC attendees had to be vaccinated to attend, but could meet the requirement with just one dose received right before the convention. And photos from the convention show plenty of people disregarding the mask mandate. It’s too early to say, but I would not be surprised if Anime NYC turns out to be a superspreading event for Omicron.
A holiday party in Norway is another likely superspreading event. About 120 people attended a Christmas party in Oslo on November 26. As of this Friday, at least 13 attendees have been identified as Omicron cases, while a number of others have tested positive for COVID-19 (and are awaiting sequencing results). “Our working hypothesis is that at least half of the 120 participants were infected with the Omicron variant during the party,” Norwegian Institute of Public Health physician Preben Aavitsland told Reuters. “This makes this, for now, the largest Omicron outbreak outside South Africa.” Notably, this superspreading event occurred even though “all the attendees were fully vaccinated and had tested negative before the event,” Reuters reports.
Omicron appears to be more likely to reinfect people who’ve recovered from a previous COVID-19 case than past variants. On Thursday, South African scientists posted a preprint study suggesting that, when compared to the Delta and Beta variants, Omicron is more capable of reinfecting people who’ve previously had COVID-19. The finding comes from an analysis of over 35,000 reinfections among millions of positive COVID-19 tests. “Although there are a lot of uncertainties in the paper, it looks like an earlier infection only offers half as much protection against Omicron as it does against Delta,” writes Gretchen Vogel in Science, paraphrasing Emory University biostatistician Natalie Dean.
Omicron might cause less severe illness than other variants, but a lot more data are needed on this topic. On Saturday, the South African Medical Research Council posted a report that aligns with some other early reports about this variant: so far, patients infected with this variant seem to be getting less sick than those infected with previous coronavirus variants. Specifically: a lower share of Omicron patients in South Africa have required intensive care, oxygen support, or ventilators than physicians there have seen in previous COVID-19 waves. But this report, like other anecdotal reports, has been based on a small number of patients, and many of them have been younger—as older South Africans have been prioritized for vaccination. The number of severe Omicron cases may be low now, but may rise sharply in the coming weeks, Financial Times reporter John Burn-Murdoch pointed out in a Twitter thread responding to the report. Also, it’s way too soon to know how many of the so-called mild Omicron cases thus far may turn into Long COVID. So, a lot of experts are skeptical that Omicron is actually more mild—basically, we need more data.
BUT: now that I’ve injected a triple-dose of nuance, here’s your exponential case chart:
Even if far less than 25% of patients require ICU this time, a small share of a rapidly increasing number can still become a big number. And numbers are going up very, very fast. pic.twitter.com/HmWooHWoDw
I’ll end the post with this excellent thread from Muge Cevik, infectious disease expert at the University of St. Andrews, discussing the many uncertainties surrounding Omicron:
🦠 There’s a lot we don’t yet understand about Omicron, including its impact on immunity and what it means for vaccines. New data will be emerging over the next few wks, which could be misinterpreted w/o context. What we might expect & how to interpret the emerging data? 🧵(1/n)
Though Omicron is making headlines, Delta is still causing 100% of COVID-19 cases in the U.S. Chart via the CDC, screenshot taken on December 5.
In the past week (November 27 through December 3), the U.S. reported about 600,000 new cases, according to the CDC. This amounts to:
An average of 86,000 new cases each day
184 total new cases for every 100,000 Americans
8%fewer new cases than last week (November 20-26)
Last week, America also saw:
45,000 new COVID-19 patients admitted to hospitals (14 for every 100,000 people)
6,000 new COVID-19 deaths (1.8 for every 100,000 people)
100% of new cases are Delta-caused (as of November 27)
An average of one million vaccinations per day (including booster shots; per Bloomberg)
Don’t be fooled by the apparent case decline in the CDC’s numbers: the U.S. is still in the midst of a new surge. The agency reported fewer cases last week due to Thanksgiving holiday delays, but we can expect cases to shoot up next week as delayed cases are added to the data.
I use the CDC for these updates because I find the national agency’s data reliable and easy to access, but the CDC does tend to be more heavily impacted by reporting delays than other sources which compile numbers from U.S. states or counties. For example, the New York Times is reporting a daily new case average of 108,000 as of December 4, while BNO Newsroom has reported over 100,000 new cases for five days in a row.
Meanwhile, hospitalizations are ticking up: with 45,000 new COVID-19 patients admitted to U.S. hospitals last week and almost 50,000 people currently hospitalized, as of December 2. Hospitalizations are one COVID-19 metric that tends to be less impacted by holidays, as the hospitals collecting these data don’t take days off.
Northern states continue to lead the country in new cases per capita. According to the latest Community Profile Report, top hotspots are New Hampshire, Michigan, Minnesota, North Dakota, and Wisconsin. New Hampshire reported over 500 new cases for every 100,000 people in the last week, and is continually setting new COVID-19 records.
Michigan is seeing more cases now than it has in any previous surge, and the state’s hospital systems—like many others—are facing dire staff shortages, along with increased numbers of flu patients. The state has almost 900 fewer staffed hospital beds now than in November 2020, according to ABC News.
While the Omicron variant has now been identified in more than ten U.S. states (more on that below), the Delta variant is still driving this current surge. According to the CDC’s latest variant data, 100% of new cases in the country are caused by Delta. In the coming weeks, we’ll see how much Omicron is able to compete.
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.”
1) My gut feeling from hearing of Omicron cases in Botswana, ex-Malawi, ex-Egypt (2 now it seems) and in South Africa is, that the variant was flying under the radar in undersequenced countries for some time until Botswana and South Africa detected it and sounded the alarm.
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.
This extremely long branch (>1 year) indicates an extended period of circulation in a geography with poor genomic surveillance (certainly not South Africa) or continual evolution in a chronically infected individual before spilling back into the population. 4/16 pic.twitter.com/8mEI46VFMn
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.”
2) This is coinciding with a wider rise in cases in South Africa.
Again, currently we’re talking about small numbers (both of B.1.1.529 and of cases in SA overall), but there’s a clear upward trend. This may be a blip, but this is how waves start. pic.twitter.com/sn9IIKtzUm
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.
Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)…there is…not much green.🧵 pic.twitter.com/yNHM55oTTH
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.
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.)
A short list of what NO ONE knows about the Nu (B.1.1.529) variant:
– We DON'T KNOW if it spreads faster than delta – We DON'T KNOW where it originated – We DON'T KNOW if it bypasses immunity/causes more severe disease
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.
But remember that our immune system has more than just neutralising antibodies in store, so none of this tells us just how much this variant is going to escape immunity and if it will mostly affect protection from infection or also severe disease.
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:
1/ FAQs I'm getting re: Omicron variant:
Q: Is Omicron more infectious than Delta? A: We don't know yet. Possibly. Or it could be "hitching a ride" with lax behavior or super spreading. pic.twitter.com/SWtUB8BjeQ
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:
What vaccine makers are saying about B.1.1.529:
-Moderna notes it's shown it can get into clinic (human trials) within 60 days; question is regulatory process from there. Manufacturing new doses could take a few months.
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.
What IS clear is that knee-jerk reactions like banning flights may be politically palatable, but will do little to slow the spread of this variant.
In the coming days more countries will identify cases. And there’s a good chance it’s already spreading here and in other places. https://t.co/YSbrSe0EdO
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.
I’ll raise you one: BY THE TIME YOU DETECT ONE VARIANT ANOTHER IS ALREADY CIRCULATING UNDER THE RADAR SOMEWHERE SO WITH A MIX OF SURVEILLANCE LAGS, LOW VACCINE UPTAKE, INEQUITABLE VACCINE ACCESS WE ARE WILL BE CHASING VARIANTS ENDLESSLY.
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?
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.
If you’re worried about your risk from omicron, get vaccinated if you aren’t already. Continue to layer other precautions. And more than anything, follow the science and advocate for collaborative global health. Travel bans won’t do shit. Vaccines and global health equity WILL.
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.
💉 7.8 billion COVID vaccine doses have been administered
👥 53% of world population with at least 1 dose
🌍 Total doses per 100 people High-income countries: 147 Upper-middle income: 146 Lower-middle income: 68 Low income: 7
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.
“Instead of solving the problem by vaccinating the world & cutting off new variants, rich countries seem prepared to fork over more money for boosters, & live in a state of endless fear,” Achal Prabhala told me back in JULY. https://t.co/Z1trCXN9Dp
A couple of weeks ago, I received a reader question from a friend of mine who recently got engaged! He and his fiancée are planning a wedding in summer 2023, and he asked me: “How likely do you think it is that (1) the COVID-19 pandemic remains a serious danger to our safety in the summer of 2023 and (2) the government still has the energy to keep enforcing COVID-19 restrictions?” I’m going to tackle these questions one at a time.
Will the COVID-19 pandemic still be a serious danger to our safety in summer 2023?
I talked to an epidemiologist last week (for an upcoming story); he pointed out that COVID-19 is incredibly unpredictable—even for the most knowledgeable experts.
We don’t know why Delta surges appear to dip after two months, for example, or why cases might pick back up again after a decline. We can hypothesize (at least in the U.S.) that cold weather and more indoor gatherings are playing a role in the current beginnings-of-a-surge, but that’s a hypothesis. And there are plenty of other questions we’re still working to answer about the coronavirus, from why some people are superspreaders to how the virus can cause symptoms that last over a year.
So, it’s hard for me to say whether we’ll see more COVID-19 surges after the one that seems likely this winter, or what those surges will look like—whether we can stave off most severe infections with vaccinations (and booster shots), or whether hospitals will become overwhelmed yet again.
At the same time, we know that the vaccines are very good at protecting people from COVID-19. Three-dose series (and two-dose series with Johnson & Johnson) are especially good at protecting people, including from infection, transmission, severe disease, and Long COVID.
These incredible vaccines were developed based on early coronavirus strains, identified in China in early 2021. And they’re still working great against pretty much all variants. In the past couple of months, I’ve asked several experts what they think future variants might look like; and the consensus is that new mutations basically will arise from Delta at this point. The virus could get more contagious (as we saw with AY.4.2), but it seems unlikely that it would evolve to evade vaccine-induced immunity.
If we let infections hang around for too long without protecting people, without decreasing the burden of infection, it would not be surprising at all [if we see] newer variants. Will this be just a more concerning mutant of Delta? It’s possible. But it also could be something completely new that we’re not able to predict at the moment.
But I think it’s also very, very hard for us to get a new variant that will evade all vaccines. With the number of vaccines we have, we can really vaccinate many, many new people very, very quickly. I think no matter what variant comes, we will be able to bring it under control.
Of course, as far as I know, nobody saw a variant as contagious as Delta coming—so this could be overly optimistic. Again, there’s still a lot we don’t understand about this virus!
Will the government still enforce COVID-19 restrictions in summer 2023?
This second part of my friend’s question gets at a concept called “pandemic offramps,” which I’ve seen discussed a lot in COVID-19 scientist circles recently. The idea is, essentially, we need to decide how to get off the current freeway of COVID-19 safety and resume some kind of “normal life.”
The New York Times recently devoted its morning newsletter to this concept, asking when Americans will stop needing to “organize their lives around COVID-19.” The newsletter argued that vaccinated people already accept risk that’s comparable to COVID-19 in other ways, such as driving in cars.
But this piece drew criticism for suggesting that the U.S. loosen restrictions more when a new surge is approaching, more than 1,000 Americans are dying of COVID-19 every day, and billions around the world are still unvaccinated.
I really do think this kind of propaganda is more dangerous than even hard denialism. https://t.co/b1Bd19AHTV
We’re clearly not anywhere close to the “end of the pandemic” right now. But at some point, our leaders will need to answer some questions, such as: When are masks no longer necessary in public spaces? What about rigid vaccination checks, or regular testing for certain schools and businesses?
In a recent article for The Atlantic, Sarah Zhang argues that the U.S. needs to agree on a new COVID-19 goal. We’re no longer striving for 70% of adults to get vaccinated by July 4, so what are we striving for? Is there a vaccination threshold that we can label “herd immunity,” or a daily case threshold that would signify the ability to loosen restrictions?
Since public health systems in the U.S. are so fragmented, these questions likely won’t be answered all at once for everyone, but will be answered individually—by states, cities, school districts, businesses, and other institutions. New Mexico has already done this, to a certain extent, with a tiered system that helps counties add or remove COVID-19 safety measures based on outbreak levels.
And of course, in some states, it seems like leaders have already decided that any level of COVID-19 cases is acceptable, as long as businesses stay open. We can see other (less conservative) leaders go in this direction, too, with the popularization of booster shots rather than, say, implementing new mask mandates.
So, my TL;DR here is: I think serious restrictions on the level of wedding cancellation are pretty unlikely. Rather, the wedding venue might require vaccines, maybe including booster shots (possibly even multiple rounds of booster shots!). Maybe it will require COVID-19 tests or masks indoors, or the wedding planners might want to impose such precautions themselves for the safety of their guests.
Personally, I hope that by summer 2023, we can at least buy rapid tests in bulk at Costco.
Recently, a new offshoot of the Delta variant has been gaining ground in the U.K. It’s called AY.4.2, and it appears to be slightly more transmissible than Delta itself. While experts say this variant doesn’t differ enough from Delta to pose a serious concern, I think it’s worth exploring what we know about it so far—and what this means for the future of coronavirus mutation.
How was AY.4.2 identified?
The U.K. national health agency first found AY.4.2 in July 2021, and has watched it slowly spread through the country since then. The agency formally designated this variant as a Variant Under Investigation (VUI) on October 22; at this point, about 15,000 cases had been identified across the country.
It’s worth noting here that the U.K.’s genomic surveillance system is incredibly comprehensive—considered to be the best in the world. The country sequences over 20,000 coronavirus samples a week; it’s consistently sequenced a large share of its COVID-19 cases since the beginning of 2021. And, since the country’s public health system integrates COVID-19 testing records with hospitalization records, primary care records, and other data, U.K. researchers are able to analyze other aspects of a variant’s performance, such as its ability to cause breakthrough cases or more severe disease.
It’s perhaps not a surprise that the U.K. noticed AY.4.2 so quickly. The country has an incredible sequencing system in place to monitor genetic changes in the virus, and researchers there have been among the global leaders in characterizing different mutations and forms of the virus. It’s possible that other Delta sublineages have similar growth rates to AY.4.2, but they’re in parts of the world where it will take longer for scientists to detect.
How does AY.4.2 differ from OG Delta?
AY.4.2 is transmissible enough that it is slowly pushing out the original Delta in some parts of the U.K. In late June, it comprised 0.1% of new U.K. COVID-19 cases; in late August, it was at 3.5%; and now it’s at 11.3%, as of the most recent data (the week ending October 24).
“It’s a slow burner,” wrote U.K. epidemiologist Meaghan Kill in a Twitter thread last week. “But Delta is already *so* transmissible, it’s notable that AY.4.2 is increasing in that context.”
It’s a slow burner 🔥
But Delta is already *so* transmissible, it’s notable that AY.4.2 is increasing in that context
• Growth rate estimates: 17% advantage for AY.4.2 over Delta
— Meaghan Kall has moved to Bluesky (@kallmemeg) October 23, 2021
Kill and other scientists estimate that AY.4.2 is between 10% and 15% more transmissible than Delta. That’s a small enough difference that scientists are not panicking about this variant, in the same way that epidemiologists sounded the alarm when Delta itself was first identified in India earlier in 2021. (For context: Delta is 60% to 80% more transmissible than the Alpha variant.)
Still, AY.4.2 is worth watching as a signal of Delta’s continued ability to mutate and spread more readily. As Joseph points out in his STAT article, some experts hypothesized that Delta might be so contagious, the coronavirus basically could not mutate further in that direction. AY.4.2 suggests that we haven’t hit that upper limit yet.
Is AY.4.2 more likely to cause breakthrough cases?
This is one piece of good news that came out in the U.K. health agency’s most recent variant report, released this past Friday: AY.4.2 is not more likely to cause a breakthrough case than the original Delta variant. (Not thus far, anyway.) This is true for both symptomatic and asymptomatic infections, as well as different ages and vaccine types.
The AY.4.2 data in this U.K. report are based on a relatively small sample size—about 13,000 people infected with AY.4.2, compared to over 350,000 people infected with the original Delta variant. Still, it’s good news that the variant appears to simply be more transmissible, not more able to break through vaccine-induced immunity or cause severe disease.
“More likely (I believe) is a slightly increased biological transmissibility,” Meaghan Kill wrote in a Twitter thread about this news. “Growth rate & secondary attack rates are refreshed with new data and findings remain the same as last week.” She predicts that AY.4.2 may be able to replace the original Delta by summer 2022.
More likely (I believe) is a slightly increased biological transmissibility.
Growth rate & secondary attack rates are refreshed with new data and findings remain the same as last week.
— Meaghan Kall has moved to Bluesky (@kallmemeg) October 29, 2021
How much is AY.4.2 spreading in the U.S.?
AY.4.2 has been identified in over 30 countries, including the U.S. But here, OG Delta continues to dominate; this variant has been causing over 99% of new cases in the U.S. for well over a month, with a couple of other Delta sub-lineages (AY.1 and AY.2) briefly popping up without getting competitive. AY.4.2 is not yet accounted for on the CDC’s variant tracker, but other estimates indicate that it’s causing under 1% of new cases in the U.S.
“We have on occasion identified the sublineage here in the United States, but not with recent increased frequency or clustering to date,” CDC Director Dr. Rochelle Walensky said at a recent COVID-19 briefing, according to STAT.
Are we prepared for a surge of AY.4.2—or another coronavirus variant?
The U.S. does not have a great track record for dealing with COVID-19 surges—whether that’s New York City in spring 2020 or Delta hotspots in the South this past summer. 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.
To illustrate this point, I’d like to share a major project of mine that was published this past week: an investigation of the Delta surge in Southwest Missouri this summer. This project was a collaboration between the Documenting COVID-19 project at the Brown Institute for Media Innovation and MuckRock (where I’ve been working part-time for a few weeks now), and the Missouri Independent, a nonprofit news outlet that covers Missouri state government, politics, and policy.
Missouri Independent reporter Tessa Weinberg and I went through hundreds of emails, internal reports, and other documents obtained through public records requests. We found that, even though Missouri had ample warnings about Delta—wastewater surveillance picked up the variant in May, and hospitals noticed increasing breakthrough cases in June—the Springfield area was completely overwhelmed by the virus. Infighting and mistrust between state and local officials also hindered the region’s response to the Delta surge.
Our major findings (copied from the article) include:
Springfield hospital and health department leaders urged the state to take advantage of additional genomic sequencing assistance to address unanswered questions about the variant’s spread. The state declined, forcing Springfield officials to seek additional data on their own.
After days of preparation for an overflow hospital for COVID patients requested by Springfield officials, local leaders decided to forego the plan after the window of need had passed — setting off dueling narratives over the reason why in public while state officials seethed in private.
When local officials pleaded for more support in addressing the Delta surge, state officials questioned the value of directing more resources to the area and even wondered whether the overflow hospital request was fueled by motivations to “pay for an expansion of their private hospital.”
And read my Twitter thread with more highlights here:
today, my first big investigative story with the Documenting COVID-19 project was published at @MO_Independent. @Tessa_Weinberg and I explained how miscommunication and a lack of preparedness hurt SW Missouri's ability to address the Delta surge this past summer. (1/17) pic.twitter.com/gQZS0WFyYX
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.
Together, this would suggest perhaps 40k or 100k deaths per year in the US from COVID at endemic state. Most infections would be relatively mild (just like flu), but there's enough of them that even a small fraction of severe outcomes add up. 15/17
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.
This is not cancer or heart disease, but it's still a substantial public health burden. That said, yearly boosters just like flu vaccine, therapeutics like molnupiravir, improved ventilation and rapid testing can all contribute to reducing this ongoing burden. 17/17
COVID-19 Data Dispatch 
