COVID-19 Data Dispatch

Tag: Omicron variant

  • BA.2 FAQ: What you should know about this Omicron offshoot

    BA.2 FAQ: What you should know about this Omicron offshoot

    BA.2 has become the dominant strain in Denmark, one of the countries that sounded the alarm about this Omicron offshoot. Chart via the Pandemic Prevention Institute, posted on Twitter on January 26.

    An offshoot strain of the Omicron variant has been making headlines this week as it spreads rapidly in some European and Asian countries. While the strain, called BA.2 by virologists, has not yet been identified in the U.S. in large numbers, it’s already spreading here, too: scientists have picked it up in wastewater samples in some parts of the country.

    This strain clearly has a growth advantage over the original Omicron strain (also called BA.1), but it’s not cause for major concern at this point. Scientists are working to identify whether BA.2 has a higher capacity for breaking through immunity from past infection or vaccination; so far, early data suggest that it does not significantly differ from BA.1 on this front, though it may have a slight advantage.

    Here’s a brief FAQ on what we know about the strain so far.

    When and where did BA.2 emerge?

    I’ve been careful not to call BA.2 a “new strain” or a “new variant” here because it’s not actually new—at least, it’s not any newer than Omicron BA.1. When South African scientists first sounded the alarm about Omicron in late November 2021, BA.2 was already present among the country’s cases of this variant.

    In fact, a paper from South African scientists describing the Omicron wave in their country, published in Nature in early January, specifies that the earliest specimen of BA.2 was sampled on November 17; the earliest specimen of BA.1 was sampled on November 8. Around the same time, South African scientists also identified a third lineage, called BA.3—this one hasn’t yet become a cause for concern.

    Why are scientists concerned about BA.2?

    In the past couple of weeks, epidemiologists have identified that BA.2 is spreading faster in some countries than BA.1, the original Omicron strain. This means BA.2 has what scientists call a “transmission advantage” over BA.1: it is capable of getting from person to person fast enough that it may be able to outcompete BA.1.

    For example, in Denmark, BA.2 became the dominant strain in mid-January, taking over from BA.1. The takeover has coincided with an additional increase in COVID-19 cases in the country after Denmark’s Omicron wave initially appeared to peak a couple of weeks ago—but it’s hard to determine whether this second increase is solely due to BA.2 or also connected to an announcement that Denmark will end its COVID-19 restrictions on February 1.

    This past week, the World Health Organization (WHO) announced that investigations into BA.2, including its potential virulence and ability to escape prior immunity, “should be prioritized independently (and comparatively) to BA.1.” The WHO has yet to designate BA.2 as a separate variant of concern from BA.1, however; at the moment, both strains are still included under the Omicron label.

    https://twitter.com/PeacockFlu/status/1483770131419443201

    How does BA.2 compare to BA.1, the original Omicron strain?

    As I’ve explained in previous posts about the variant, Omicron has the most antigenic drift of any coronavirus variant identified thus far—meaning that it’s the most genetically different from the initial Wuhan version of the virus. Omicron BA.1 has about 60 mutations compared to the Wuhan strain, but BA.2 has even more: about 85 mutations, according to a recent Your Epidemiologist post.

    BA.2 is clearly more transmissible than BA.1, as we’ve seen from its rapid spread in countries including Denmark, the U.K., France, the Netherlands, India, and the Philippines. Scientists estimate that “BA.2 may be 30% to 35% more transmissible than BA.1,” STAT News reports.

    The question scientists hope to answer, then, is why BA.2 has this transmission advantage over BA.1. Do BA.2’s additional mutations lend it some adaptation in how it interacts with human cells, enabling faster spread? Or is BA.2 more capable of evading protection from past infection or vaccination compared to BA.1, leading it to cause more reinfections and breakthrough cases?

    While we don’t know the answers to these questions yet, early data are indicating that there’s no major difference in disease severity between BA.1 and BA.2. In other words, BA.2 isn’t more likely to cause severe symptoms.

    “There is no evidence that the BA.2 variant causes more disease, but it must be more contagious,” Danish Health Minister Magnus Heunicke said at a news conference last week, Reuters reported.

    Why do some articles call BA.2 a “stealth variant?”

    You might have seen some headlines referring to BA.2 as a “stealth variant” or a “stealth version of Omicron.” This is because of one major difference between BA.2 and BA.1: while BA.1 can be identified with a PCR test due to a key mutation that’s visible on PCR test results, BA.2 does not have this mutation.

    As a result, BA.2 can be more time-consuming for COVID-19 testing labs to identify: labs need to sequence a sample’s genome to identify this strain rather than simply look out for an indicator on a PCR test. It’s unclear how much of a difference this will make in the U.S.’s ability to track BA.2, however, as many labs across the country are already performing routine full-genome sequencing of coronavirus samples.

    How well do vaccines work against BA.2?

    So far, it seems like there is no significant difference in vaccine protection between BA.1 and BA.2, at least when it comes to severe symptoms—which makes sense, scientists say, given how well vaccines have worked against every major variant to emerge thus far.

    Early findings in this area come from the U.K., which designated BA.2 as a “Variant Under Investigation” (separate from BA.1) about a week and a half ago. This past Friday, the U.K.’s Health Security Agency released a report with information on BA.2, including how it compares to BA.1 or original Omicron.

    Overall, U.K. epidemiologist Meaghan Kall wrote in a Twitter thread summarizing the report, early evidence suggests that “BA.2 is no more immune evasive than Omicron,” though confidence in this statement is low. The report found that, for Brits who had received booster shots, vaccine effectiveness against symptomatic COVID-19 disease was 70% for BA.2 and 63% for BA.1. The confidence intervals on these effectiveness estimates overlapped, indicating that vaccines perform similarly against BA.2 and BA.1.

    When it comes to disease severity, Kall wrote, the U.K. doesn’t have enough data to compare BA.2 and BA.1; early data on this topic (suggesting BA.2 is not more severe) have come from Denmark and India.

    How will BA.2 impact the U.S.’s COVID-19 trajectory?

    BA.2 has already outcompeted BA.1 in some parts of Europe and Asia, and epidemiologists expect that countries like the U.K. and the U.S. could also follow this pattern—though it will likely be a longer, slower replacement process compared to the intense way Omicron pushed out Delta. A bigger unknown here is what effect this strain may have on case numbers, hospitalizations, and deaths.

    Countries and regions now passing the peaks of their Omicron BA.1 waves have extremely high levels of population immunity. As a result, people who are fully vaccinated with boosters and/or recently infected with Omicron BA.1 likely will have a lot of immune system protection against BA.2, though we don’t yet have good data on exactly how robust this protection is.

    So, could BA.2 cause the current downturn in U.S. COVID-19 cases to reverse? It’s possible, explains Andrew Joseph in a recent STAT News article. However, thanks to our high immunity levels, a further spike in cases could be “broadly limited to infections” rather than causing major increases in hospitalizations and deaths. In the coming weeks, we’ll get a better sense of how well prior Omicron infections protect against BA.2 and other key information that will inform our understanding of how this strain may change the country’s COVID-19 trajectory.

    Right now, COVID-19 experts are closely monitoring BA.2, but they’re not hugely concerned. As Dr. Jetelina put it in a recent Your Local Epidemiologist post, the bigger worry right now is that another variant could “pop out of nowhere” like Omicron did in November.

    More variant reporting

  • Omicron updates: Where will these massive case numbers leave us?

    Omicron updates: Where will these massive case numbers leave us?

    Omicron went from 1% of U.S. cases to nearly 100% of cases in about six weeks. Chart via the CDC, retrieved January 23.

    Major news items for this week include the potential peak of the U.S.’s Omicron surge and real-world data from the CDC on how well booster shots work against this variant.

    • Omicron is now causing nearly 100% of new COVID-19 cases in the U.S. The latest CDC estimates of variant prevalence put Omicron at 99.5% of new cases in the U.S. as of January 15, with Delta causing the remaining 0.5% of cases. I have to say, it’s incredibly striking not only how quickly Omicron outcompeted Delta (it went from 1% of new cases to nearly 100% in just six weeks), but also how both of these highly contagious variants have dominated the country so thoroughly that they’re now the only two variants present here at all. For comparison, Alpha only got to 70% of cases at its peak. These trends show how drastically both Delta and Omicron changed the trajectory of the pandemic.
    • While the U.S. may be peaking, massive numbers of people are getting infected. As I noted in today’s National Numbers, America’s Omicron wave may have peaked this week, with the country’s massive case growth appearing to turn around. Computational biologist Trevor Bedford wrote a recent Twitter thread about this peak, pointing out that a huge share of the U.S. population was infected with Omicron in the past month: “between 18% and 23% of the country was infected by Omicron by Jan 17, with the large majority infected in a span of just ~4 weeks,” he hypothesized. By mid-February, Bedford says, this number could be “36%-46%.”

    • The high infection numbers may give us “a bit of a break from the Covid roller coaster.” With so many people infected in such a short time, Omicron will have a huge impact on the “immunological landscape” of the U.S, Helen Branswell explains in a recent article for STAT News. Millions will have immunity from a recent infection, vaccination, or both; and Omicron’s unique biology may mean that people who caught this variant will be protected from other strains. As a result, the end of this wave may lead into “a bit of a break” from COVID-19, Branswell writes, with low case numbers for a few weeks or months. It’s hard to say whether this “break” will constitute the end of the pandemic, though—we don’t know how long post-Omicron immunity lasts.
    • Rapid at-home tests work well at detecting Omicron, though they’re far from perfect. As I’ve noted in past issues, there have been some questions recently about how well rapid antigen tests work at identifying Omicron infections. In a recent Your Local Epidemiologist post, Dr. Katelyn Jetelina walked through the data from several recent studies on this topic. The highlights: rapid tests likely won’t work well in the very beginning of an infection, so wait to test until five days after an exposure; if you test positive, trust the result; test repeatedly for higher accuracy; and, if you have the tests, wait for two negative results before coming out of isolation.
    • New CDC wastewater report shows how early Omicron was spreading in the U.S. The CDC published a report this week sharing findings from wastewater surveillance systems in a few states and localities. (Wastewater surveillance means the states are regularly testing samples from sewage to identify coronavirus levels coming from residents’, well, waste.) In New York City, Omicron was first detected in wastewater on November 21, the weekend before Thanksgiving. In California, Colorado, and Houston, Texas, the variant was detected in late November or early December.
    • An additional booster shot may not be enough to completely prevent Omicron infection, a small Israeli study suggests. Israel was one of the first countries to offer third vaccine doses to its residents, and now it’s also one of the first countries offering fourth doses. A new study presents the impact of these shots among about 270 healthcare workers. The additional doses produced more antibodies in the patients, but “this is probably not enough for the Omicron,” one of the study’s authors told Reuters—at least when it comes to completely preventing infection.
    • But: booster shots still reduce chances of infection significantly, compared to people who are unvaccinated. Another new CDC report published this week compares COVID-19 cases among vaccinated, boosted, and unvaccinated people in 25 U.S. jurisdictions. In late December, after Omicron started spreading widely, adults who were unvaccinated had a five times higher risk of COVID-19 infection compared to those who were fully vaccinated with a booster shot, the CDC found.
    • Booster shots also have a huge impact on risks of severe symptoms and hospitalization. One more CDC report released this week: scientists analyzed the impact of booster shots on emergency department visits and other hospitalization metrics in ten states. When both Delta and Omicron were the dominant variants in the U.S., the CDC researchers found, third doses had 94% efficacy rates in protecting people against COVID-related emergency department visits, and 82% efficacy rates in protecting against urgent care visits. Efficacy against hospitalization was also over 90%. In short: if you’re eligible for your booster, go get it!
    • Booster shots of Pfizer and Moderna vaccines could be critical for countries that used other brands. Last week, I shared a report that found 22 million mRNA vaccine doses are needed as booster shots in low-income countries, to protect the world against Omicron. This past week, a new study in Nature supported this report: a group of scientists in Hong Kong found that Pfizer doses are safe and highly effective booster shots for people who initially received the Chinese CoronaVac vaccine. The authors suggest that mRNA vaccines should be used as boosters in countries that originally distributed CoronaVac.
    • New research identifies a mutation that may contribute to Omicron’s super-contagiousness. A new study from the National Institutes of Health (NIH) found that a mutation present in the Alpha and Delta variants allows the coronavirus to more easily bind to human cells. When the coronavirus binds more easily, it can spread faster within the body; this rapid multiplication helps the virus quickly spread outside the body as well, increasing contagiousness. Though this study was done before the Omicron variant emerged, Omicron has this same mutation, explained lead author Dr. Lawrence Tabak in a post for the NIH Director’s Blog.

    More variant reporting

  • National numbers, January 23

    National numbers, January 23

    Has Omicron peaked in the U.S.? Nationally, it seems possible, but the situation is more complicated at the state and local level. Chart via the CDC, retrieved on January 23.

    In the past week (January 15 through 21), the U.S. reported about 5.2 million new cases, according to the CDC. This amounts to:

    • An average of 745,000 new cases each day
    • 1,588 total new cases for every 100,000 Americans
    • One in 63 Americans testing positive for COVID-19
    • 5% fewer new cases than last week (January 8-14)

    Last week, America also saw:

    • 147,000 new COVID-19 patients admitted to hospitals (45 for every 100,000 people)
    • 12,200 new COVID-19 deaths (3.7 for every 100,000 people)
    • 100% of new cases are Omicron-caused (as of January 15)
    • An average of 300,000 vaccinations per day (per Bloomberg)

    Has Omicron peaked in the U.S.? Looking at the national data, you might think so: new COVID-19 cases in the U.S. have dropped 5% from 5.5 million last week to 5.2 million this past week. While those numbers are astronomically high compared to past pandemic waves, it’s encouraging to think that they might not get higher.

    Hospitalization data also seem to have reached a peak; while about 150,000 Americans are currently hospitalized with COVID-19, according to the HHS, this number is no longer rapidly increasing. Patient numbers are starting to decline in the states and cities that were first hit by Omicron.

    It’s too soon to say that we’re actually coming down on the other side of the Omicron curve, though. For one thing, as Dr. Katelyn Jetelina pointed out in a recent issue of Your Local Epidemiologist, holiday reporting and test capacity could be playing a role here.

    Last Monday was Martin Luther King Jr. Day, a federal holiday that many health agencies and test providers took off—though not a holiday on the reporting disruption level of Christmas or New Year’s. And tests are incredibly hard to find in some parts of the country, meaning that our current system simply isn’t catching a large number of COVID-19 cases. (Remember: most COVID-19 case counts do not include cases identified with at-home antigen tests.) In short, the current trend is encouraging, but we’ll have to see next week if it continues.

    While the national picture is hard to interpret, it’s clear that the Northeast states that dealt with Omicron first are now on the decline. In New York City, the case rate has been reduced by over a third, from 3,500 new cases per 100,000 in a week at the beginning of January to 1,000 new cases per 100,000 in the last week. Case rates are also going down in New Jersey, Maryland, D.C., Connecticut, and Massachusetts.

    At the same time, other parts of the country are still in the first half of their Omicron surges. Cases rose by over 40% from last week to this week in Wisconsin, Wyoming, Oklahoma, Idaho, Ohio, and New Mexico, according to the latest Community Profile Report. In fact, Wisconsin now has one of the highest per capita case rates in the country, at 2,800 new cases per 100,000 in the week ending January 19.

    A recent NBC News article explains that the urban regions first exposed to Omicron have higher vaccination rates and more available hospital beds, making them more prepared to weather the variant. But now, Omicron is beginning to reach rural parts of the country that are less vaccinated, less capable of taking on patients, and still reeling from Delta. For these communities, the next few weeks are bound to be rough.

    more national numbers
  • Omicron updates: Possible peaks, viral loads, vaccines

    Omicron updates: Possible peaks, viral loads, vaccines

    Has Omicron peaked in NYC? It sure seems like it, according to city data; screenshot retrieved from NYC Health dashboard on January 16.

    These update posts are getting shorter as time goes on, but we’re still learning about this variant! A few news items from this week:

    • Omicron is now causing almost 100% of new COVID-19 cases in the U.S. In the CDC’s latest variant proportions update, the agency estimated that 98% of new COVID-19 cases were caused by Omicron in the week ending January 8. The CDC also revised estimates for previous weeks, though the revisions were not as significant as they have been in the past—suggesting that the numbers are now fairly close to accurate, but will continue to be tweaked as more sequencing data come in.
    • Major Northeast hotspots appear to be peaking. Last week, I wrote that New York City’s Omicron wave seemed to have reached its peak. The trend has continued into this week: the new case rate and test positivity rate have both fallen consistently since peaking on January 3. Similarly, in Boston, the Omicron levels detected in the city’s wastewater have declined steeply since early January. The daily case rate is also going down in Washington, D.C., and in the Northeast region overall. Still, hospitals are still overwhelmed throughout the region, and it’s unlikely that cases will go down as quickly or as decisively as they went up.

    • New NYC report provides data on the city’s Omicron wave. Speaking of NYC: the city’s public health department recently put out a new report detailing the variant’s impact. The variant “has accounted for nearly all coronavirus samples sequenced in NYC” since Christmas, the report’s authors write. Also, while a smaller share of Omicron cases led to hospitalization compared to the Delta wave, more people have been hospitalized overall because of sheer case numbers. Unvaccinated New Yorkers, Black New Yorkers, and those over age 75 have been most likely to require hospitalization.
    • Real-world study suggests rapid at-home tests work well at detecting Omicron. A new study from the University of California, San Francisco, released this week as a preprint, analyzed rapid antigen tests’ capacity to detect Omicron by comparing rapid test results to PCR test results. The results: antigen tests correctly identified 95% of cases with high viral loads and 98% of symptomatic cases. In about one-third of the cases identified through PCR, patients tested negative on antigen tests; but this is in line with the tests’ accuracy for other variants.
    • Data from the NBA suggest Omicron’s viral load is pretty variable. Another new study posted as a preprint this week analyzed data from the National Basketball Association (NBA). The league’s regular testing policy allowed Harvard researchers to study viral loads in Omicron-positive patients, revealing that this variant had “lower peak viral load and more variable early viral growth durations than Delta,” according to one of the authors. In other words, some of the basketball players were highly contagious early into their Omicron infections, while others were less so; and the players had less virus in their bodies overall at the peak of their infections than in previous Delta infections. Also, a large number of the players were still contagious five days after they were diagnosed—which doesn’t bode well for the CDC’s new isolation guidance.
    • More confirmation that vaccinated people are protected from severe disease from Omicron. Another new study, this one published in Nature through the journal’s advance preview system for COVID-19 reports, confirms previous research about T cell response to Omicron. T cells are a key part of the immune system’s long-term memory apparatus; they help protect against severe symptoms and death. The study found that, in patients who were fully vaccinated (or, to a lesser degree, had a previous infection), T cells could recognize Omicron and protect people against its worst impacts.
    • Omicron adds urgency to the need to vaccinate the world—ideally, with mRNA vaccines. A report from advocacy groups PrEP4All and Partners In Health, written with scientists at Harvard, Columbia, and other institutions, found that 22 billion additional mRNA vaccine doses are needed to control the pandemic, now that Omicron has become the dominant variant in the world. The report specifies that mRNA vaccines are needed because other vaccine types are not capable of preventing Omicron infection, and likely are less effective against severe disease. “Future viral variants may become even more transmissible, immune evasive, and virulent than Delta or Omicron,” the report cautions.

    More variant reporting

  • Omicron updates: the surge is here, but peaks might be in sight

    Omicron updates: the surge is here, but peaks might be in sight

    Antigenic drift posed by Omicron. Figure from Sanders et al., posted to Medrxiv on January 3.

    As the Omicron surge continues, we are still learning more about this variant. Here are the major updates from this week:

    • Omicron is now causing more than 90% of new cases in the U.S. In the latest update of the CDC’s variant proportions estimates, the agency found that Omicron caused 95% of new COVID-19 cases nationwide in the week ending January 1. The CDC also revised estimates for previous weeks, bringing us to 77% Omicron for the week ending December 25 and 38% Omicron for the week ending December 18. While these estimates continue to be based on weeks-old data, it the CDC now has enough sequencing information to make Omicron estimates with lower confidence intervals than it did a few weeks ago—suggesting that these numbers are closer to reality than the estimates we saw in December.
    https://twitter.com/jaspar/status/1478773556435730432

    • Omicron is causing the vast majority of cases in every state. Also included in the CDC’s variant proportions estimates: regional numbers. The latest figures estimate that, as of January 1, Omicron prevalence across the country ranges from 82% in the Northeast to 98% in New York/New Jersey and the Gulf states region (Texas, Louisiana, Arkansas, Oklahoma, and New Mexico). These numbers align with recent calculations from computational biologist Trevor Bedford based on sequences posed to the public repository GISAID. In short: Omicron is everywhere.
    • Evidence that Omicron is less likely to cause severe symptoms continues to mount. A combination of real-world hospitalization and lab data continue to suggest that Omicron is less likely to cause severe COVID-19 symptoms than past coronavirus variants. The hospitalization data: in Omicron hotspots, hospitalization numbers are not rising at the same rate as case numbers, nor are the numbers of patients who require intensive care or ventilators. “Despite steep rises in cases and patients, the number on ventilators has barely risen,” wrote Financial Times data journalist John Burn-Murdoch in a recent thread about U.K. data.
    • And the lab data: a growing number of studies show that Omicron is less capable of infecting patients’ lungs compared to past variants—meaning the worst respiratory symptoms are rarer. At the same time, people who catch Omicron after gaining immunity from vaccination and/or prior infection are protected against severe symptoms thanks to T cells and other aspects of immune system memory. Note that, however, we still don’t know about the risk of Long COVID following an Omicron case.
    • Still: U.S. Hospitals are now incredibly overwhelmed with Omicron and Delta cases. In the U.S. so far, the “decoupling” phenomenon (in which hospitalizations and ICU admissions don’t rise as fast as cases) has been less visible than in other countries hit by Omicron. Several states have already set hospitalization and/or ICU records during the Omicron surge. This is likely because many parts of the U.S. have lower vaccination rates than other countries like the U.K. At the same time, accounts from hospital workers show the toll that this surge is taking: “Thankfully the Covid patients aren’t as sick. BUT there’s SO many of them,” wrote NYC ER doctor Dr. Craig Spencer in a recent Twitter thread.

    • Omicron has more antigenic drift than any other variant. “Antigenic drift” is a virology term referring to the small mutations in virus genetic material that cause these viruses to change slowly over time. As I noted in early Omicron updates, this variant didn’t evolve out of Delta (as many experts were expecting) but rather showed up seemingly out of nowhere; it might have emerged from a part of the world with limited variant surveillance, an immunocompromised person, or even an animal host. We don’t know Omicron’s origin yet, but we now know that it is further apart, genetically speaking, from the original coronavirus than any other variant so far.
    • London’s Omicron surge may have peaked. According to U.K. data, both case numbers and hospital admission numbers have slowed in their increases, the Washington Post reports. “For the moment, we can probably say London appears to be over the worst,” U.K. hospital executive Chris Hopson said last week. Other U.K. health officials are more skeptical though, according to the Post: while case numbers are falling for teenagers and younger adults, London is still reporting increasing cases among seniors.
    • New York City also might be on the verge of peaking. Another tentative peak report: data from NYC’s health department suggest that case numbers might be starting to fall in the city. The citywide seven-day average for new cases fell from 3,261 per 100,000 people on January 2 to 2,754 per 100,000 on January 4, and NYC’s positivity rate is also trending down. Reduced COVID-19 testing over New Years and other reporting uncertainties are likely playing a role here, but still—NYC cases jumped right back up after Christmas, but haven’t yet jumped up after New Years. I am cautiously optimistic!
    • New research maps out South Africa’s intense Omicron wave. This recent study caught my eye when it was published in Nature this week through accelerated approval. Nearly 100 scientists in South Africa, Botswana, the U.S., Switzerland, the U.K., and other countries collaborated to analyze Omicron’s genetic makeup and the variant’s rapid spread through South Africa, including its ability to cause breakthrough cases and reinfect people who’ve previously had COVID-19. The paper is just one example of the immense collaboration that has taken place over the past month as scientists work to quickly understand this variant. Thank you, scientists!

    More variant reporting

  • National numbers, January 9

    National numbers, January 9

    The national average case rate for the U.S. is twelve times the CDC’s benchmark for “high transmission” (100 new cases per 100,000). Chart via the January 6 Community Profile Report.

    In the past week (January 1 through 7), the U.S. reported about 4.1 million new cases, according to the CDC*. This amounts to:

    • An average of 586,000 new cases each day
    • 1,251 total new cases for every 100,000 Americans
    • One in 80 Americans testing positive for COVID-19
    • 86% more new cases than last week (December 25-31)

    Last week, America also saw:

    • 115,000 new COVID-19 patients admitted to hospitals (35 for every 100,000 people)
    • 8,700 new COVID-19 deaths (2.7 for every 100,000 people)
    • 95% of new cases are Omicron-caused (as of January 1)
    • An average of one million vaccinations per day (including booster shots; per Bloomberg)

    *Here at the COVID-19 Data Dispatch, we’re back to our regular schedule of national updates based on Friday data, as the CDC has resumed weekly reports following its holiday hiatus.

    Omicron continues to drive record cases across the U.S., as we move from tense holiday gatherings to extremely fractured schools and workplaces. This week, the CDC reported 4.1 million new cases—almost double last week’s number, and about 2.5 times the case peak reported during last winter’s surge.

    Put another way: 4.1 million cases amounts to about one in eighty Americans testing positive for COVID-19 in the past week. And that number doesn’t include the vast majority of rapid, at-home tests that continue to be in high demand across the country.

    At the same time, hospitalizations are increasing rapidly, with over 100,000 current COVID-19 patients now reported by the CDC. We appear to be on track to pass last year’s peak, 124,000 COVID-19 patients in beds nationwide.

    I’ve seen a lot of discussion in recent days about hospitalizations “with” COVID-19 versus hospitalizations “for” COVID-19. As Omicron is less severe and more transmissible than other variants, the argument goes, aren’t a lot of those 100,000 COVID-19 patients people who have mild or asymptomatic cases, but tested positive for COVID-19 upon going to the hospital for a different condition?

    While it’s true that some COVID-19 patients in hospitals are “incidental,” meaning their cases were caught during routine hospital screening, these cases can still have a major impact on the hospital system. Healthcare workers need to separate these patients from non-COVID patients, take extra care with their PPE, and utilize other resources. Plus, a lot of patients that, at first, appear to “incidentally” have COVID-19 may see the disease worsen their chronic conditions, such as diabetes or COPD.

    To better understand the strain on hospitals right now, I recommend reading Ed Yong’s latest feature in The Atlantic—which gets into the “with” versus “for” issue, hospital staffing challenges, and other problems.

    When it comes to hotspots: the Northeast continues to see the highest case rates. New Jersey and New York are leading the pack, both with over 2,400 new cases for every 100,000 residents reported in the last week according to the latest Community Profile Report. (Reminder: the CDC threshold for “high transmission” is 100 new cases per 100,000, so New York and New Jersey are at 24 times the rate of this benchmark.)

    Rhode Island, Puerto Rico, D.C., Delaware, Massachusetts, and Florida also have incredibly high case rates, over 1,800 per 100,000 in the last week. Meanwhile, cases are rising rapidly in a number of other Southern and Western states: Texas, the Carolinas, Utah, Arkansas, California, Oregon, and Mississippi have all reported more than 150% case increases in the past week.

    If you are able to work from home and avoid public spaces as much as possible, now is the time to do so. January is going to be rough.

    more national numbers
  • Omicron updates: ‘mild’ cases can still mean a nasty surge

    Omicron updates: ‘mild’ cases can still mean a nasty surge

    Image
    Data from South Africa and the U.K. suggest that Omicron patients are less likely to require intensive hospital care than those infected with previous variants. Chart posted on Twitter by Paul Mainwood.

    It’s now been over a month since Omicron arrived in the U.S., and the variant’s impact is clear: January is about to be nasty. Here are the major updates from this week:

    • Omicron continues to cause the majority of new cases in the U.S., but the CDC revised its estimates down this week. On Monday, the agency updated its variant proportions estimates; according to the new data, Omicron caused 59% of new cases in the U.S. in the week ending December 25. Notably, this was lower than the previous week’s estimate of 73%. As I explained in a Twitter thread, the CDC’s variant proportions data are estimates with very wide confidence intervals, based on sequencing data that are reported with a lag of multiple weeks. And the agency’s slow pace of updates means that its estimates are unlikely to match the actual variant situation in the U.S. anyway. Still, the CDC data do tell us that Omicron is causing the majority of U.S. cases right now, and that it became dominant over Delta in under one month.
    • Outdoor concerts in Puerto Rico were a superspreading event for Omicron. Puerto Rico has been a pandemic success story, with one of the highest vaccination rates in the nation. But the territory is currently reporting record COVID-19 cases thanks to Omicron, with an increase of over 5,000% in the space of two weeks. One reason for the increase: a series of concerts by the Puerto Rican rapper Bad Bunny, which have now been connected to at least 2,000 cases according to Puerto Rico’s Office of Epidemiology. The concerts took place in an outdoor stadium, and audience members had to be vaccinated and wear a mask to attend. The high number of cases connected to this event indicates Omicron’s high transmissibility, even in outdoor settings.
    • South Africa’s Omicron wave continues to decline, and London may be seeing a similar pattern. Omicron cases have now been decreasing in South Africa for more than two weeks, with a 30% decline from December 18 to 25. The country’s leaders recently lifted a curfew from midnight to 4 AM, though public gatherings are still restricted to 1,000 people indoors and 2,000 outdoors. A similar decline may be starting in London, another major Omicron hotspot—though holiday reporting delays and high testing demand make it hard to say for sure.

    • Continued evidence that Omicron cases are more likely to be mild. Data out of South Africa continue to show that patients infected with Omicron have a lower risk of severe symptoms than those infected in past waves. One study, published this week in JAMA, finds that the country’s fourth wave has impacted younger patients with “fewer comorbidities, fewer hospitalizations and respiratory diagnoses, and a decrease in severity and mortality.” As I’ve written before, this is likely thanks to South Africa’s high prevalence of immunity from past infections. But a growing number of lab studies are also showing that Omicron may have inherent biological qualities that make it more mild, including a reduced capacity to infect lung cells compared to past variants.
    • It is worth noting, however, that mild, in the clinical sense, means that your case does not require hospitalization. A patient could have a high fever, become bed-bound for days, and even face Long COVID symptoms while still fitting the “mild disease” classification, as Nsikan Akpan discusses in this Gothamist article about his own experience with Omicron. Reminder: we still have next-to-no data on how Omicron may impact the likelihood of Long COVID.
    • Studies continue to indicate that vaccines protect against severe disease from Omicron, though protection against infection is less robust. A new preprint posted this week finds that “most of your T cell responses from vaccination or previous infection still recognize Omicron,” explained study author Wendy Burgers in a Twitter thread. T cells are a type of immune system cell that participates in long-term response; their recognition of Omicron means that vaccinated people are still well-protected against severe disease. At the same time, a new study set to be published in Nature found that vaccinated people who’d received two doses had limited protection against infection, while people with three doses or multiple doses and a prior infection were better protected.
    • Antibodies made during an Omicron infection could provide protection against Delta. In Omicron hotspots, people who recently caught Delta have been readily infected by the new variant. But an Omicron infection may lead to anti-Delta antibodies in your immune system, according to a new preprint from South African scientists who tested blood samples from Omicron patients in the lab. “The researchers found, unsurprisingly, that the patients’ blood contained a high level of antibodies potent against Omicron,” explained Carl Zimmer in the New York Times. “But those antibodies proved effective against Delta, too.” If other studies back up this finding, it could mean that regions with Omicron waves will be protected from Delta resurgence.
    • Pediatric hospitalizations are rising as Omicron spreads, but the variant is not necessarily inherently worse for children. In New York City, one of America’s Omicron hotspots, pediatric hospitalizations increased four-fold from the beginning of December through last week, according to the New York State health department. State leaders are encouraging parents to get their kids vaccinated, as less than one-third of children in the five to 11 age group had received at least one dose as of December 24. As the New York Times points out, low vaccination rates for young kids, combined with the sheer number of cases caused by Omicron, are likely to blame for this increase—rather than some inherent quality of Omicron making it more severe for children.
    • The Omicron surge will be bad in the U.S., but it may boost nation-wide immunity for a few months afterwards. I highly recommend reading through this story by STAT’s Megan Molteni, which walks through several potential scenarios for the Omicron winter surge in the U.S. Some highlights: while South Africa’s short wave is promising, it might not translate to the U.S.; the country will be “in a viral blizzard nationwide” for the next few weeks; massive numbers of Americans will be infected (though their cases may be mild and go unreported); the whole world may be in a similar situation; and those huge case numbers could translate to a lot of immunity in the future. “The thing Omicron will do, because it’s going to infect 40% of the entire world in the next two months, is it will raise population-wide immunity for a while,” Chris Murray, director of IHME, told STAT.

    More variant reporting

  • National numbers, January 2

    National numbers, January 2

    While COVID-19 case numbers in many parts of the country have shot past last winter’s records, hospitalizations and deaths have remained relatively low. Chart via the New York Times, shared on Twitter by Benjamin Ryan.

    In the past week (December 24 through 30), the U.S. reported about 2.2 million new cases, according to the CDC.* This amounts to:

    • An average of 316,000 new cases each day
    • 674 total new cases for every 100,000 Americans
    • 79% more new cases than last week (December 17-23)

    Last week, America also saw:

    • 71,000 new COVID-19 patients admitted to hospitals (22 for every 100,000 people)
    • 7,700 new COVID-19 deaths (2.4 for every 100,000 people)
    • 59% of new cases are Omicron-caused (as of December 25)
    • An average of 1.3 million vaccinations per day (including booster shots; per Bloomberg)

    *This week’s update, like last week’s, is based on Thursday data (as of December 30) because the CDC has once again taken Friday through Sunday off.

    It’s difficult to interpret COVID-19 data in the wake of any major holiday, as public health officials and testing sites alike take well-deserved time off. The weeks after Christmas are particularly tricky: the numbers are just starting to recover from one holiday when New Year’s hits, causing another round of delays. This year, the CDC took three-day weekends over both Christmas and New Year’s.

    All of that said, we have enough data to say that cases are rising incredibly fast across the U.S. The country reported over 300,000 new cases a day this week—the highest seven-day average of the entire pandemic so far. Over 500,000 new cases were reported on Friday alone.

    https://twitter.com/alexandraphelan/status/1476919027670962176

    New York City continues to be a major Omicron hotspot. Last week, I wrote that one in every 100 New Yorkers had tested positive within a seven-day period, according to NYC data; this week, that number is one in 50. NYC’s positivity rate is over 25%, indicating that one in every four PCR tests conducted in the city is returning a positive result—but also indicating that the city is not testing enough to actually identify all cases. City data don’t include rapid at-home tests, contributing to the data gap here.

    NYC’s case rate seems to be slowing down, suggesting that the city may soon follow South Africa in seeing an intense, yet short Omicron surge. But “growth is still growth,” as analyst Conor Kelly points out:

    Meanwhile, plenty of other places in the U.S. are facing rapid growth from Omicron. In Florida, cases increased by almost 1,000% in the last two weeks of December—bringing the state from the lowest per-capita case rate in the country to the fourth-highest. Several other Southern states have also seen cases more than double in the last week: Georgia, Alabama, Louisiana, California, Mississippi, Washington, and Maryland, among others.

    There is some good news in this surge, though: while COVID-19 cases surge to record highs, hospitalizations remain much lower than they were at this point last year. The CDC currently reports about 67,000 COVID-19 patients in hospitals nationwide, compared to a peak of over 120,000 in January 2021. Omicron hotspots like NYC and DC are similarly reporting hospitalization numbers that, while rising sharply, are not following cases as closely as they did last year. 

    COVID-19 experts call this phenomenon “decoupling”: thanks to vaccinations, treatments, and (possibly) some inherent biological qualities of Omicron, hospitalization increases no longer directly follow case increases. Still, a smaller percentage of cases requiring hospitalization can still mean a lot of hospitalizations, when case numbers are as high as they are right now. And hospitals, already facing dire staffing shortages, were in crisis mode before Omicron hit.

    more national numbers
  • Omicron updates: A major surge is underway in the U.S.

    Omicron updates: A major surge is underway in the U.S.

    Within a week, Omicron has jumped from causing an estimated 13% of new COVID-19 cases in the U.S. to 73% of new cases. Chart via the CDC.

    The majority of new COVID-19 cases in the U.S. are now caused by Omicron, and a massive surge is underway. But there’s good news: the variant continues to appear less likely to cause severe disease than past coronavirus strains, and South Africa’s wave may have already peaked.

    Here are the highlights of Omicron news this past week:

    • Omicron is now causing the majority of cases in the U.S. Last week, I wrote that the CDC’s estimates of new COVID-19 cases caused by different variants were providing a delayed, incorrect look at Omicron in the U.S. This past Monday, the ramifications of that delay were made clear: the CDC updated its estimates, showing that 73% of new cases in the week ending December 18 were caused by Omicron. (The agency’s previous estimate: 3% of new cases.) The agency also updated its estimates for prior weeks, to 13% in the week ending December 11 and 1% in the week ending December 4. It’s important to note that, as Trevor Bedford points out in this STAT News interview, these numbers are estimates generated by CDC algorithms. New sequencing data are always reported with a lag, and the true share of cases caused by Omicron is almost certainly even higher by now.
    • The Yankee Candle Index shows a major rise in COVID-19 cases. One of the most common COVID-19 symptoms is loss of smell. As a result, COVID-19 surges in the U.S. tend to correspond with increases in one-star reviews of Yankee Candles, in which reviewers complain that they can’t smell their candles—a phenomenon known as the Yankee Candle Index. And in the past few weeks, those one-star Yankee Candle reviews have shot up again, to higher levels than even last winter. This SFGATE article provides a nice summary of the situation.
    https://twitter.com/zornsllama/status/1473575508784955394
    • In South Africa, Omicron cases continue to go down. COVID-19 case numbers in South Africa dropped by about 20% between December 15 and December 22, prior to any holiday reporting interference. Several South African scientists have said that the country appears to be “over the curve,” with similar case patterns observed in the Omicron hotspot of Gauteng. This news is puzzling for some researchers—and might be tied to insufficient testing and/or high numbers of mild and asymptomatic cases—but it still bodes well for Omicron outbreaks in other countries. London may be seeing the beginning of a case drop right now, as well.
    • It’s tough to say whether Omicron is more mild because of inherent biology or prior immunity. As the scientists studying Omicron in the lab continue to share their findings—and South Africa continues to see low numbers of cases requiring hospitalization—evidence is growing that Omicron seems to be less likely to cause severe disease than past variants. But scientists remain skeptical, as this recent piece in Science magazine explains. Some aspects of Omicron’s biology, like its reduced capacity to infect lung cells, may make it inherently less virulent. At the same time, vaccines and prior infections confer protection against severe disease, particularly in the form of T cells.
    • Omicron might be making people sick—and contagious—faster than past variants. Scientists call the gap between exposure to a virus and the beginning of symptoms the “incubation period.” For the original coronavirus, this period was five or six days, Katherine J. Wu writes in The Atlantic. For Omicron, it may be as short as three days. While it’s challenging to study incubation periods, Wu writes, early data indicate that Omicron makes people sick in less time than prior variants—thus shortening the time that we have to identify and stop infections. Her piece also discusses the implications that this shorter incubation period has for testing.

    • Oral swabs may be more accurate than nasal swabs in identifying Omicron infections. In the past few days, I’ve seen some discussion on Twitter about swabbing one’s throat in addition to one’s nose when rapid testing for a potential Omicron infection. One recent preprint from South Africa suggests that Omicron might cause more viral shedding in saliva and less in the nose than past variants, meaning tests that rely on samples from the throat could be more likely to catch Omicron infections than tests that rely on nasal swabs. If you’d like to try the saliva swab method yourself, this video from Public Health England is helpful.
    • Omicron protection from booster shots may be short-lived. In the latest Omicron briefing from the U.K. Health Security Agency, one finding stuck out: while booster shots provide additional protection against Omicron infection, this protection begins to wane several weeks after vaccination. “Updated vaccine effectiveness analysis shows mRNA boosters beginning to wane from one month (week 5-9) for Omicron, and as low as 30-50% effective from 10 weeks post-booster,” wrote Meaghan Kall in her Twitter thread summarizing the briefing. If you haven’t gotten your booster shot yet, definitely do so—the shots also increase protection from severe disease, and that doesn’t wane. But this finding suggests that Omicron-specific boosters may be needed in the coming months.
    • Antiviral pills for COVID-19 will soon be available, and they work against Omicron. This week, the FDA authorized two antiviral COVID-19 pills for emergency use in the U.S.: one pill made by Merck (about 30% effective against hospitalization and death in clinical trials), and the other made by Pfizer (about 90% effective). Both pills are designed to prevent severe disease in vulnerable adults, such as the immunocompromised, and both work well against Omicron infections—since they target pieces of the coronavirus outside of the heavily-mutated spike protein. While the pills require a positive COVID-19 test for prescription (a challenging task, as testing demand continues to increase), their authorization is still a source of hope as the variant spreads.
    • IHME predicts “enormous spread of Omicron,” but with most cases mild or asymptomatic. The Institute of Health Metrics and Evaluation (IHME) at the University of Washington has predicted that the U.S. could see 140 million new coronavirus infections between January and March 2022, with a peak of 2.8 million infections a day. That could amount to 60% of the U.S. getting infected, the IHME director told USA Today. Note, however, that the institute predicts infections, not reported cases; the modeling suggests that the vast majority of these cases will be mild or asymptomatic. This prediction is in line with estimates of existing COVID-19 immunity in the U.S.: for example, Trevor Bedford said that 80% to 90% of Americans currently have some degree of protection from vaccination or prior infection in the STAT News interview linked above.
    https://twitter.com/JuliaRaifman/status/1472972206246440971

    More variant reporting

  • National numbers, December 26

    National numbers, December 26

    The seven-day average for new COVID-19 cases in the U.S. on December 23 has passed the peak of the Delta surge. Chart via the CDC.

    In the past week (December 17 through 23), the U.S. reported about 1.2 million new cases, according to the CDC.* This amounts to:

    • An average of 176,000 new cases each day
    • 376 total new cases for every 100,000 Americans
    • 42% more new cases than last week (December 10-16)

    Last week, America also saw:

    • 55,000 new COVID-19 patients admitted to hospitals (17 for every 100,000 people)
    • 8,500 new COVID-19 deaths (2.6 for every 100,000 people)
    • 73% of new cases are Omicron-caused (as of December 18)
    • An average of 1.4 million vaccinations per day (including booster shots; per Bloomberg)

    *This week’s update is based on data as of Thursday, December 23; I typically utilize the CDC’s Friday updates, but the agency is not updating any data from Friday through Sunday this week due to the Christmas holiday.

    Last week, the Omicron surge had clearly arrived; this week, it’s picking up steam. Nationwide, the U.S. reported well over one million new cases this week—more than a 40% increase from last week. 244,000 cases were reported on Thursday alone, and the daily new case average is now higher than at any point during the Delta surge.

    Hospitalization and death numbers have yet to increase so sharply: the number of new COVID-19 patients admitted to hospitals this week is up less than 1%, and the number of new COVID-19 deaths is up by about 4%.

    But when Omicron reaches those Americans who are more vulnerable to COVID-19, they’ll arrive at hospitals already overwhelmed from Delta, the flu, and nearly two years of pandemic burnout. At the same time, Omicron’s incredible capacity to spread will likely cause staffing shortages for many hospitals, as workers get breakthrough cases. On Thursday, the CDC announced that healthcare workers who get sick may shorten their quarantines if their facilities are facing shortages.

    New York City continues to be a major Omicron hotspot: according to city data, one in every 100 New Yorkers has tested positive for COVID-19 in the last week. In Manhattan, the number is one in 60. And these numbers don’t include people who tested positive on rapid at-home tests and weren’t able to confirm it with PCR. The city’s test positivity rate is over 10%, indicating that a lot of cases are going unreported in official data.

    Washington, D.C. has also emerged as a Omicron hotspot this week, with an average of over 1,000 new cases reported daily in the week ending December 22. That’s more than three times higher than the city’s case record at any other point during the pandemic. Meanwhile, several states have seen their case rates more than double in the past week, according to the latest Community Profile Report: Hawaii, Florida, Louisiana, Georgia, and Maryland.

    As Omicron sweeps across the country—aided by holiday travel and gatherings—we are about to face the reporting delays that come with every holiday. Public health workers from local agencies to the CDC are taking time off, while testing sites close for Christmas and millions of rapid tests go unreported.

    Erin Kissane, co-founder of the COVID Tracking Project, wrote about holiday data issues in The Atlantic this week. Her piece concludes:

    In this information vacuum, some of us will tend toward caution and others toward risk. By the time Americans find out the results of our collective actions, the country will have weeks of new cases—an unknown proportion of which will turn into hospitalizations and deaths—baked in. In the meantime, the CDC’s COVID Data Tracker Weekly Review has wished us all a safe and happy holiday and gone on break until January 7, 2022.

    more national numbers