COVID-19 Data Dispatch

Tag: omicron

  • 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
  • COVID source callout: The CDC’s slow variant updates

    COVID source callout: The CDC’s slow variant updates

    Due to reporting delays, the CDC’s variant data fails to convey Omicron’s rapid spread through the country. Chart retrieved on December 19.

    On Tuesday, the CDC updated the Variant Proportions tab of its COVID-19 data dashboard. This update included some alarming information: Omicron had jumped from causing about 0.4% of cases in the week ending December 4, to 2.9% of cases in the week ending December 11. In the New York and New Jersey area, it was causing 13% of cases.

    At this rate of increase, we can anticipate that, as of yesterday (December 18), Omicron is already causing roughly 21% of cases in the U.S.—and more than 90% of cases in New York and New Jersey. But because of the CDC’s delayed updates, the majority of people who go look at the CDC’s dashboard anytime before its next update, this coming Tuesday, would likely presume that Omicron is still causing a tiny minority of cases.

    I’ve written before about the delays in collecting and reporting coronavirus sequencing data. It can take weeks for a COVID-19 test sample to go from a patient’s nose to a nationwide sequencing database, which leads to inevitable lags in the U.S.’s genomic surveillance. This is understandable. But in a crisis moment, when Omicron is here and spreading rapidly, the agency should clearly label the lags and update its projections to provide a more accurate view of the variant’s growth. 

    What’s more, the CDC’s data update on Tuesday was not communicated widely; Director Dr. Rochelle Walensky gave a TODAY Show interview, and that was about it.

    more source spotlights
  • Omicron updates: Spreading rapidly in the U.S.

    Omicron updates: Spreading rapidly in the U.S.

    We keep learning about this dangerous variant as it spreads through the U.S. and the world. A few major updates from this week:

    • Omicron is spreading rapidly in the U.S. Last Tuesday, the CDC announced that Omicron had gone from causing 0.4% of new COVID-19 cases nationwide in the week ending December 4, to 2.9% of cases in the week ending December 11. That’s a seven-fold increase over the course of a week; the variant appears to be doubling every two to three days, based on data from the U.K. We can assume that it will be the dominant variant in the U.S. by the end of December, if not sooner.
    • U.K. data provides information on just how fast Omicron can spread. The U.K.’s comprehensive genomic surveillance system, combined with its unified national public health system, allows British researchers to analyze their country’s Omicron cases in high detail. According to the latest briefing from the U.K. Health Security Agency (summarized by Meaghan Kall): risk of reinfection with Omicron is three to four times higher than with Delta; risk of household transmission with Omicron is two to three times higher than with Delta; and the variant is doubling every two days—or even every 1.5 days, in some parts of the U.K.
    Omicron’s rapid spread in London, compared with prior Delta cases. Chart by Theo Sanderson; see his Twitter for the full animated version.

    • New research from Hong Kong provides insight into why Omicron spreads so fast. Preliminary data from a Hong Kong University research team suggests that, within 24 hours of an Omicron infection, the virus “multiplied about 70 times faster inside respiratory-tract tissue than the Delta variant,” reports Megan Molteni at STAT News. More virus in the respiratory tract means more virus getting out into the air, Molteni explains. At the same time, the variant seems to be worse at multiplying within lung tissue, which may contribute to milder disease. While the Hong Kong study has yet to be peer reviewed, this finding aligns with reports of superspreading events among fully vaccinated people.
    • Skepticism about “Omicron being mild” continues despite more reports. Early this week, the largest health insurance company in South Africa posted results of a study examining the country’s Omicron wave. The study found that risk of hospitalization was 29% lower for Omicron patients than it had been during the country’s spring 2020 COVID-19 surge. While this finding follows other reports out of South Africa, experts are still skeptical: in part because it can take weeks for a coronavirus infection to progress to hospitalization, and in part because South Africa’s population has a lot of prior immunity from past surges and vaccinations. Also, a “milder” variant that’s more transmissible can still lead to significantly more hospitalizations.
    • We’re getting more evidence that vaccination protects against severe disease from Omicron. Basically: two shots are good, three shots are better. “Though these data are preliminary, they suggest that getting a booster will help protect people already vaccinated from breakthrough or possible severe infections with Omicron during the winter months,” writes NIH Director Dr. Francis Collins in a recent blog post summarizing both laboratory and real-world studies. If you’re eligible for a booster and haven’t yet gotten it, now is a great time.
    • But: We don’t know how well vaccines protect against Long COVID from an Omicron infection. As many experts continue to say that Omicron cases are mild for those who are vaccinated, the Long COVID experts and advocates I follow have pointed out that a mild breakthrough case can still lead to this prolonged condition. “Omicron is a huge individual threat,” wrote Long COVID researcher Hannah Davis on Twitter recently. “A 15-30% chance of being disabled for at least a year, but likely for the rest of your life, is a bigger threat than most of us ever faced ever before the pandemic.”
    • New York City is an Omicron hotspot in the U.S. As I noted in today’s National Numbers post, this variant has clearly hit NYC, as seen in record case numbers and felt in long lines for testing throughout the city. According to CDC estimates, Omicron was causing about 13% of new cases reported in New York and New Jersey in the week ending December 11. One week later, knowing how fast Omicron has outcompeted Delta in the U.K. and elsewhere, we can assume that it’s now causing the majority of cases in this region.
    • Other U.S. states and regions may be behind in their Omicron sequencing, so assume it’s spreading in your area even if it hasn’t been officially identified yet. As I’ve written before, genomic surveillance in the U.S. is geographically very spotty. NYC is a clear hotspot, but it’s also a city with a lot of sequencing infrastructure. In other parts of the country, Omicron may not have been formally identified yet—but that doesn’t mean it isn’t spreading. Take Orlando, Florida as an example: wastewater sampling in the surrounding county found that Omicron was completely dominating the community this week, according to AP, even though “practically no cases of clinical infection” have been reported.
    • Good news: South Africa’s case numbers are now trending down. As of yesterday, COVID-19 case numbers in Gauteng, the center of South Africa’s COVID-19 outbreak, as well as in other parts of the country, seem to be turning around. Computational biologist Trevor Bedford offered some potential explanations in an interview with New York Magazine: limited testing capacity and milder disease may lead to underreporting of COVID-19 cases in South Africa; less of the population may be susceptible due to prior immunity; and the variant may spread so fast that it can quickly burn through social networks and other avenues of transmission. We’ll need to see whether South Africa’s decline holds, and whether we see similar patterns in other Omicron hotspots.
    • The U.S. is not prepared for an Omicron surge. If you haven’t yet, take some time today to read Ed Yong’s latest feature in The Atlantic, which discusses how the U.S. has failed to learn from past COVID-19 outbreaks and prepare for the Omicron surge that has already arrived. “Rather than trying to beat the coronavirus one booster at a time, the country needs to do what it has always needed to do—build systems and enact policies that protect the health of entire communities, especially the most vulnerable ones,” Yong writes.
    • Omicron has altered the trajectory of the pandemic. Another piece to take time for today is this article in Science by Kai Kupferschmidt, discussing the “really, really tough winter” that scientists now see coming. Kupferschmidt explains that, even if many Omicron cases are mild, the variant is still spreading fast enough that it could land a lot of people in the hospital. In addition, the variant “may bring other, unpleasant evolutionary surprises” if future coronavirus variants evolve out of Omicron, Kupferschmidt writes.

    More variant reporting

  • National numbers, December 19

    National numbers, December 19

    COVID-19 cases have increased sharply in New York City in the past week, to over 500 new cases for every 100,000 people city-wide. Chart via NYC Health, retrieved December 19.

    In the past week (December 11 through 17), the U.S. reported about 860,000 new cases, according to the CDC. This amounts to:

    • An average of 122,000 new cases each day
    • 261 total new cases for every 100,000 Americans
    • 2% more new cases than last week (December 4-10)

    Last week, America also saw:

    • 55,000 new COVID-19 patients admitted to hospitals (17 for every 100,000 people)
    • 8,300 new COVID-19 deaths (2.5 for every 100,000 people)
    • 2.9% of new cases are Omicron-caused (as of December 11)
    • An average of 1.6 million vaccinations per day (including booster shots; per Bloomberg)

    The Omicron surge has arrived in the U.S. While national COVID-19 cases are not significantly up from last week to this week, last week’s bump in the numbers from delayed Thanksgiving reporting has been replaced with a true increase, thanks to the combined pressures of both Delta and Omicron.

    Hospitalizations are also increasing, with about 60,000 Americans hospitalized with COVID-19 nationwide as of December 15—a 9% increase from the previous week. The number of Americans dying from COVID-19 each day is increasing as well, now at about 1,200 deaths a day.

    Omicron’s impact feels particularly pronounced in New York City, where I live, as the city’s case rate more than doubled in the first two weeks of December. This past week, the city’s test positivity rate doubled in the span of three days. Yesterday, New York state reported a record number of new COVID-19 cases (about 22,000), with more than half of those cases reported in NYC.

    To be fair, the case rates reported in NYC this week are probably lower than the true case rates during spring 2020, as testing wasn’t widely available during the city’s first COVID-19 surge. But on a personal level, this city’s current Omicron surge is undeniable: testing lines stretch around the block, and everyone from my old college friends to my local City Council representative is reporting a breakthrough case. I personally have yet to catch “the Media Variant,” but I’m rapid testing frequently and avoiding indoor activities as I prepare to visit my parents for Christmas.

    Omicron was causing 13% of new COVID-19 cases in New York and New Jersey in the week ending December 11. By today, it’s likely causing the majority of new cases. But the NYC region isn’t the only part of the country seeing rapid case increases: Hawaii, Florida, Connecticut, Maine, and D.C. have all reported more than a 30% increase in cases from the previous week to this one, according to the latest Community Profile Report. Rhode Island, New Hampshire, Maine, and other Northern states have the highest cases per capita.

    Vaccines, particularly booster shots, can protect against this dangerous variant (more on that later in this issue). While 61% of Americans are fully vaccinated, according to the CDC, less than 30% have received booster doses. This includes about 53% of Americans over 65, even though seniors were one of the first groups become eligible for boosters—and are among those most in need of this additional protection.

    more national numbers