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.
  • 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.

More variant reporting

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Last week, I introduced you to BA.2.86, a new Omicron variant that’s garnered attention among COVID-19 experts due to its significant mutations. We’ve learned a lot about BA.2.86 since last Sunday, though there are many unanswered questions to be answered …
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