Omicron updates: What we’ve learned since last week

Within days of its first identification, the Omicron variant has been found on every continent except Antarctica. Chart via GISAID, retrieved December 5.

There is still a lot we don’t know about the Omicron variant, first identified in Botswana and South Africa in late November. For the most part, what I wrote last Sunday remains true: this variant is spreading quickly in South Africa and has a number of mutations—some of which may correspond to increased capacity for transmission or evading prior immunity—but we don’t yet have enough information to determine how it may shape the next phase of the pandemic. 

Still, we’ve learned a few new things in the last week. Here’s a quick roundup:

  • More than 30 cases have been detected in the U.S., with the earliest detection in states with robust genetic surveillance. The first U.S. case was identified in California, in a San Francisco resident who had recently traveled to South Africa. As I pointed out on Twitter, California is one state that’s sequencing a lot of coronavirus genomes; combine that with San Francisco’s large international airport, and it may be unsurprising that the variant was first picked up there. The second U.S. case was identified in Minnesota; this state, too, has sequenced a lot of cases, with a lab at the University of Minnesota providing sequencing services for other Midwest states.
  • Omicron is spreading rapidly in South Africa. On Friday, South African scientists said that the variant may be spreading “more than twice as quickly as Delta,” according to the New York Times, though it may also be less contagious than Delta. This announcement aligns with modeling by computational biologist Trevor Bedford, who wrote on Saturday that Omicron appears to have a transmission advantage over Delta. “These are still very early estimates and all this will become more clear as we get comparable estimates from different geographies and with different methods,” Bedford wrote. “But ballpark current Rt of Omicron in South Africa of between 3 and 3.5 seems pretty reasonable.” Rt refers to how fast the virus is spreading; for context, Delta’s Rt when it first hit the U.S. was about 1.5.
  • Anime NYC may have been a superspreading event. The Minnesota resident who became the second Omicron case identified in the U.S. had attended Anime NYC, an anime convention held at the Javits Center between November 19 and 21. City and state officials urged other attendants of the convention to get tested; and a number of the Minnesota resident’s friends have tested positive, according to The Washington Post, though sequencing results are not yet available for these cases. Anime NYC attendees had to be vaccinated to attend, but could meet the requirement with just one dose received right before the convention. And photos from the convention show plenty of people disregarding the mask mandate. It’s too early to say, but I would not be surprised if Anime NYC turns out to be a superspreading event for Omicron.
  • A holiday party in Norway is another likely superspreading event. About 120 people attended a Christmas party in Oslo on November 26. As of this Friday, at least 13 attendees have been identified as Omicron cases, while a number of others have tested positive for COVID-19 (and are awaiting sequencing results). “Our working hypothesis is that at least half of the 120 participants were infected with the Omicron variant during the party,” Norwegian Institute of Public Health physician Preben Aavitsland told Reuters. “This makes this, for now, the largest Omicron outbreak outside South Africa.” Notably, this superspreading event occurred even though “all the attendees were fully vaccinated and had tested negative before the event,” Reuters reports.
  • Omicron appears to be more likely to reinfect people who’ve recovered from a previous COVID-19 case than past variants. On Thursday, South African scientists posted a preprint study suggesting that, when compared to the Delta and Beta variants, Omicron is more capable of reinfecting people who’ve previously had COVID-19. The finding comes from an analysis of over 35,000 reinfections among millions of positive COVID-19 tests. “Although there are a lot of uncertainties in the paper, it looks like an earlier infection only offers half as much protection against Omicron as it does against Delta,” writes Gretchen Vogel in Science, paraphrasing Emory University biostatistician Natalie Dean.
  • Omicron might cause less severe illness than other variants, but a lot more data are needed on this topic. On Saturday, the South African Medical Research Council posted a report that aligns with some other early reports about this variant: so far, patients infected with this variant seem to be getting less sick than those infected with previous coronavirus variants. Specifically: a lower share of Omicron patients in South Africa have required intensive care, oxygen support, or ventilators than physicians there have seen in previous COVID-19 waves. But this report, like other anecdotal reports, has been based on a small number of patients, and many of them have been younger—as older South Africans have been prioritized for vaccination. The number of severe Omicron cases may be low now, but may rise sharply in the coming weeks, Financial Times reporter John Burn-Murdoch pointed out in a Twitter thread responding to the report. Also, it’s way too soon to know how many of the so-called mild Omicron cases thus far may turn into Long COVID. So, a lot of experts are skeptical that Omicron is actually more mild—basically, we need more data. 

I’ll end the post with this excellent thread from Muge Cevik, infectious disease expert at the University of St. Andrews, discussing the many uncertainties surrounding Omicron:

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