Omicron updates: BA.2, vaccine effectiveness, and more

As of February 5, the CDC is now including BA.2 in its variant prevalence estimates. Screenshot from the CDC dashboard.

A few Omicron-related news items for this week:

  • The CDC added BA.2 to its variant prevalence estimates. As I mentioned in today’s National Numbers post, the CDC is now splitting out its estimates of Omicron prevalence in the U.S. into original Omicron, also called B.1.1.529 or BA.1, and BA.2—a sister strain that’s capable of spreading faster than original Omicron. BA.2 has become the dominant variant in some parts of Europe and Asia, but seems to be present in the U.S. in fairly low numbers so far: the CDC estimates it caused about 3.6% of new cases nationwide in the week ending February 5, with a 95% confidence interval of 1.8% to 6.8%. The remainder of new cases last week were caused by original Omicron.
  • CDC describes its expanded genomic surveillance efforts in an MMWR study released this week. Between June 2021 and January 2022, the agency has extended its ability to monitor new variants spreading in the U.S., incorporating public repositories like GISAID into CDC data collection and developing modeling techniques that can produce more timely estimates of variant prevalence. (Remember: all variant data are weeks old, so the CDC uses modeling to predict the present.) According to the MMWR study, genomic sequencing capacity in the U.S. tripled from early 2021 to the second half of the year.
  • Vaccine effectiveness from a booster shot wanes several months after vaccination. In another MMWR study released this week, the CDC reports on mRNA vaccine effectiveness after two and three doses, based on data from a hospital network including hundreds of thousands of patients in 10 states. During the U.S.’s Omicron surge, researchers found, vaccine effectiveness against COVID-19 hospitalization was 91% two months after a third dose—but declined to 78% four months afterward. It’s unclear whether this declining effectiveness is a direct result of Omicron getting past the vaccine’s defenses, or whether we’d see similar declines with other variants. Also, the CDC’s findings are not stratified by age or other factors that make people more vulnerable to severe COVID-19.
  • Updated monoclonal antibody treatment from Eli Lilly gets FDA authorization. During the Omicron surge, one challenge for healthcare providers has been that, out of three monoclonal antibody treatments authorized by the FDA, only one retained effectiveness against this variant. (Monoclonal antibody treatments provide a boost to the immune system for vulnerable patients.) This week, however, the FDA authorized an updated version of Eli Lilly’s treatment that does work against Omicron, including against the BA.2 lineage. The federal government has purchased 600,000 courses of this new treatment.
  • More data released on South Africa’s mild Omicron wave. A new paper published in JAMA this week, from researchers at a healthcare provider in South Africa, compares COVID-19 hospitalizations during the Omicron surge to past surges. Among patients who visited the 49 hospitals in this provider’s network, about 41% of those who went to an emergency department with a positive COVID-19 test were admitted to the hospital during the Omicron surge—compared to almost 70% during South Africa’s prior surges. The paper provides additional evidence that Omicron is less likely to cause severe COVID-19 than past variants, though this likelihood is tied in part to high levels of vaccination and past infection in South Africa and other countries.
  • Omicron has been identified in white-tailed deer. New York City was an early Omicron hotspot in the U.S.; and the variant has been passed onto white-tailed deer in Staten Island, according to a new preprint posted this week (and not yet peer-reviewed). Scientists have previously identified coronavirus infections in 13 states, but finding Omicron is particularly concerning for researchers. “The circulation of the virus in deer provides opportunities for it to adapt and evolve,” Vivek Kapur, a veterinary microbiologist who was involved in the Staten Island study, told the New York Times. 

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More variant reporting

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Across the U.S., COVID-19 spread continues at a moderately high plateau as newer versions of Omicron compete with XBB.1.5. Officially-reported cases and new hospitalizations declined by 7% and 8% respectively, compared to the prior week.
National numbers, April 16
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National numbers, April 9
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