More Omicron mutation in South Africa and the U.S.

Variants in Missouri sewersheds, shared on Twitter by Marc Johnson.

As cases rise in the U.S. and other parts of the world, Omicron subvariants are a continued culprit. Experts are watching closely to see if further mutations of the virus may become even more contagious, or may gain the ability to evade immunity from prior infections and vaccinations.

BA.4 and BA.5 in South Africa

When South African scientists sounded the alarm about Omicron in November, they identified three versions of the variant, called BA.1, BA.2, and BA.3. BA.1 first spread rapidly through South Africa and the rest of the world in December and January; BA.2 then outcompeted BA.1 to become the dominant strain globally.

Now, South African scientists are sounding the alarm again: this time about new Omicron lineages, dubbed BA.4 and BA.5. These two lineages have driven another new surge in the country, with both cases and hospital admissions rising sharply in recent weeks. The surge might be starting to slow, as of late this week, but it’s unclear if this trend will continue.

South Africa saw a huge BA.1 surge in November and December, then didn’t see much of a BA.2 bump—likely because so many people infected with BA.1 had immunity to this variant. But BA.4 and BA.5 may be a different story, according to a preprint from Alex Sigal and colleagues at the Africa Health Research Institute.

Sigal and his collaborators tested neutralizing antibodies—a commonly-studied aspect of immune system protection—from BA.1 against BA.4 and BA.5. They found that a BA.1 infection offered relatively limited protection against BA.4 and BA.5, especially if the person who had BA.1 was unvaccinated. “BA.4 and BA.5 have potential to result in a new infection wave,” the authors wrote.

This study is a preprint, not yet peer-reviewed. But it’s still a major warning sign for the U.S. and other countries: watch out for BA.4 and BA.5.

BA.2 subvariants in the U.S.

Meanwhile, here in the U.S., BA.2 continues to mutate and spread rapidly. The BA.2.12.1 subvariant, first identified by the New York State health department in mid-April as a sublineage that spreads even faster than BA.2, is now causing more than one-third of new COVID-19 cases in the country, according to CDC estimates.

In New York and New Jersey, BA.2.12.1 is causing over 60% of new cases; it’s no coincidence that these states are also reporting some of the highest case and hospitalization rates in the country right now. New England, mid-Atlantic, South, and Midwest states are also seeing high proportions of BA.2.12.1.

The CDC’s variant proportions estimates don’t yet include BA.4 and BA.5, but other reports suggest that these subvariants are already in the U.S. and starting to compete with our homegrown BA.2 lineages. Marc Johnson, a leading wastewater expert in Missouri, posted on Twitter yesterday that he’s seeing “a circus of Omicron sublineages” in his state, including BA.4 and BA.5.

Also worth noting: a new U.S. study (shared as a preprint last week) found that, actually, Omicron is not inherently less severe than other variants. In comparing hospitalization and mortality risks after accounting for vaccination and medical risk factors, the researchers behind this study found little difference between the Omicron wave and prior periods. While this study also has yet to be peer-reviewed, it doesn’t bode well for future Omicron-driven surges.

More variant data

HV.1, JN.1: Variants to watch this fall and how we’re tracking them
As winter approaches, pretty much every public health expert I follow is anticipating a COVID-19 surge. The size and severity of that surge may depend in part on SARS-CoV-2 variants. As a result, experts are closely watching a few current …
National numbers, September 17
For the second week in a row, available data suggest that the current COVID-19 surge may be turning around, or at least heading for a plateau. But there’s still a lot of coronavirus going around—and this will likely remain true …
New data on BA.2.86 suggest the fall booster may work well
Since BA.2.86 emerged a couple of weeks ago, scientists around the world have been racing to evaluate this variant. Several teams posted data in the last week, and the news is promising: while BA.2.86 does have an advantage over past …
Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows us
This week, the health department in New York City, where I live, announced that they’d identified new variant BA.2.86 in the city’s wastewater. I covered the news for local outlet Gothamist/WNYC, and the story got me thinking about how important …
Variant Q&A: Why scientists are concerned about BA.2.86, and which questions they’re still investigating
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 …
BA.2.86 is the latest variant to watch; send me your questions
Last week, several variant experts that I follow on Twitter started posting about a new SARS-CoV-2 variant, first detected in Israel. They initially called it Omicron BA.X while waiting for more details to emerge about the sequence; it’s now been …

Leave a Reply