Still around 13 new cases per 100K per day, still climbing at about 30 percent per week. The only change today is that now, all the regions of the U.S. are showing increases in cases.
The more interesting news is that CDC is tracking a new sub-strain of Omicron (BA.2.12.1). The incidence of this new strain appears to explain why New York/New England has had such a rise in cases, while much of the rest of the country has not.
Data source for this and other graphs of new case counts: Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 4/20/2022, from https://github.com/nytimes/covid-19-data.” The NY Times U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
I just happened to glance at the CDC’s COVID variant proportions page — as one does, from time to time — and noticed that it didn’t look the way I expected it to look. Based on what showed up last week, I expected it to be more-or-less one solid strip of son-of-Omicron (BA.2). So much so that I didn’t even bother to check it when the new data came out on Tuesday, because I assumed there’d be nothing new.
Last week’s variant mix:
Source: CDC COVID data tracker, accessed circa 4/12/2021.
But instead, this week, there’s a brand new strain that the CDC projects will have accounted for about 20% of the most recent cases. It’s BA.2.12.1, which makes it the grandson of son-of-Omicron.
(Each “.” separates a distinct sub-mutation, so BA.2.12.1 is the first recognized sub-mutation, of the 12th recognized sub-mutation, of son-of-Omicron BA.2. You’re only allowed three “.”, after which, if there’s yet another substrain, you give its parent a new letter-based designation and keep going. The original strain of COVID-19 that spread to most of the world was designated B. The original Omicron strain was B.1.1.529. But when that had a significant sub-mutation, they assigned the letters BA to B.1.1.519, and that particular submutation (son-of-Omicron) became known as BA.2. So BA.2 is equivalent to B.1.1.529.2. This new strain is equivalent to B.1.1.529.2.12.1. It is now six generations removed from the original (Wuhan) strain of COVID-19.)
This week’s variant mix:
Source: CDC COVID data tracker, accessed circa 4/21/2021.
By this time, we all know the drill. Natural selection drives the virus to be ever-more-contagious. And when a variant comes out of nowhere and grows like a weed, that’s because it’s more contagious than whatever it is displacing. And, plus-or-minus the uncertainty in the estimate, it looks like BA.2.12.2’s share of new cases is doubling every week.
The only figure I see cited is “27% more contagious than BA.2”. At this point, the chain of estimated R-nought values for these viruses has gotten so long that I’ve lost track of where we are. Last I recall, Delta had an R-nought of about five. Omicron came in at 15, which is why the Omicron wave was so huge compared to all prior waves. Then son-of-Omicron (BA.2) was something like a 21. So this latest one would come in around 26-ish? Even further off-the-charts for infectiousness than the prior strains were.
There’s also some controversy as to whether this is more contagious (higher R-nought), or just somewhat better at getting past the body’s immune system (“immune escape”). I’m not even really sure what the academic issue is there, except that you’ll see a different set of infected individuals if it’s merely more contagious (no impact on relative protection provided by vaccine), versus higher immune escape (vaccine provides relatively less protection).
In any case, the interesting thing is that this may provide some explanation for why the New England/Mid-Atlantic area has been hardest hit so far in the second U.S. Omicron wave. I’ve noted in the past that son-of-Omicron itself (BA.2) did not seem to explain regional differences in new-case growth. But, by eye, regional variation of this sub-strain does appear correlated with recent new-case growth:
Source: CDC data tracker accessed 4/21/2022
In particular, focusing on the red segment of the pie charts above, note the highest concentration in the Northeast, and the near-complete absence in the south-central region (centering around Texas). Obviously, this one factor doesn’t explain all the variation in growth, but at least it aligns with the fastest-growth and slowest-growth regions of the U.S.
In terms of severity of illness, all that anyone will say is that it doesn’t appear to generate cases that are any more severe than the BA.2 strain that it replaces. And that’s unfortunate, because if, by chance, this one turned out to be even milder than BA.2, that would give us the final piece of the puzzle. That would explain why the rise in hospitalizations is not keeping pace with the rise in cases.
But, so far, nobody is saying that. All they’re saying is that there’s no evidence that it’s any worse.
In any case, the emergence of this new strain offers some explanation of why the U.S. Northeast was the first to enter the second Omicron wave, and why the South Central region was the last.
