SARS-CoV-2 Update for April 26th
My concern for a potential new wave is at its highest since last fall. Vaccination, ventilation, and/or high-quality masks remain effective tools regardless of what happens.
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Throughout the pandemic, I’ve attempted to follow the data, read a broad range of experts, disregard preconceptions and biases, and reason toward conclusions, whatever they were.
On November 14th, I wrote “The Winter Wave Is Already Here,” arguing that, despite a plateau in national cases, the first signs of another wave were detectable. The emergence of the Omicron variant a few weeks later only poured gasoline on the fire, and this past winter was the largest wave of cases of the entire pandemic.
In the previous update on February 27th, I argued that the American ‘immunity wall’ would hold strong “for the next several months” due to a combination of an extreme number of Omicron infections, the majority of the country being vaccinated, and the spring’s warmer weather. Since then, while many nations have succumb to a large Omicron BA.2 wave, America hasn’t.
The United Kingdom publishes detailed reports on vaccine effectiveness (latest here, full archive here) and it’s clear that the vaccines have similar effectiveness against both BA.1 and BA.2 (below). Moreover, re-infection by BA.2 after BA.1 infection is rare. Taken together, this suggests that BA.2’s displacement of BA.1 is mainly a transmission advantage, not an immune-escape advantage (i.e. it spreads more rapidly between people without immunity, but mostly doesn’t circumvent prior immunity).
In other words, since the United States did an extremely poor job handling both the Delta1 and Omicron BA.1 variants, our ‘immunity-wall’ was much stronger than other nations’ toward BA.2.
However, cases in the United States have been trending upward, and rather significantly. The seven-day average of daily cases is 51,279. This almost double the recent nadir on April 5th of 26,526.
If you follow me on Twitter, you’ll have seen multiple posts since March about the potential for a small, regionalized wave, just like the Alpha wave in April 2021 wave that was concentrated in Michigan.
And for the most part, this is what has occurred (current case map below), with the concentration of cases in the Northeast and Puerto Rico.
Given that both Michigan and the Northeast are in the northern latitudes of the United States, this might suggest that seasonal effects in April are not strong enough to keep cases under control in the northern parts of the Eastern US .
While it is quite possible that the wave remains small and fades as we move deeper into spring, I believe that there is a real chance that we’re in the beginning of a serious wave.
Omicron BA.2.12.1
Evolution doesn’t stop. As BA.2 spread, it branched into (so-far) nearly two dozen sub-lineages. Moreover, BA.3, BA.4, and BA.5 evolved.
As we’ve covered in the past, most mutations have little-to-no effect. Sometimes, they have a large effect (think the Alpha, Beta, Delta, etc. variants).
While it is still early, the evidence suggests that subvariant BA.2.12.1 could potentially be the next major variant-of-concern and it’s spreading rapidly within the United States, now accounting for ~29% of total sequences in the nation.
Now, a rapid rise in a variant doesn’t necessarily signal a wave. We just discussed how BA.2’s rise left the United States mostly unscathed (though it hit many other nations hard).
What is concerning about BA.2.12.1 relates to BA.4 and BA.5.
BA.4 and BA.5 have rapidly displaced BA.2 from South Africa (which has a great genomic surveillance program; remember that South African teams were the first to identify Omicron). This displacement is also leading to an exponential increase in cases in a nation that has already had four major waves.
This is potentially concerning because BA.4 and BA.5 have mutations (specifically the 486V mutation) that confer additional immune-escape relative to BA.2. In other words, they can get around prior immunity to some degree.
While BA.2.12.1 does not have that specific mutation, it does carry several distinction mutations from BA.22 (here is an image that maps important mutations in BA.2, BA.2.12.1, BA.4, and BA.5).
If BA.2.12.1’s set of mutations provide additional immune-escape, like BA.4’s and BA.5’s do, then both vaccine-immunity and BA.1-immunity may not confer significant protection from infection (though it is almost certain that both still protect from severe disease and death). Thus, BA.2.12.1 could cause the next meaningful wave of cases.
Dr. Trevor Bedford has published charts of genomic surveillance from New York and Massachusetts (below, note the log scales on the Y-axis). Just as BA.2 displaced BA.1, BA.2.12.1 is displacing BA.2. And BA.2.12.1 growth more closely mirrors the total case growth in these states (i.e. total cases were still declining in NY in late Feb, when BA.2 was rising, and started to increase in early-to-mid March, when BA.2.12.1 emerged).3
I’ll reiterate that this is still very early and much is left to be researched. It is unknown how all of these mutations affect transmission and immunity. But there is concern; cases have doubled in the United States in the past three weeks.
Dr. Trevor Bedford believes that a “flu-like” scenario is most likely (i.e. small wave that fades into summer, like the 2021 Alpha wave) but leaves open the possibility of an “Omicron-like” event (i.e. significant immune-escape that will cause a moderate-to-severe wave of breakthrough infections).
I agree with Dr. Bedford and believe a small wave is most likely. I haven’t provided an update since late February because I did not believe BA.2 was a significant threat to the United States. But I’m updating now because this is also the most concerned that I have been since I wrote “The Winter Wave Is Already Here” last November.
I will be watching the situation closely.
Regardless of how the situation develops, the three best things you can do to protect yourself are:
Schedule your next vaccination if you’ve not received the recommended number for your age group (4th doses have been approved for the elderly and at-risk).
Focus on ventilation and air circulation, especially as the weather improves.
Wear high-quality masks (KN94/95s or N95s) and make sure they are tight around the nose and mouth.
Pandemic lessons will continue! Sorry, I’ve been busy with work and the farm. If you missed the first edition, it can be found here: “Pandemic Lesson #1: Ashes to Ashes, Dust to Dust.”
Prior infection from Delta provides significant protection from Omicron re-infection.
For BA.2.12.1, the focus in on the L452R mutation. To explain this shorthand, L452R means “the 452nd amino acid changed from a leucine to an arginine.”
This can really be seen in the first image from this section, the CDC’s variant tracker. The nadir of national cases was on April 5th and they have roughly doubled since then. It’s been BA.2.12.1 that has been taking share since April 5th.