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JWeiland Profile picture
@JPWeiland
Aug 9, 2024 • 5 tweets • 2 min read • Read on X
August 9th update:

Estimated daily infections reach 1 million. Remarkable infection rates for a summer surge. Only BA.2->BA.5 was higher in the 2022 summer.

🔸1,000,000 new infections/day
🔸1 in every 33 people currently infected
🔸74% higher than 12 month avg. Image
Prevalence by region:

Every region increasing in wastewater levels. Both the South and West are at roughly 12 month highs.

Midwest: 1 in 42 ⬆️
South: 1 in 25 ⬆️
Northest: 1 in 58 ⬆️
West: 1 in 22 ⬆️ Image
Make no mistake- though waning is a very important driver of waves, variant evolution plays a large role in the differences between years.

Last summer was "just" F456L mutation on XBBs.

This year we had FLiRT->KP.3->KP.3.1.1 back to back, each quickly overtaking the last. Image
This was part of the concern with the Pirola variant tree: a huge evolutionary jump on the spike may allow for a lot more optimization in the months after arrival. We saw the same thing with Omicron: many meaningful mutations in the first 9 months after it arrived.
@cml199002 Also note: this data is for the US, not Alberta. I don't know what the current stats are for Alberta.

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More from @JPWeiland

JWeiland Profile picture
May 19
XFG* looks to me like the likely summer wave generator. From modeling NY growth:

🔸️~65% wkly advantage
🔸️Fastest since JN.1 or KP.2
🔸️Slower than the combo of KP.2/KP.3/KP.3.1.1
🔸️Dominance in NY within 2 weeks
🔸️Dominance in US in June Image
I focused on New York state because XFG* is far ahead there relative to anywhere else, and they still have a lot of sequencing. It will take some time to evaluate it in other places to confirm the growth rates.
I used @RajlabN 's Tableau to determine sequence frequencies over time. Thanks Raj
Read 4 tweets
JWeiland Profile picture
Apr 27
I'm not sure if we'll get quite as low in transmission this spring as the minimums the last 2 years because of a very low winter peak not as efficiently cleaning up the susceptables. A bit of uncharted territory, since immunity is waning but we don't have strong variant growth. Image
Even without a strongly growing variant, I'm still confident we will have a decently sized summer wave. Parts of the south and west basically had no wave at all in the winter, thus the susceptibility is slowly increasing. Image
But the question is, how long will the decline hold on until we start the summer increase without a new fast variant? If the decline hangs on until late May or June, we may get below 2023/24's lows.
Read 5 tweets
JWeiland Profile picture
Apr 14
🧬 Variant Evolution Rate Since 2020

We witnessed a huge weekly growth advantage in new variants for the first year after Omicron arrived, and then to a lesser extent after Pirola. Now we have 9 months of the lowest growth advantages since 2020. 🧵 Image
Both Alpha and Delta had only moderate divergence from their predecessors, but they increased transmission in a time with a mountain of people with no immunity to severe disease. Their waves of cases were moderate, but the waves of death and hospitalization were huge. Image
Omicron came in and wiped more than half of immunity to infection without heavily impacting resistances to severe disease. What it also did was open up a lot of new evolutionary potential for immune escape, and BA.2, BA.5, and XBBs demonstrate that impact well
Read 6 tweets
JWeiland Profile picture
Mar 11
▶️ An interesting saltation was found yesterday by variant trackers.. 3 samples of a highly divergent BA.3 in South Africa with 57 AA spike mutations. Samples were taken Nov-Jan, so it doesn't have a ton of speed (at least yet), but is worth watching. 1/ Image
It currently lacks both 455 and 456 mutations that have been critical for immune escape in the last 16 months. If it is able to find those before its candle runs out, I think it has a chance to outcompete the current variants. 2/
I completely agree with this take from @LongDesertTrain - I was pessimistic about BA.2.87 due to the uphill battle against JN.1. The current relatively slow movement of variants could give this new BA.3 enough time to evolve mutations to jump start spread
Read 5 tweets
JWeiland Profile picture
Jan 20
How accurate are my infection estimates? The calibration is based on 2020-early2022 historical WW&case data, so we have no easy way to validate today's calibration in the US.

But we do have *measured* UK prevalence in December 2023 that arrives very close to my US estimates. Image
This is unfortunately about as good of validation as we can have since we don't measure prevalence directly in the US. UK and US are obviously not the same entity, but they do tend to spike together in December each year. Their data was not used to feed my calibration, so it..
..is reassuring that they arrived at very similar numbers on their actual prevalence measurements.

It would be great if the US did a similar measured prevalence study of their own, but we don't have anything like that at the moment.
Read 4 tweets
JWeiland Profile picture
Dec 27, 2024
The sequence from the 2nd severe H5N1 case in North America (Louisiana) has been released, and again, ⚠️has mutations that favor a2,6. Is it simply a coincidence that both severe cases have 2,6 favoring mutations? Or is this an indication of severity with 2,6?
I don't like this. Image
Link to the CDC update: cdc.gov/bird-flu/spotl…
@HelenBranswell wrote about this development further in STAT
Read 4 tweets

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