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JWeiland Profile picture
@JPWeiland
Aug 17 • 5 tweets • 2 min read Twitter logo Read on Twitter
August 17th update (Biobot): US community spread is back up to "high" with an estimated 610,000 daily new infections.

Similar levels in all 4 US regions.

🔸610,000 new infections/day⬆️
🔸1 in every 550 new people were infected today
🔸1 in every 55 people currently infected Image
This rise is still due to EG.5.1, FL.5.1, and XBB.1.16.6 along with some immune waning.

It is not due to the new, heavily mutated variant BA.2.86. There was the US' first sequence reported today (Michigan). We are watching this one *very* closely.

Slide from @jbloom_lab Image
As some of us suspected past week, the "surprising" jump in Midwest cases last week was indeed an anomaly. It's back to matching the increases in the other 3 regions.

https://t.co/L6HifRTlOb
Image
The BA.2.86 variant that has very high "potential" could land anywhere in the bubble on this chart (note: not a probability map). First 4 sequences in a few short days on 3 contents is not a great sign. I'm still hoping it's just a "scariant" Image
The recent wave seen in wastewater is tracking pretty well to the model from a month ago. This wave was not unexpected.

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More from @JPWeiland

JWeiland Profile picture
Aug 14
The variants we've seen since 2022 each only have a few S mutations at a time, so their potential was limited.

This unnamed new one has 24.
Omicron had 32.

We don't know yet where this will land on this chart. Given the mutation profile, it has a much larger range of outcomes. Image
Maybe our exposure to other Omicrons will stunt it, and maybe it made too many advantage tradeoffs to be highly successful like Omicron initially was. We don't know yet. But we know it's quite different. Here is my count for new S mutations from EG.5.1 (blue also new). Image
@LongDesertTrain is one of the top experts on mutations. I trust his expertise on evaluating the new mutations.

He's been saying effectively the same thing: it has a high "potential" but we won't know until more sequences come in.

Read 5 tweets
JWeiland Profile picture
Jul 20
Model for next 5 weeks:

Anticipating increases into August, driven by EG.5.1, FL.1.5, and XBB.1.16.6.

Each of these have advantage over XBB.1.16, XBB.2.3 etc.

The lack of cases for the last 4 months is expected to have increased the number of people susceptable to infection. Image
It also makes sense that the Northeast is seeing the biggest uptick on wastewater, considering their levels of the faster variants are higher than the rest of the US.

21 day seq data from @RajlabN dashboard
Image
Image
The common driver between these variants seems to be the F456L mutation on the spike. They also have various other escape mutations.
Read 6 tweets
JWeiland Profile picture
Jul 14
I made a simple Omicron simulation with the following assumptions: R0=8 and avg. protection after infection is 9 months. No seasonal effect etc.

Then I applied NPI that cut the chance of infection per interaction by 7 in 10.

Found the results really interesting!
1/ Image
🔹️3 to 4 waves are expected per year with 0 NPI, even though about 1 infection/yr/capita
🔹️70% effective NPI reduces frequency of waves just less than 2 per year
🔹️But total infections over time were only reduced ~30%
🔹️All the waves started to dampen to flat over time
2/ Image
I didn't anticipate the difference in wave frequencies, but I did expect that the total reduction would be much less than 70%. The pool of susceptibles grows high enough to still create sizable waves.suppressed.
3/
Read 7 tweets
JWeiland Profile picture
Jul 9
This data is preliminary (so a lot of uncertainty still), and there isn't a ton of sequencing data, but:

There appears to be a new variant related to XBB.1.9 called FL.1.5.1 that appears to be growing rather quickly in the Dominican Republic.
I haven't been interested in any new variant in a good while, but this one might stand out. It appears to have gone from first sequenced case to dominant in less than a month.

I'll be keeping an eye on it and update as needed. More sequencing could show this is just a blip
The reason I'm posting about it is the apparent rapid rise in proportion coincides with a sudden increase in cases in the DR, even with presumibly less testing. This is additional indication that this variant could be important.
Read 5 tweets
JWeiland Profile picture
Jul 2
Okinawa is experiencing an unusual spike in hospitalizations..

We have almost 0 sequencing coming out of there.

It's so critical to keep timely global sequencing efforts going to get an early warning. 🧵
Because of sequencing:

It was obvious with Japan's waves last year that the variants spreading were not a threat to other nations.

It was also obvious in South Africa that the new variant there (Omicron) was a cause for global concern.
Listen, we might be out of the woods in terms of a Delta like severity strain reappearing. But we might not be. Early warning systems help hospitals prepare if we ever ran into that situation again

Sequencing is a huge tool for that, and those efforts are slowly evaporating
Read 4 tweets
JWeiland Profile picture
Jun 9
New Model for next 7 weeks, out to August:

The rise of the XBB.1.16* along with XBB.1.9* and XBB.2.3* should halt the decline of caseloads start to creep them back up.

XBB.1.16* with a 31% weekly advantage over background
This is what we've seen play out with XBB.1.16*. From the same starting point, India was far, far more affected by this variant.

The US has seen a 17% weekly rise of XBB.1.16 vs ~100% weekly rise in India. And that compounds.
The cause for the dramatic differences lie in recent experience with similar variants. The US has seen enough waves of similar variants in the past to retard the growth.

This is precisely what I've been predicting since April. Now we have data that proves it.
Read 7 tweets

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