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. Link to the CDC update: cdc.gov/bird-flu/spotl…

PSA (again): *Never* use the last 3 or 4 days of WWscan averages. They're always wrong, and I keep seeing this mistake being made. Half the time it's a straight line up or down. The midwest showed a vertical spike a couple days ago then it got reduced by 40% a day later.

https://twitter.com/CovidDataReport/status/1870158477332496828

@WastewaterSCAN is a fantastic resource, but it has an averaging issue in the latest few data points, as they dont have samples from all of their sites yet, so it's not comparing apples to apples. They should consider averaging to tmax-4 days in their algorithm.

Dec 16th update:

Increasing numbers this week as the holiday season kicks in. I believe the prior week was undersampled and this week was oversampled. ED data shows a slower rise over 2 wks (next post)

🔸286,000 new infections/day
🔸1 in every 112 people currently infected Emergency department data is currently 5 more days up to date than WW, and the trend looks quite different. Slow, steady increases. The reality may lie somewhere between them. I didn't post a WW update last week because I thought the decrease was a mirage.

Updated December-Early January Forecast:

Given recent data, the expected peak has decreased even further, and the range has shrunk.

This is now guaranteed to be a record low for Holiday infection rates, hospitalization, and deaths. A comparison of Holiday surge estimates from 2020 to 2024 shows just how unusual this prediction is.

Ok, this is actually concerning. The sequence of the hospitalized teen with H5N1 has been released. Both of these mutation sites are known to impact α2,6 binding that is needed for human to human transmissibility.

Need top experts on H5N1 to immediately to look into this.

https://twitter.com/jbloom_lab/status/1857817755199877451

⚠️The right mutations at these sites can, on paper, significantly increase h-h transmission. That's why there needs to be immediate focus on this sample. It's somewhat unclear if the mutations occurred in this patient or prior to their infection.

FYI:
All of the news stories of the sudden jump in severity of XEC comes from a dentist in the UK (Dr. Snieguole Geige) who most likely does not even know that it's only been 1/6 infections over the past month.

It's nearly impossible to judge any severity change this early.
This is not a knock for dentist speaking about covid. This is not my day job either. Sci/docs have made important contributions studying this virus even though it's outside their field. The issue:
🔸️Big claim
🔸️No data in hand
🔸️No evidence this Dr studies covid

Outlook for Fall and Winter:

This is not an official forecast, rather a general idea of how I anticipate fall and winter Covid trends to look at the moment, with XEC being the main growing variant.
⚠️A strong new variant would change this relatively positive outlook. The winter wave would be lead by the Northeast followed by the Midwest in terms of prevalence.

Note: I've been sitting on this outlook for 3 weeks, but waited to post it until we could see if XEC had stronger competition. That hasn't happened yet.

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. 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 ⬆️

July 19th update:

Another substantial increase this week (+26%). Wastewater signal now higher than last summer's peak, and over a month earlier.

🔸780,000 new infections/day
🔸1 in every 43 people currently infected
🔸45% higher than 12 month avg. Ratio of people currently infected by region:

Midwest: 1 in 59 ⬆️
South: 1 in 34 ⬆️
Northest: 1 in 73 ⬆️
West: 1 in 25 ⬆️

Largest spike AA evolutionary jumps from 2020-2024, plotted:

BA.1 Omiron's top spot was followed closely by JN.1 Pirola, and both stand well above the rest over the past 4 years. Viewed from a different lens of total AA spike divergence from the current lineages, JN.1 takes the top spot. This is branch to branch distance. Also note BA.2 divergence from BA.1.

The cost of preventing a pandemic is far lower than the cost of dealing with a pandemic. The current response to H5N1 in bovine needs to be dramatically increased.
1) Federal funds for compensation of lost profits on H5N1 farms (increases cooperation)
2) Abundant sequencing of.. H5N1 positive cows and mammals on or near outbreak farms
3) Ramp up testing of farms and farm animals
4) Detailed sequencing metadata: date, location, etc.
5) Guarantee privacy on any humans with symptoms, test, trace, isolate, seq any positives
6) Guarantee immunity for...

What is "FLiRT"?

FLiRT is the clever nickname for two mutations on the spike protein of the highly mutated variant "Pirola", that accounts for >99% of all Covid right now.
F->L at position 456 and R->T at 346.
Both escape mutations were present last year, but never on Pirola. The two mutations are like makeup and lipstick to disguise the virus a bit more to sneak past some of your antibodies from prior infection and vaccination. And she wears it well.

A set of 8 highly mutated variant designated BA.2.87.1 were released from South Africa today from Sept-Nov 2023.

While this deserves close watch, at this point, I don't think it's as concerning as the arrival of Pirola. I'll explain my reasoning:

1/

https://twitter.com/Tuliodna/status/1752996491948327126

It's apparently been 4 months since the first sample collection date, and it still hasnt been detected in any other country that does sequencing.

When Pirola first appeared, there were sequences spotted all over the world within a week or two of first detection.

2/

Biobot update 1/23/2024:

Wastewater receding quickly off of the peak, though still near 1 million new infections a day in America. Decline will continue.

🔸990,000 new infections/day
🔸1 in every 330 became infected today
🔸1 in every 33 people currently infected My latest model run forecasts a steady decline of infections, with no variants competing for dominance against JN.1.

https://twitter.com/JPWeiland/status/1749233202663768282

Wastewater update:

Biobot had adjusted their last two weekly estimates down a bit. My Nov. 30th model missed the peak number by 0.6% 😅. Numbers still very high but dropping.

🔸1,270,000 new infections/day
🔸1 in every 26 Americans currently infected

https://twitter.com/JPWeiland/status/1730709723983261975

This model was made on Nov 30, when our last biobot data point was from 11/22, 5 full weeks out from the peak readings.

In my opinion, 68% XBB is misleading. TODAY it's already less than 50% and dropping like a rock. People probably don't care what the situation was 3 weeks ago.

They want to know what's happening *now* and what is going to happen.

No mention of the fast growth from JN.1.

https://twitter.com/WHO/status/1736340999918535150

This is very simple to explain. The BA.2.86 descendent JN.1 is quickly outcompeting and displacing the XBB sublineages, and is pushing metrics upwards in many countries.

Why are we dancing around the facts?

This is why we haven't changed Pirola's name for JN.1. This quick evolution was actually predicted by our team as part of Pirola. Even the exact site it needed (S:455) was predicted by members of this team (see @SolidEvidence quote in next tweet from September)

https://twitter.com/JPWeiland/status/1697383732540236275

BA.2.86 was able to compete equally with any of the fastest lineages out there, even though it was still very weak against class 1 antibodies. Marc Johnson noted the 455 mutation would give Pirola its full potential, before it even evolved.

https://twitter.com/SolidEvidence/status/1707099377641415036

I can help explain with models why trajectory changes "around 50% prevalence" from a growing escape variant/group and why it's a useful *rule of thumb*.

Plot it on a log chart. 40-60% is where the elbow is. Doesn't guarentee a wave, but a change in trajectory, absolutely.



The faster the growth, the *sharper* the elbow. Slower growth? Weak elbow. Multiple variants growing at different speeds? Multiple smaller elbows. JN.1 has enough growth to push numbers up in most countries.

Emergency room visits for Covid seeing a sharp increase in Ile-de-France, where Pirola (JN.1) has recently gained dominance.

We've been expecting this while we watched JN.1 grow. We also see new hospital admissions increasing. The Pirola wave has arrived in Ile-de-France.

Note the data source unfortunately only goes back to week 52 of 2022.

Why did XBB.1.5 not cause as big of an impact as BQ or the F456L group this summer, though it had a stronger growth advantage? I think we have some answers.

First off, it hit at an ideal time, right after the holiday surge, but I don't think that's the full explanation.

1/3 We also have to consider why each variant has growth advantage.

XBB.1.5's "trick" was that it had better ace binding, not that it had better immune escape. So it didn't open up a new pool of susceptibles, it just cleaned up the current pool faster.

We now have updated data from the CDC and Biobot to compare to the forecasts I've put out. This thread are the results vs model, including all my models from earlier this year.

Please evaluate to check my forecast accuracy!

First, the hosp "range" near the peak. Next, an "true infections/day" wastewater calibration forecast. Current numbers are almost spot on from my forecast after 3 additional weeks of data. As I expected, the "upswing" in late Sept. was a mirage.