Solid Evidence

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

The fear is that with time the virus will adapt to mammalian transmission and start infecting other mammalian species, which is happening already (and we aren’t doing much about it). 12/ www.propublica.org/article/bird...

telegraph.co.uktelegraph.co.uk

Among those species is human. So far there hasn’t been sustained human-to-human transmission, but if we keep giving the virus chances, it is just a matter of time. 13/13 www.telegraph.co.uk/global-healt...

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

Here’s the other disappointing part. This is a phylogenetic tree of the H5N1 lineages since the start. Notice how all of the sequences from this year cluster together? 10/

If you look at where those sequences came from you see that they are from all over the country. That means the virus is not contained, it’s continuing to move across the country. 11/

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

aphis.usda.govaphis.usda.gov

The USDA tried to contain the outbreak by preventing the transport of lactating cattle across state lines unless they test negative for H5N1. It wasn’t enough though. 8/ www.aphis.usda.gov/sites/defaul...

This should have ended 2 years ago. It is SUPER easy to screen herds for the virus (bulk milk testing). Infected cattle clear the virus after a few weeks. The outbreak could have been stopped (and still can be) if we had the will to enforce strict quarantines. We don’t. 9/

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

It took several months to figure out this was happening, and by then the virus had spread to herds across the country. nextstrain.org/avian-flu/h5... 6/

Pasteurization kills H5N1, so there haven’t been any human cases from drinking pasteurized milk. However, it caused a lot of damage and maintained an enormous outbreak in mammals (not where we want it circulating). 7/

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

There were a number of spillovers from H5N1 into various mammals, but most of these were fairly contained. 4/

Then something completely unexpected happened. In late 2023 or early 2024, H5N1 started showing up in the mammary tissue of dairy cattle. It was a major outbreak. 5/

There is something really concerning (and disappointing) going on in the US right now. A dangerous and preventable situation. Let me explain. nextstrain.org/avian-flu/h5... 1/

In early 2022 a new variant of H5N1 bird flu made its way to the US. It wasn’t subtle. It quickly swept the country and caused massive bird mortality among all different bird types. 2/ www.nature.com/articles/s44...

Remember a few years ago when eggs were more expensive than beef? H5N1 was the reason. It is extremely pathogenic to chickens. 3/

PSA. Flu season is starting very early this year. WW numbers aren't very high yet, but they are a couple of months ahead of schedule just about everywhere. Almost entirely H1N1. If you are getting a flu shot, don't put it off.

21 Sept

Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites). COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.

PJ.3.2 seems to be hitting the accelerator. These are the wastewater samples deposited in just the last week where it was present (based on 439K marker).

I meant PJ.2.1

PJ.3.2 seems to be hitting the accelerator. These are the wastewater samples deposited in just the last week where it was present (based on 439K marker).

Even more from the G24077A+T24079A screen.

WTH, I think I found a BA.3.2 cryptic (I hope it isn't circulating anyway). Standard RBD + A435F, S438F, P463F. Wonder if that improves ACE2 binding? It was 100% of the sequence from one sewershed. @ryanhisner.bsky.social

10 Sept

I picked up a carton of milk from the store this week that had H5N1 influenza in it. >150 million copies/liter! Thankfully, it was safe to drink because the milk was pasteurized, so I’m not saying what brand. Takehome: DON’T DRINK RAW MILK.

Cryptic (gain-of-function) lineage update. There are currently 7 cryptic lineages in the US that I consider ‘active’. This is a rundown. Warning, I’m going into the weeds. Nerds only. 1/ bsky.app/profile/soli...

Solid Evidence@solidevidence.bsky.social

This thread is a quick summary about cryptic lineages (for ongoing reference). In short, cryptic lineage are unique, anachronistic, evolutionarily advanced, SARS-CoV-2 lineages detected from wastewater from an unknown source. 1/

Variant #1, the Lincoln variant. Detected in almost every sample from Lincoln for the last few years. Lineage is pre-Delta, so at least a 5.5-year infection. This lineage has the most divergent RBD on record. 11/ bsky.app/profile/soli...

Solid Evidence@solidevidence.bsky.social

Speaking of gain of function, the Nebraska lineage appeared 3 more times in the last month. The SARS-CoV-2 Spike RBD looks more like a bat Sarbecovirus (RaTG13) than the Nebraska lineage. Think our immune systems would recognize it?

We still don’t know most of the basics about these patients. What makes them predisposed to these persistent infections? What are their symptoms? What are the long-term consequences? Can they be treated if we knew who they were? Hopefully some day. 12/12

Solid Evidence@solidevidence.bsky.social

freakonomics.comWater, Water Everywhere — But You Have to Stop and Think - FreakonomicsWater, Water Everywhere — But You Have to Stop and Think - Freakonomics

This is different than the Ohio variant that I talked about on Freakonomics. That one never came back. 9/ freakonomics.com/podcast/wate...

Variant #2. Charlotte, NC. I thought this one was gone too. I hadn’t seen it since last year, but then it popped up again in July. We now know this is a Delta-derivative (roughly a 5 year infection). It is NC-2 and NC-3 on the dashboard. 10/

Solid Evidence@solidevidence.bsky.social

Variant #4. California, sewershed population 14,465. I mentioned this one before. 7/ bsky.app/profile/soli...

Solid Evidence@solidevidence.bsky.social

New cryptic from California. Not sure where, population 14,465. Looked like an early Omicron, but not enough coverage to tell for sure. Check out the M domain. Two different insertions. 2/

dholab.github.ioSARS-CoV-2 Cryptic Lineage Visualizations

Variant #3. Cleveland, OH. I’ve been seeing this variant for a while. I thought it was gone, but it popped up again in May. It’s OH 2 on the dashboard. Another BA.1-derivative (4.5 year infection). 8/ dholab.github.io/public_viz/0...

Solid Evidence@solidevidence.bsky.social

Variant #5. La Plata county, Colorado. Appeared about a month ago. This one is a BA.1 derivative, so about a 4.5-year infection. Not a lot of coverage, but it has the s2m fix. 5/

And unsurprisingly, Colorado also has 1795Q. 6/

Solid Evidence@solidevidence.bsky.social

Variant #6. California, sewershed population 1.4 million. Showed up once in March of this year. Very little coverage, but there was a very telling snippet from the N gene. 3/

All modern lineages look more like this. The lineage is pre-B.1.1, so it least a 4.5 year infection. 4/

Solid Evidence@solidevidence.bsky.social

Variant #7. Little Rock. This one showed up a few times this Spring. XBB-derived, so 2.5-3.5 year infection. RBD picked up 417T, 440R, 450R, 452M, 462R, 475V, and 496S. Haven’t put it on the dashboard yet. 2/

Update. I was wrong, the sequence was normal. They just got a one-off really high sample (a hot turd). It happens.

Solid Evidence@solidevidence.bsky.social

There have been hints of a cryptic lineage from Anchorage for years. Who thinks they finally popped? bsky.app/profile/soli...

20 Aug

I'm off on the next metagenomic curiosity. Can we recover viral sequences from wine? And if so, will they be mostly plant, yeast, or insect viruses? Is there a 'viral terroir'? We shall see; I started with bottles of cheap MO and CA wine. Any predictions?

lung.fishLungfishDedicated to improving environmental surveillance and tackling viruses through innovative detection strategies.

20 Aug

I can finally reveal the rest of our World Cup surveillance. While we were working away on wastewater metagenomics, the other side of lung.fish was on the ground doing air sampling with team Canada. Preprint just out. www.medrxiv.org/content/10.6...

19 Aug

Another appearance of the Charlotte variant. A minor branch from last time is dominant this time with the addition of [483A-484V-485S-486A]. bsky.app/profile/soli...

Solid Evidence@solidevidence.bsky.social

The Charlotte Gain-of-function lineage is back, last seen in Dec, 2025. It’s from a different sewershed, but same city. Although this is clearly the same lineage as ‘NC-2’, I decided to designation this as ‘NC-3’ on my dashboard so you can see ‘how much it’s grown’. 1/

19 Aug

Stupid SC2 lineage. SV.2 is surging and it is clogging up one of my cryptic lineage screens.

18 Aug

There have been hints of a cryptic lineage from Anchorage for years. Who thinks they finally popped? bsky.app/profile/soli...

Solid Evidence@solidevidence.bsky.social