Molecular virologist, Professor, and wastewater detective. Same handle on bsky. Opinions are my own and do not reflect those of my employer or anyone else.
Columbia, Mo.
Joined January 2022
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We released our latest metagenomics preprint. I’m really excited about this study.
The unofficial title is ‘conquer the dark matter, volume 1’
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medrxiv.org/content/10.64898…
Summary of the H5N1 situation.
The USDA is now reporting infected herds in 6 states (up from just 1 or 2 states not that long ago).
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aphis.usda.gov/livestock-pou…
That does not count the outbreak on the mink farm in Utah, which is clearly linked to dairy infections.
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theweek.com/health/a-bird-fl…
Thank you @nextstrain for updating the phylodynamic tree.
I thought someone had said that the WA cases were an independent introduction, but they are associated with the other 2026 sequences.
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nextstrain.org/avian-flu/h5n…
Three human cases, one death. Can we please start taking this outbreak seriously.
yakimacounty.us/DocumentCent…
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/h5n…
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In case you were wondering, we haven't detected this ebola strain in US wastewater, at least not yet.
bbc.com/news/articles/cj5ynr…
Hey flu experts. Is H5N1 more likely to reassort with H1N1 than lineages, or is that predictable?
Seeing as H5 seems to be resurging and we are heading into a super early flu season that is almost exclusively H1N1.
@andrewpekosz
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/h5n…
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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.
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nature.com/articles/s44298-0…
Have the USDA H5N1 dashboards stopped working, or is my browser having a problem?
aphis.usda.gov/livestock-pou…
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.
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).
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.
@LongDesertTrain
New lineage to add to the 'active' list.
The TX lineage reappeared (BA.1-derivative); hadn't seen it in a year.
Classic mutations: K1795Q, K417T, H182D, S37P, s2M-fix, etc.
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.
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xitter.twitterapi.xyz/SolidEvidence/status/2…
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.
Multiple fresh appearances of the Lincoln, Charlotte, and Cleveland variants this month.
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.
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xitter.twitterapi.xyz/SolidEvidence/status/2…
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.
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xitter.twitterapi.xyz/SolidEvidence/status/2…
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.
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Update. I was wrong, the sequence was normal. They just got a one-off really high sample (a hot turd). It happens.
There have been hints of a cryptic lineage from Anchorage for years.
Who thinks they finally popped? @JusDayDa
xitter.twitterapi.xyz/SolidEvidence/status/2…
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?
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.
medrxiv.org/content/10.64898…