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.
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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…
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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.
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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).
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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
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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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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.
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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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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.
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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.
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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?
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