Hey Cornhuskers, you’ve got one heck of a cryptic lineage. This one matches the longest COVID infection that I’ve seen (~4 years). 1/ - ThreadSky

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solidevidence.bsky.social • 10 days ago

Hey Cornhuskers, you’ve got one heck of a cryptic lineage.
This one matches the longest COVID infection that I’ve seen (~4 years).
1/

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ann154.bsky.social•9 days ago

Somehow this doesn't surprise me.

solidevidence.bsky.social•10 days ago

Background: cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater. We are pretty certain that cryptics come from people with very long persistent infections, but they generally are not contagious.
2/
https://twitter.com/SolidEvidence/status/1587551682388295680

solidevidence.bsky.social•10 days ago

We’ve been detecting this cryptic from Lincoln, Nebraska since last July, but it was usually low coverage and the Nebraska group only sequences Spike, so I only knew so much about the lineage.
3/

solidevidence.bsky.social•10 days ago

Earlier this month Verily (NWSS) picked up the lineage in their surveillance. Same mutations, same sewershed.

What jumped out is that is lacked the classic B.1.1 mutations in the N gene, which means it was a very early lineage.
4/

solidevidence.bsky.social•10 days ago

The lineage also had 28869T, 29733A, 29294C, and 28472T.
5/

solidevidence.bsky.social•10 days ago

This means the lineages was almost certainly derived from B.1.2, a lineage that circulated until about March 2021.

This means they have been infected for about 4 years.
6/

solidevidence.bsky.social•10 days ago

Interestingly, the cryptic had deleted its s2m almost identically to the currently lineages; the deletion was just 2 nt shorter.
7/

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