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Marc Johnson Profile picture
@SolidEvidence
Apr 24 • 6 tweets • 2 min read Twitter logo Read on Twitter
Help me solve a COVID cryptic lineage mystery.

Cryptic lineages are distinct SARS-CoV-2 lineages that we detect in wastewater, but do not know their source. We believe they are from patients with very long COVID infections.

Here is more backstory.



1/
We recently discovered a cryptic lineage in Ohio. It appears to be derived from a person that was infected over 2 years ago. It is a B.1.1 derivative, but is highly divergent.

We first detected this lineage in a sample from last summer, and as recently as last month.

2/ Image
The one thing we know for sure it that this person is shedding a ton of viral material. I suspect that they have a SARS-CoV-2 GI infection and may think they have something like IBD or chronic diarrhea.

3/
What is different about this cryptic lineage is that has been regularly detected in two different sewersheds over the same time period, and it is definitely the same lineage.

I’m guessing this means we are detecting the viral material shed at home and at work.

4/
The two sewersheds are Columbus and Washington Court House, Ohio, which are about 40 miles apart.

I want to emphasize that this is all information gathered from a public database. I have no insider information.

5/ Image
If you know anyone that might be the source based on where they live and work, ask them to do this. The next time they go to the bathroom (#2), stick the swab from a COVID rapid antigen test into the dirty water and test it like normal.

I'd love to know if it is positive.

6/

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More from @SolidEvidence

Marc Johnson Profile picture
Mar 25
What's next for COVID?

I projected a few weeks ago that XBB.1.9* would be the next dominant lineage in the US.

This lineage was a little over 4% of US sequences over the last 2 weeks, and the numbers are doubling roughly every 8 days.

It's in almost every state.

1/
The competition.

XBB.1.16 remains the fastest growing lineage. Worldwide it is doubling about every 5 days. (world data shown)

However, it is less than 1% of US sequences in the last 2 weeks, and only seen in 13 states so far (including Missouri).
2/
If trends hold, XBB.1.9 will still become the dominant lineage in the US in late April, but it won't hold the position for long.
3/
Read 6 tweets
Marc Johnson Profile picture
Mar 21
Update on Polio.

After the detection of Polio in NY last year, there was some pressure to do wastewater testing in Missouri.

So we developed a few polio wastewater assays. One generic enterovirus screen, and 2 polio-specific (targeting the 5’UTR and the Capsid)
1/14
None of the Missouri samples had any sign of Polio, so we decided to throw the net a little bit wider and looked at other samples.

Don’t ask me where they were from. Most of them were de-identified so I couldn’t tell you if I wanted to, but they were from all over.
2/14
We only had one surprise, which was from Utah. I’m revealing the location only because it was recently reported in the press. (It was NOT a false positive, by the way.) Polio was about 2% of the sequence in our generic enterovirus screen.
3/14
deseret.com/utah/2023/3/20…
Read 14 tweets
Marc Johnson Profile picture
Mar 6
Brief commentary about the origins of Omicron (and SARS-CoV-2).

I think I’ve posted most of this before, but it’s worth repeating.
1/13
I’ve heard increasing chatter lately about the theory that SARS-CoV-2 was engineered, and even that Omicron was engineered.

I don’t have any direct evidence about either, but I do have evidence from studying cryptic lineages about what kinds of things we should expect.

2/13
First of all, cryptic lineages are evolutionarily advanced SARS-CoV-2 lineages that we detect from wastewater that do not match anything that has been seen in patients. They are always derived from lineages that are no longer in circulation.

3/13
doi.org/10.1038/s41467…
Read 13 tweets
Marc Johnson Profile picture
Mar 4
1. Missouri COVID wastewater update.
Cumulative numbers from over 90 sites were up about 8% from last week, so basically flat; I haven't corrected for flow.

The numbers aren't that low overall. There must be a fair number of people infected that probably don't know it.
2. We sequenced 72 sites this week and over 80% of the total was XBB.1.5.
BTW, we added a probe to check for XBB.1.9.1. There were two sites with a little bit last week, but this week none at all. It really is XBB.1.5.
3. Other lineages present were BQ.1.1, BQ.1, BN, CH, BF.7, CQ.2 and a tiny hint of BA.5 in one sewershed.
Other than the BA.5, these are all contemporary lineages, meaning they are derived from recent infections.
Read 5 tweets
Marc Johnson Profile picture
Feb 25
We found a new cryptic lineage this week.

This time it's from Dallas (I think). The same sequence was in two different samples from January.
The lineage is a B.1 derivative (pre-Alpha).

The RBD is R346T/A372T/N388S/K417T/N460K/E484A/S494P/Q498H/H519N

This is a pretty 'classic' cryptic RBD.
It also has some of the other hallmark cryptic mutations outside of the RBD: 828 and some Orf3 mutations (a few people will know what I'm talking about).
Read 4 tweets
Marc Johnson Profile picture
Feb 15
Interesting facts about Orf9b and XBB.1.9.1

OK, I missed it. There is a third mutation in XBB.1.9.1 that differentiates it from XBB.1.5 - Orf9b: I5T (T28297C).

Thanks colleagues for pointing it out.

@CarlottaOlivero @RajlabN @siamosolocani @PeacockFlu
Orf9b is an alternative reading frame within the N gene that starts at 28284 (within the 4th codon of N).

Several confusing things threw me off, the first being the fact that cov-spectrum does not call out the AA changes of this gene along with the nt change.
Adding to the confusion, the GISAID reference sequence calls this gene Orf9a, and gives the Orf9b name to a downstream ORF in N.
Read 10 tweets

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