Share this page!

Enter Twitter Thread URL to Unroll

Needs to be the full URL like: https://twitter.com/threadreaderapp/status/1644127596119195649

How to get URL link on Twitter App

  1. On the Twitter thread, click on or icon on the bottom
  2. Click again on or Share Via icon
  3. Click on Copy Link to Tweet
  4. Paste it above and click "Unroll Thread"!
  5. More info at Twitter Help
Marc Johnson Profile picture
@SolidEvidence
May 19 • 11 tweets • 4 min read Twitter logo Read on Twitter
Our updated manuscript with @dho about a SARS-CoV-2 cryptic lineage from Wisconsin is now online.
1/
 medrxiv.org/content/10.110…
A cryptic lineage is a SARS-CoV-2 sequence detected from wastewater that is distinct from anything that has been seen before and is of unknown origin.

At the start of this investigation I thought these lineages probably came from an animal reservoir.

I was wrong.
2/
The WI lineage was continually detected from Jan 2022 until Jan 2023. It was probably present earlier, but that is when we first detected it.

The sequence was diverse (mixed), evolutionarily advanced, and looked nothing like circulation lineages.
3/ Image
We first detected the lineage from a large sewershed, but gradually narrowed the signal to a single set of toilets in a business. It was coming from a person.

This took extraordinary cooperation with the municipal wastewater authorities, WSLH, UW, WIDPH, and the CDC.
4/ Image
As we got closer to the source, the signal got stronger and the cryptic lineage proportion increased.

The final samples collected close to the source were as pure (and as concentrated) as a patient nasal sample. It was by far the highest wastewater signal I have ever seen.
5/ Image
The sequences from this lineage partially foretold the future of circulating lineages. Many of the changes that we detected in the cryptic lineage were later acquired by Omicron VOCs.
6/ Image
Part of the reason it took us so long to resubmit this manuscript is because we had hoped that we would have a conclusion (find the source). That has not happened, and the we haven't detected the lineage again since January. (Everyone tested by nasal swabs was negative.)
7/
The person might have left their job, they might have cleared the infection (after 2 years), or the virus might have subsided but is still be active. I have seen particular cryptic lineages disappear for as long as 7 months only to reappear with additional mutations.
8/
For now we have learned a lot about cryptic lineages, but there are still many questions.

What is the health status of carriers? Do they have long COVID?

Where is the virus replicating?

How widespread are these chronic infections, and how are they affecting patients?
9/
I think these questions are important to answer for the sake of the individuals and for public health in general.

There is another active cryptic lineage in Ohio that we are monitoring. Hopefully we will get more answers there.
I'm hopping on a flight back to the US after the @nidovirus2023 meeting in Switzerland. Sorry if I'm slow to respond to any questions.

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Marc Johnson

Marc Johnson Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @SolidEvidence

Marc Johnson Profile picture
Apr 29
I’ve started doing a deeper dive looking at the genome of the latest cryptic lineage from Ohio.

Warning – I’m going deep into the weeds.

Lay summary: cryptic lineages have a lot of convergent mutations, and for the most part we don’t what they mean.
1/
 Image
I repeated the screen of ALL of the wastewater samples to specifically look for this lineage. Still only from Ohio, but I found 2 more positive samples from Columbus. These two were from the sewershed on the North side of town. Both were from December.
There have been 20+ samples that contained the cryptic lineage so far. I took the top 15 and compared what mutations were present.

Theses samples had about 200 different mutations (not all were consensus changes) that are extremely rare in circulating lineages.
Read 15 tweets
Marc Johnson Profile picture
Apr 24
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/
Read 6 tweets
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

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

Send Email!

:(