Marc Johnson Profile picture
Sep 18, 2022 19 tweets 7 min read Read on X
SARS-CoV-2 lineages, Cryptic lineages, and a prediction of what the next dominant VOCs will be.
We sequence SARS-CoV-2 from wastewater using a different approach than most. We sequence smallish fragments of the genome so that we can tell if particular mutations are derived from the same virus. This way we are better able to determine if there is anything new circulating. Image
About a year and a half ago we detected something from a St. Louis sewershed that didn't make sense. SARS-CoV-2 lineages whose sequence did not match anything that had been seen from patients. We called these 'cryptic lineage'. Image
Wanting to know if this kind of thing was common, we started collaborating with @DrJDennehy to see if we could find anything similar in other places. NYC also had cryptic lineages. Not the same lineages, but lineages with similar characteristics.
nature.com/articles/s4146…
By the end of 2021, we had identified 9 sewersheds (out of about 180 that were being routinely surveyed) that contained cryptic lineages, including a lineage from California with @RoseKantor.
medrxiv.org/content/10.110…
My obsession with finding and characterizing these cryptic lineages accelerated in 2022. To date we have screened wastewater from around 700 sewersheds. In total we have found 24 putative lineages. I say putative because some of them we have only seen once.
We still didn't know where these lineages were coming from. I was convinced of an animal reservoir. What changed my mind is when we tracked a lineage in Wisconsin with @dho all the way to a single set of bathrooms. There is no animal contribution. It is from a person. Image
What we think is happening is that cryptic lineages are very long-term infections in people (often >1 year). Perhaps GI infections. The hosts are obviously mounting an immune response, but are not able to clear the infection.
Because there are no genetic bottlenecks from spreading from person-to-person, these viruses basically push the evolutionary fast-forward button.
What can these lineages tell us about circulating viruses? These are the sites in the Spike RBD that are most commonly changed in the cryptic lineages. We had seen lineages with these changes long before they were seen in Omicron. Image
When Omicron arrived (shown in red) it had mutations at many of the same sites. The main exceptions were L452 and N460, which were common in cryptic lineages, but were not in Omicron (BA.1). Image
About six months later we started seeing Omicron lineages with mutations at L452. Highlighted in red are the changes in BA.4/5 (which has L452R), but there were also lineages with L452Q, L452M, and others. These lineages took over, but there were still no changes at N460. Image
Finally, a few months ago N460K appeared in an Omicron lineage (BA.2.75). However, it was not combined with any of the L452 mutations. Nonetheless, BA.2.75 and its derivatives have continued to expand and slowly displace other lineages. Image
A few days ago, a new lineage appeared in a MO wastewater sample. Omicron with L452R+N460K (and K444M). This appears to match a new lineage that was just designated as BU.1 a few days ago. Currently there are only 13 sequences in GISAID with this combination of mutations. Image
However, I recently learned from @CorneliusRoemer that I was behind in my lineages. There is another completely independent lineage that arrived at almost exactly the same combination. This lineage is designated BQ.1.1. This group has L452R+K444T (rather than K444M).
In addition, BQ.1.1 has also picked up R346T (also in BA.4.6). We haven't focused as much on this region of spike, but most cryptic lineages that we have checked also have a mutation at this site. It seems to be pretty critical. BQ.1.1 is new, but it seems to be taking off.
There you have it. BQ and BU. I don't know if they will cause a spike in total cases, but barring something completely new appearing, I predict that they will be the dominant VOCs in the coming months.
Addendum. It seems a few other lineages have hit very similar 'jackpot' combinations very recently. In addition to BU and BQ:

BW.1 (BA.5.6 derivative)
BS.1 (BA.2.3 derivative)
BR.2 (BA.2.75 derivative)
other undesignated

They all have N460K, L452R + other changes.
Real pango experts, please correct me if I botch any of these, or have missed any. @CorneliusRoemer @PeacockFlu @siamosolocani @LongDesertTrain

• • •

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

Dec 15
What are really the most prevalent SARS-CoV-2 lineages and which are increasing?

This is our latest wastewater analysis.

1/ Image
We downloaded and analyzed seqs from over 3,000 US wastewater samples collected since Oct 16.

We only analyzed the US samples because there weren't any other sites we could find that covered the time period. This represented at least 80M people.
2/
ncbi.nlm.nih.gov/sra/
For the analysis we compared the frequency of every non-consensus change in Spike during the first 3 weeks (10/16-11/5) to the frequency in the second 3 weeks (11/6-11/26).

3/ Image
Read 10 tweets
Dec 7
I'm working on a new strategy to track lineages by making composites of all of the recent wastewater sequences.
1/ Image
We downloaded about 1600 samples from the last month (~1 TB of data) and compared the frequency of mutations in the first 2 weeks versus the second 2 weeks.
2/
KP.3.1.1* is still on top with 50-55% of sequences and dropping slowly.
XEC* is next at 30-35% and rising slowly.
2/
Read 7 tweets
Nov 29
GISAID vs SRA/WW
I thought I would do a little comparison to see how wastewater sequencing data compares with patient sequencing data in evaluating viral trends.
1/
cdc.gov/nwss/index.html
For WW I took all of the samples from our most recent SRA download that were collected in the last month (~500 samples). This wasn’t normalized.

For the patient side I used Cov-Spectrum data (because it's public) from the last month (8,302 sequences).
2/
cov-spectrum.org/explore/World/…
There are about 50k patient samples collected for sequencing each month, but there is always a delay before they are all sequenced and uploaded.

In this regard, the WW data is much faster.
3/
Read 12 tweets
Nov 28
Maryland variant, retrospective analysis.

I decided to have a more careful look back at the evolution of the Maryland cryptic lineage.
1/ Image
Standard explanations and disclaimers.
Cryptic lineage: unique, evolutionary advanced SARS-CoV-2 lineages detected in wastewater from an unknown source.
Cryptics are not from animals, they are long term infections.
2/
Cryptics generally are not contagious and we think they are probably GI infection.

The virus in wastewater is not infectious.

3/
Read 12 tweets
Nov 22
If anyone wants to follow along with the Maryland variant (or doesn't believe my analysis), have a look for yourself.

1/
Go to
Type in SRR31400336 and start alignment.

This is a sample from the Maryland sewershed collected on November 7 of this year.
2/deeperseq.genomium.org
This is the RBD region of the Maryland sewershed, below is a normal sewershed.

It doesn't take a molecular virologist to see that one doesn't look like the other.

3/ Image
Read 4 tweets
Nov 20
Maryland folks, I need another favor.
There is a person from Anne Arundel county that has been infected with SARS-CoV-2 for about 3 years (Delta infection).

They probably don’t even know they are infected, but they are shedding a ton of viral material in wastewater
1/ Image
I’m trying to find this person without invading their privacy, if they are willing to be found.

Here are a few threads I’ve written about this variant if you want to read up.

x.com/SolidEvidence/…
x.com/SolidEvidence/…
x.com/SolidEvidence/…
2/
We figured out that the signal is from the Patuxent sewershed (78k people). We’ve been detecting the variant there since this Spring.

Interestingly, the COVID WW spikes were dates when the cryptic sequence was highly prevalent.

Those spikes were driven by one person!

3/ Image
Read 8 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!

:(