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

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More from @SolidEvidence

Nov 5
I'm doubling down on MV.1*

This lineage has been growing rapidly recently, but it's been hard to tell if it would be a real contender since most of the infections were from Singapore.

In North America its growth has been more questionable.

But I have new data.
1/ Image
You probably know that our team screens all of the wastewater sequences submitted to SRA for cryptic lineages.

One of the 'cryptic-specific' changes we look for is S:F456V, which is common in cryptic, but hadn't been seen much in circulation until recently.
2/
MV.1* has a reversion at S:478 back to T, which is right next door to 456V, so its easy for me to check if the 456V sequences are in fact MV.1*

3/ Image
Read 5 tweets
Oct 28
Cryptic lineage quarterly update, last update for now.

I save the weirdest for last. Read to the end.
1/ Image
A lineage popped up in our cryptic screen because most of the seqs did not have the s2m deletion (meaning it was from 2022 or earlier).

The sample was from 9/30 in Texas. Population is 780, so it isn’t even on the NWSS map.

I don’t know where the sample was from.
2/ Image
So next I checked the RBD, and it was virtually blank. Decent coverage, but no mutations to speak of.
Very weird.
3/ Image
Read 9 tweets
Oct 26
Cryptic lineage quarterly update, part 3
Cleveland variant.
If you missed part 1 and 2, they are here.
x.com/SolidEvidence/…
x.com/SolidEvidence/…
1/
My favorite way of finding cryptic lineages by screening for what I call the ‘s2m fix’.
s2m is an RNA element at the end of the SC2 genome that has been deleted from all lineages in circulation for over 2 years.
If you see the s2m sequence, you know it is an old lineage.

2/
A distinctive thing about cryptic lineages is about a third of the time they pick up a very specific mutation in their s2m sequence. T29758G. It’s actually a reversion to the sequence found in bats.

More about s2m here, if you are interested.


3/
Read 11 tweets
Oct 23
Cryptic lineage quarterly update, part 2
BA.1 and Delta
If you missed part 1, it is here.

1/
BA.1 cryptics. BA.1 infections all occurred in late 2021-early 2022. If there is good coverage, BA.1 lineages are easy to spot because they have a unique Spike insertion that no other lineages have had.
2/ Image
There were hints of a few BA.1 lineages across the country, but there were only 2 that were really clear, one in San Diego and one in Western Colorado.
3/
Read 12 tweets
Oct 22
Cryptic lineage quarterly update, part 1
Recent BA.2-XBB cryptics

Cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater from an unknown source.

1/ Image
We are almost certain that these lineages are derived from individuals that have been infected with SARS-CoV-2 for several years that are shedding a ton of viral material.

If you want to know why we think these are from humans, read this thread.

2/
Or read our paper on the lineage we almost tracked down.

3/
sciencedirect.com/science/articl…
Read 14 tweets
Oct 2
Update on the Bavarian cryptic lineage that @LongDesertTrain spotted.

This lineage first popped up in August but has been consistently present since.


1/ cov-spectrum.org
Image
The lineage is derived from BA.5.1.10, but taken at face value, it has over 90 additional mutations and deletions.

2/ Image
BA.5.1.10 stopped circulating back in January, 2023 in Germany, so this person was presumably infected for at least 18 months before they 'popped' and started showing up in wastewater samples.

3/ Image
Read 4 tweets

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