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Marc Johnson Profile picture
@SolidEvidence
Oct 2 • 4 tweets • 2 min read • Read on X
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
This really makes you wonder how many more persistent infections are out there that we don't know about.

BTW, if you think you may have a persistent GI infections since having COVID, we are still enrolling.

4/4

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More from @SolidEvidence

Marc Johnson Profile picture
Aug 17
I'm giving the variant update at the SAVE meeting on Monday so I thought I'd put out a preview for comment.

We are now at our 4th 'high water' mark since the Omicron wave based on wastewater surveillance.

1/ Image
I thought I would give an abbreviated summary of the last year in variants.

A little over a year ago BA.2.86 started circulating, a lineage that was almost certainly derived from a persistent infection.
2/ Image
BA.2.86 was pretty fit, but it was still sensitive to a lot of Class 1 antibodies.

However, it quickly picked up S:L455S (making it JN.1), which evaded these antibodies, and it was off to the races.
3/ Image
Read 15 tweets
Marc Johnson Profile picture
Jul 24
Just returning from the CEIRR influenza annual meeting.

Here are my takeaways.

1/
First the bad news.

2.3.4.4b (which the H5 in cattle is derived from) is a bad ass. In birds it is ridiculously contagious, ridiculously promiscuous, and pretty darn deadly. It spread through typical and atypical US bird populations practically instantly.

2/
Now the good news.

The lineage has mixed pathogenicity in mammals (don't let your pet ferrets play near wild birds), but generally is very poor at mammalian respiratory spread, even in species where it is highly pathogenic.

3/
Read 6 tweets
Marc Johnson Profile picture
Jul 6
MO COVID wastewater update. Although it's not major, there has been a noticeable uptick on COVID levels the last few weeks.

1/ Image
In my thinking, there are 3 things that contribute to these fluctuations: the viral lineage, host immunity, and human behavior.
2/
I don't think the viral lineage has much to do with this uptick. We've been experiencing a gradual takeover of a scattering of JN.1 derivatives, but they have been with us for a while and don't seem to correlate with the increase.
3/
Read 7 tweets
Marc Johnson Profile picture
Jun 7
Update on the Maryland variant, the highly diverse Delta variant from a sewershed South of Baltimore.
1/ Image
This sewershed only started sequencing earlier this year, so I don't know how long it has been around, but it is clearly Delta-derived, which means the infection probably occurred in the second half of 2021, nearly 3 years ago.
2. Image
The lineage has been showing up pretty consistently in the first sewershed, but on May 21 it also appeared in the sewershed just to the West. Daytrip.
3/ Image
Read 8 tweets
Marc Johnson Profile picture
Jun 5
Update on the unexpected H5 detections from wastewater.

Thanks to all that helped figure this out.

1/
There were 4 sewersheds that had detectable H5 from states that have not been reported to have infected herds. Those 4 were from Minnesota and Iowa.

2/
 data.wastewaterscan.org/tracker?charts…
The easiest to explain is Mankato. They have a Dairy plant.



MN is not supposed to be in MN herds, but the milk could have been trucked in from SD.
3/ mda.state.mn.us/minnesotadairy…
Image
Read 7 tweets
Marc Johnson Profile picture
May 4
A few points about the H5N1 outbreak that I'd like to share.

1. If we had a pan-influenza wastewater screen in place nationally that differentiates the influenza sources by sequencing (which isn't that hard to do), we probably would have detected this outbreak months ago.
1/
BTW, we submitted a CDC proposal earlier this year to do exactly this, but the topic was pulled from the BAA so the proposal wasn't even reviewed.
2/
2. We should not panic about the current outbreak in cattle. You aren't going to get influenza from pasteurized milk, and this virus isn't ready for human-to-human spread (yet).
3/
Read 9 tweets

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