Molecular virologist, Professor, and wastewater detective. Same handle on bsky. Opinions are my own and do not reflect those of my employer or anyone else.
Columbia, Mo.
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We released our latest metagenomics preprint. I’m really excited about this study.
The unofficial title is ‘conquer the dark matter, volume 1’
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medrxiv.org/content/10.64898…
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I knew there were a lot of fake accounts on this platform, but they are usually obvious. I had no idea how intricate and complex the ruse could be.
Get a load of this story.
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This is getting complicated. We're now detecting 6 different Omicron sub-lineages in MO wastewater.
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Ohio cryptic lineage update.
We’ve made no progress identifying the individual, but we have learned a few things.
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We developed an assay for testing for H5N1 from wastewater over a year ago. (I wasn't expecting it in milk, but I figured it was going to poke up somewhere.)
However, I was just on a call with the CDC and they are advising us NOT to use it.
I need a drink.
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This is unbelievable.
H5N1 is banging at the door and we're firing the 'disease detectives'?
Funny thing about pathogens, they will kill you even if you don't know they are there.
statnews.com/2025/02/14/trum…
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We are now officially into year 5 of the SARS-CoV-2 pandemic/endemic.
I gave a lecture to my virology class this Fall about the history of the pandemic through the lens of viral genotypes.
I thought I would share that lecture as a thread.
This is a long one.
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Last month there was an announcement that I thought was a major advancement in world health, but it got little attention.
I thought I would tell you all a little bit about it and why it is so important.
1/25
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Called it. CDC is now recommending that all wastewater surveillance groups develop and implement protocols to specifically test for H5N1.
👏👏👏
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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
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So it’s all a fake, but why?
This is a paid account. It doesn’t seem to be political, or monetary, or porn. It’s all about science.
What’s the end game? Can someone explain?
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I think this is a record. Seven co-circulating Omicron lineages from a single wastewater sample:
BA.4.6, BQ.1, BQ.1.1, BU, XBB, CH and CK (and no BA.5).
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This is absurd.
If this goes into effect, it would end medical research in this country as we know it.
I'm not being hyperbolic, it really would.
49.8% of the popular vote should not give you a mandate to do that.
grants.nih.gov/grants/guide/…
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Perhaps one of the people that follow ‘her’ has gone further down the rabbit hole and can explain.
Has ‘Julia’ been chatting you up too?
I’m curious where the conversation went.
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However, when I went to the journal itself, the papers were real, but the authors were different.
The ResearchGate profile was all a fake.
They had taken the CV of some Iranian scientist, changed the name on the papers, and created a fake ResearchGate account with them.
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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.
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Once I knew it was a fake, other mistakes jumped out.
One doesn’t study Organic Chemist, it would be chemistry.
CALS is on the Ithaca campus, not NYC.
Chemistry isn’t even in CALS. (I did my postdoc at Cornell)
What grad student has 63 pubs going back to 2007?
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What's more, if we can figure out how these infections occur, and how to treat them, it could potentially help out a whole lot of people.
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Two comments I should have made in my thread.
Washington Court House is a town of 15k (not an actual courthouse).
I haven't invaded anyone's privacy. Approximately 1600 people commute between Columbus and WCH. That isn't enough information to pinpoint the source.
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First, the signal is almost always present in the Columbus Southerly sewershed, but not always at Washington Court House. I assume this means the person lives in Columbus and travels to WCH, presumably for work.
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My point is that this patient is not well, even if they don’t know it, but they could probably be helped if they were identified.
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Third, I’ve tried to calculate how much viral material this person is shedding. (Multiply the cryptic concentration by the total volume). I’ve done this several times and gotten pretty consistent results.
They are shedding a few trillion (10^12) genomes/day.
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I checked, and there really was a Julia Allen that got her PhD in Chemistry at Cornell, but she graduated in 2011. I tried to reach out to her to let her know about this account.
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Second, the signal is increasing with time. Washington Court House had its highest SARS-CoV-2 wastewater levels ever in May, and the most recent sequencing indicates that this is entirely the cryptic lineage.
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The pubs she listed were all those of a scientist in Iran.
I also emailed him to let him know about this account.
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I do not know of any persistent infections that shed this much virus without killing the patient. (Correct me if I’m wrong). The closest would probably be HCV, an infection that often ends in liver cancer.
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The person kept trying to chat with me, but it was just a little ‘off’. I figured it was just an awkward scientist (common), or someone had hacked their account and this wasn’t really the account owner messaging me.
This used to happen on FB all the time.
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Look what we found in Ohio. Present in at least 20 sewershed samples over the last 6 months.
B.1.1 derivative (person infected for over 2 years).
About 94 genome changes (71 non-synonymous). Highly accumulated in Spike.
Many familiar cryptic mutations.
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What does this tell us? How much tissue is infected? It’s impossible to know for sure. Chronically infected cells probably don't release much, but acutely infected cells produce a lot more. I gather a typical output in the lab is around 1,000 virus per infected cell.
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Don’t get me wrong. The intestines have a huge surface are and 3 square feet is a tiny fraction of the total.
But it’s still a massive infection, no matter how you slice it.
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About a week ago I got a DM from an account asking me a benign but specific question about my research.
This happens to me all the time. I’ve met some interesting people this way.
Sometimes people even look up my number and call my office. It happens.
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If you are the individual, let me know. There is a lab in the US that can do 'official' tests for COVID in stool, and there are doctors that I can put you in contact with that would like to try to help you.
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I finally solved the mystery of why there are so many cryptic lineages in Northern Ohio.
This is a mystery I’ve been working on for the last 18 months.
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Oh shit.
The NCBI and NIH websites are down.
If that isn't a fluke, it is REALLY bad.
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Anyone who follows me know that when something doesn’t seem right, I don’t let it go.
I decided to look the person up, email them, and just ask them if the DMs were ‘real’.
It wasn’t hard to find them at all.
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You wonder why official COVID cases are low.
I know a guy that went to urgent care yesterday because he had crackling in his lungs, though he felt OK.
They took a chest X-ray, which looked OK, and sent him home. No tests.
Once home he took COVID test.
Positive, of course.
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How do you figure out if you have a COVID GI infection. Most rapid antigen test are not explicitly for stool. However, I know of at least one that is. The instructions from that test say to mix a ‘matchhead’ worth of feces with the buffer.
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dyonmedical.com/en/corona-ag…
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They had a profile on ResearchGate (sort of like linkedin for scientist).
The picture looked similar and the profile identical. Lots of pubs, but no email.
I decided to look up the pubs where the email address of authors is often listed.
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If we assume we are getting 1,000 viral particles per infected cell, that would mean there are at least a billion infected cells. The density of monolayer epithelial cells is around 300k cells/sq cm. A billion cells would represent around 3.5 square feet of epithelial tissue!
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I didn't know this. After Trump tried to cut NIH indirects in his first term congress added this appropriations rider to the budget to stop anyone from trying again. The rider remains in effect today.
I'm not a lawyer, but this seems to be a pretty open and shut case.
nytimes.com/2025/02/10/us/po…
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I’m pleased to share that we FINALLY submitted our latest manuscript on SARS-CoV-2 cryptic lineages and what they tell us about the origins of COVID-19.
This was a ton of work.
medrxiv.org/cgi/content/shor…
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If it were spreading it would not remain precisely restricted to 2 sewersheds for almost a year.
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The account looked legitimate. They are a paying account (I’ve never seen a bot that pays).
They’ve been on the platform for over 2 years.
They have 52 followers, some of whom I recognize, and they compulsively repost interesting science posts (including some of mine).
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If you do get a positive reading, I would suggest having someone else try with the same kind of test with their feces to be sure it isn’t a false positive. Weird shit happens.
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For those of you that have asked me why I am convinced that cryptic lineages are coming from people, I can finally point to a pre-print with @dho and many fantastic collaborators in the UWisc and Wisc Public Health.
medrxiv.org/cgi/content/shor…
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Interesting that there are considerably more people masking at a wastewater surveillance conference in Atlanta than there were at a flu conference in New York City.
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I'm done manually logging the week's sequencing results for 76 sewersheds that averaged 5-8 different lineages per sewershed. Kind of exhausting.
I'm noticing an overall shift in SARS-CoV-2 diversity.
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storymaps.arcgis.com/stories…
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These are the locations where we have detected cryptic lineages from wastewater so far. Number of lineages is in yellow.
I'm sure this is the tip of the iceberg.
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Do you think you've had long-term GI problems since having Covid?
We are performing a study examining the characteristics of viruses, specifically persistent SARS-CoV-2 infections, in stool samples.
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I can tell you that with very positive wastewater samples we got a positive by just sticking the swab into the wastewater before adding it to the buffer. Either way, it is essential to use the buffer provided or the test doesn’t work.
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BTW, David Ho still maintains a very active research lab at Columbia University, which apparently now has all of its NIH grants frozen.
Let no good deed go unpunished.
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science.org/content/article/…
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Ohio Cryptic lineage update.
The lineage is still present, but as far as I know the person still does not know they are infected.
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I'm anxious to learn what all of this fluA activity in California is.
CA has not been reported to have any H5-infected herds, they don't have a lot of wild birds contributing to their wastewater, and this isn't flu season.
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It’s pretty clear the most sweeping SARS-CoV-2 lineages to date have been Delta, BA.1, and now JN.1.
Fun fact: as far as I am aware, our laboratory (with our collaborators) was the first to detect all three of these lineages from US wastewater.
Why were we always first?
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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.
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I've always found this frustrating.
You or your child has a respiratory infection. It's not flu or COVID. Your doctor can only tell you, 'you have a virus'.
Could it be a little bit more specific?
We hope to help answer this question, non-invasively, and for free.
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Oh shit.
I mentioned before that I was worried that BA.2.86 would pick up S:456L because that is the one place where BA.2.86 is more sensitive to neutralizing antibodies than EG.5 and the like.
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I keep doing this search. This is the first time in the pandemic when I have been anticipating a specific mutation.
Spike_L452W, F456L
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Another human H5N1 case.
From a hospitalized patient,
with no known animal exposure,
and from Missouri, which has no known infected cattle.
This is not good.
The only good news is that they recovered.
cdc.gov/media/releases/2024/…
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Never mind wastewater, this is virus from a chronic infection collected in the last few weeks.
A Delta derivative!
35 non-synonymous changes, highly concentrated in S1.
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However, if you’ve had GI issues for the last three years and you live and Cleveland but you occasionally visit Akron and Dayton, I have a free and confidential study you can enroll in to find out if this is you.
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Do you think you've had long-term GI problems since having Covid?
We are performing a study examining the characteristics of viruses, specifically persistent SARS-CoV-2 infections, in stool samples.
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They say it will only add to the confusion because we won't know where it is coming from.
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This is amazing.
Can cryptic lineages tell us anything about the origins of SARS-CoV-2 (SC2)?
The answer may surprise you, it surprised the hell out of me.
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6. Most important, we shouldn't shy away from surveillance because we want to avoid a panic. There is still time to stay ahead of this, but if we aren't careful I think it's just a matter of time before H5N1 makes it to humans.
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However, the news got even better last month when it was announced that lencapavir could be used for PrEP with as little as one treatment per year.
That is a treatment that could actually work!
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aidsmap.com/bulletin/confere…
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3. What we should be concerned about is that fact that the viruses is getting way too many chances. It keeps expanding its tropism. The more animals it replicates in, the more chances it gets to sample new configurations.
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I was starting to believe the H5N1 outbreak from dairy cattle was winding down.
I was wrong.
I hadn’t detected H5N1 in CA wastewater in 6 months, and then 4 samples in a row came up positive. The sequences were all B3.13 (the dairy cattle lineage).
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5. In my opinion we should be focusing our attention on wastewater testing downstream of meat processing plants (for all types of animals). It wouldn't matter what tissue the virus is in, it would end up in the water and give us an early warning.
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Persistent infections are training grounds for pathogens.
People worry about ‘gain of function’ work, but failing to continue treating the 40+ million people in the world living with HIV would be the largest and most dangerous gain of function ‘experiment’ in history.
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Despite what you might have heard, Omicron is not a milder lineage.
The milder disease was because of differences in the population (immunity), not the virus itself.
academic.oup.com/jid/advance…
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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.
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We still don't know which person is the source (most were tested by nasal swabs and were negative), and more importantly, we don't know why the lineage is not spreading.
We suspect that the source is a long-term COVID infection of someone's GI tract.
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There are 5 known infected workers from the H5N1 poultry outbreak in Colorado, and they were all symptomatic.
Of the >1,000 poultry outbreaks in the last few years, this is the first case I know of where the exposed humans are symptomatic.
It's starting.
aphis.usda.gov/livestock-pou…
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SARS-CoV-2 lineages, Cryptic lineages, and a prediction of what the next dominant VOCs will be.
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4. When the virus makes it way it to pigs, that is when we need to start getting really nervous. Pigs are a mixing vessel where flu is more likely to adapt to respiratory spread in humans.
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Update on the unexpected H5 detections from wastewater.
Thanks to all that helped figure this out.
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So what's happening with medical research in the US? This is the cumulative award count from the NIH for the year.
Doesn't look so good.
But it gets worse.
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That’s the good news.
Please indulge me for a moment to get on my soap box to tell you why we should really care about continuing to fight the war on HIV, even though not that many people are dying of HIV in the US.
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Yeah, but it was the second account they created just in case someone tried to look them that surprised me.
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To put this in layman's terms:
A person in Dallas has been infected with COVID for about 2 years.
The virus has mutated a lot in those 2 years.
The patient is shedding so much virus that it was the dominant SARS-CoV-2 sequence from wastewater in a sewershed with 900k people.
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This dream recently became a reality with the development of the drug lenacapavir, a capsid inhibitor where a single dose could last as long as 6 months.
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science.org/content/article/…
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The breakthrough came in 1996 when HIV researchers such as David Ho found that they could treat HIV if patients received a cocktail of antivirals all at once.
HIV went from being a death sentence, to being a life-long treatable disease.
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Fun fact.
The first time NB.1.8.1 was detected in US wastewater was 2/26/25 from Sacramento, CA (reported 3/6/25).
The first time it was found in a person was 3/18/25 from Alameda County, CA (reported 5/12/25).
One of these techniques is faster (and cheaper) than the other.
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BTW, earlier this year PEPFAR activities were abruptly halted.
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nytimes.com/2025/01/27/healt…
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That brings it to 6 cases from 3 continents.
The three Denmark cases were from different parts of the country and had no known contact with one another.
This is looking more and more like an avalanche.
BA.2.86. Three cases of the new SARS-CoV-2 variant now detected in Denmark. The subvariant differs significantly from the other omicron variants that have been seen in the past, and it is designated as ‘Variant under monitoring’ by the WHO. en.ssi.dk/news/news/2023/thr…
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Do you think you've had long-term GI problems since having Covid?
We are performing a study examining the characteristics of viruses, specifically persistent SARS-CoV-2 infections, in stool samples.
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But there is a reason that is even more important. Patients with untreated HIV become severely immune suppressed, and immune suppressed patients are breeding grounds for new pathogens and variants.
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Although HIV became treatable in 1996, the world death rate from HIV didn’t start to go down until almost a decade later. Why then?
A big part of the reason was the program PEPFAR, which was launched by George W. Bush in 2003. This program focused on getting lifesaving drugs in the hands of people who needed them.
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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.
nitter.app/SolidEvidence/status/1…
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For those of you that have asked me why I am convinced that cryptic lineages are coming from people, I can finally point to a pre-print with @dho and many fantastic collaborators in the UWisc and Wisc Public Health.
medrxiv.org/cgi/content/shor…
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Records were meant to be broken.
Our longest detected cryptic lineage is now 2.5 years (30 months).
It is mind boggling how much SARS-CoV-2 material this person has shed.
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I’ve found cryptic lineages from sequencing wastewater.
I’ve found cryptic lineages from screening databases.
This is the first time I’ve found a cryptic lineage from social media.
This was an interesting story.
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Need a little help.
Does anyone know someone that works at the Patuxent Water Reclamation Facility in Crofton, MD that they could put me in touch with?
Here's why.
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We've started a project where we are doing unbiased sequencing of the wastewater 'virome'.
SARS-CoV-2 was the 6th most common human virus we detected.
Who can guess the top 5?
Note - only human viruses count, not counting plant and bacteria viruses (which there are tons of).
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Time to update my lineage cheat sheet.
This virus is doing some strange things.
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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).
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Our NIH grant to study cryptic lineages was triaged this week.
Easy solutions: if you don't want to find something, don't fund anyone to look for it.
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