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Welcome to the People CDC webinar on waste water surveillance for detecting COVID-19. I'm Dr.
Edgar. And we are honored to have Dr. Mark Johnson who you'll be introduced to have Dr.
Mark Johnson who you'll be introduced to and his great research from the great state of Missouri with us.
And also of course all our other comrades from the people CVC. But us, Nemos, who's, the person who's going to keep us on the tech side.
Kenzie Cantrell, graduate student from CUNY, epidemiologist and you know we are happy to have that comrade here and Dr.
Yes.
Rob Walis troublemaker extraordinaire the guy who told you what was gonna happen. He wrote it a couple of times. You're right.
I did, I did. You should have listened. You should listen, but here we are.
They should have listened. And of course, our, there we are. Of course, our port, Laureate and sociologist, our favorite sociologist, Dr.
Sam Friedman from New Jersey, the great state of New Jersey, we're on Yale from Lobs coming in from Minnesota.
Kenzie is coming in from Brooklyn and we know that FRODOS is coming in from, you know, Story of Queens.
We're in a, we continue to be in this crisis of the pandemic. It's not over despite what the major media is saying.
I've noticed that both the Los Angeles Times, the Washington Post and the New York Times have had articles saying, well, things are sort of turning and things might be bad and sort of sort of mini mouth really but at least aware that something's coming or should talk.
And again, we really encourage people to keep our masking, to using all the non-forters, pharmaceutical interventions you can as well as to keep on putting fresher on different institutions in the federal government to make sure that masks are in hospital settings, political settings, educational settings, and we also ask you to be active because this thing ain't over and as we see what's
happening throughout the world thinking about Hawaii today but I be thinking about another country you know next week the catastrophe climate change and sort of the the agro industrial climate change and sort of the the agro industrial policies that have led to these kind of zoonosis, and viruses and there will be more.
We're gonna inform you, we're here to be with you just to company you in this process and it's so good to have Dr.
Mark Johnson here and because he is from Missouri he's going to show us today and can see is going to introduce him to headcom right Kenzie, fresh from the People's Republic.
Hi everyone, I'm Kenzie. It is my pleasure to introduce Professor Johnson today.
Mark Johnson is a molecular, sorry if you can hear sirens in the background too, I live in Brooklyn, very busy.
Mark Johnson is a molecular. Viologist and associate professor of molecular microbiology and immunology at the University of Missouri.
His lab studies, the interactions that occurred between viruses, particularly HIV. And their host to provide new avenues for the development of antiviral drugs.
A self-proclaimed sewage stage and waste water with wizard. Mark Johnson has published extensively on the utility of waste water monitoring and surveillance of COVID-19 and other infectious diseases.
And he helped develop the coronavirus sewer shed surveillance project, a collaboration between the Missouri Department of Health and Senior Services, the Missouri Department of Natural Resources and the University of Missouri.
The project which tracks spiral genetic material and wastewater is one of the world's most advanced programs in tracking Covid-nineteen and identifying emerging variants.
And in today's presentation, he'll be taking taking us through the basics and the cutting edge of such surveillance.
With that, I'll hand it over to Professor Johnson.
Thank you. Can you hear me okay?
Yes.
Can you give me a thumbs up? Can see? Okay, thanks. Alright, cool.
Yes, yes, we can. We can hear you, Mark.
Let's see. Where do I share screen share screen? Just do this. Real pleasure to be back.
I'm gonna go into a bit more, of the. Sort of the underwater this time they did last time.
So here's the overview of what I'm gonna talk to you about. The first is gonna be stuff we all know about that we can use waste water to detect and quantify SARS Cov 2, talk a little bit about when that's useful and.
Kind of where we've gotten. Second part will be the classification and tracking the idea that we can not only say what, you know, how much virus there is, but which viruses and what's happening with them through wastewater.
And then the last part is about wastewater and chronic infections. This is the totally unexpected part of my talk that if you follow me on Twitter, you've probably heard about it's there's a lot more going on than is obvious from our standard surveillance that waste water is helping to review and I'll spend some time talking about that because a lot of what I think about these days.
So this is we were mentioned university, collaboration between. Yeah, University of Missouri, Missouri Department of Health and Senior Services and Department of Natural Resources, for the main surveillance project.
And I have a counterpart who does pretty much half of everything, which is Chung. Who was, an environmental chemist who has also roped into this project at the beginning of the pandemic.
So just This is just illustrate what we get is, you know, we get waste water samples from.
Hey, at 1 point upwards of a hundred sites per every week. And what we give is about a quarter cup and little tubes that look like this.
I threw in this slide because I don't have a new one yet for our new concentration.
But what we do is basically we just take it, we concentrate everything this in there. We extract the nucleic acid and then we do the same thing that they do in labs.
We do, queue or digital PCR and it tells us how much is there. And by looking at that in a big picture we can learn that what is happening in individuals who are shed.
Starting things going up, things going down and so forth. These were the sites we were sampling.
We had a pretty good geographical coverage of the state and every other metric you can think of.
We tried to get Everyone covered. We obviously don't have everyone in the state because there's a lot of septic systems in our state and a lot of small towns and we're not ready to go door to door yet but we we cover probably 60% of the state at this point.
We have a public dashboard. I fought really hard for this and, it's, we were one of the first to have a public dashboard, which is cool and appropriate since where the show me state as was mentioned but it's you know in the very beginning a lot were a lot of people were nervous about having public dashboards that there would be stigmatism.
Associated with. Finding things in certain locations. But I guess it we haven't gotten any push back.
There's really been. Widely appreciated by the public that they can go on a site and get an unbiased readout of what's going on.
You can go to any sewer shed in the state and look at where we are compared to the entire pandemic up till date.
One of the nice things is we, that, the health department also got detailed geographical data on all the sewer sheds that they can combine with all of the patient data they get.
So when there is a patient in the state, they can ping it to a certain sewer shed.
So we know very well how many patients were diagnosed in each sewer shed, which was really helpful in the beginning when we were trying to figure out whether this works or not.
What we did is we would just take a period of time and we would count up the total amount of RNA, SARS Cov 2 RNA that was in the sewer shed and we compared that with a total number of patients that were logged in that sewer shed and it formed a straight line and actually it was it got to be really useful not only to validate that this was working but whenever there was a point
that didn't fit in the line, if it seemed like there was too much or too little, we could usually go in and figure out why and I could give a whole other seminar just talking about the weird stories of finding out what kind of weird shit was happening that caused the numbers from assured said to be off, yeah, it's, a really good reflection in almost every case of what's going on in
the population.
But it's not static. And, I wanna take a minute on this slide. To explain it.
So this is, you can look at this. This is on our dashboard. This is all of the numbers, the cumulative numbers since the beginning.
So the orange line is the cumulative wastewater numbers, week to week since the beginning.
The blue bar graphs are the total number of diagnosed cases and the the yellow is the number of cases specifically in our sewer shed.
They are covered by waste water surveillance. And so whether you look at the entire state or just our shore sheds, they very much mimic each other.
But what I want you to notice is how In the first wave, there was this big difference we saw way more a lot of RNA compared to the number of cases compared to what we saw later.
So this was sort of the original wave when we came out of lockdown. And then we had this second wave, which was Delta.
And you realize this this RNA was not that much higher, but then came the Omicron wave and now they were about even and then with each wave.
The the amount of RNA that we got per diagnosed, not diagnosed case seems to be going down.
And I think that's actually what's happening. Is that it when you have. Less waste wire signal per diagnose case.
It either means there's less RNA per infection or there's more cases being diagnosed.
And I don't think the cases were really going diagnosis was going up that much. I think it's that, you know, as people were getting vaccinated or getting their second or third infection, the amount of RNA that was being shed per case was reducing, which is what you'd expect actually.
And that, continued to go on with every wave until about The beginning of this year, as was mentioned, you know, when we once again decided that the pandemic was over and we basically stopped testing, it reversed again.
So. Now we're back to where we were before where there's way more RNA we're detecting than actually diagnose case but I'm sure this because there's no cases are being diagnosed.
So I think a lot of groups. I think fairly think that wastewater is waste bar and hospitalization.
Records are probably the most reliable ways of knows, knowing what's really going on with the with the virus at this point.
So now that I know that was a short part that was part one that was. Just basic waste wire surveillance.
Part 2 is about, well, what else can we learn? So, starting in late 2022, we decided to someone raised their hand.
Should I answer questions now? No.
You're too fine.
Okay, I'll keep going unless someone says otherwise. Okay, so. About. Yeah, 6 months into it.
We, so maybe we could get some more information about the virus than just. How much is there and at that point there was really no establish protocols for sequencing a virus and waste water.
So we kind of developed our own. So what we do is actually a little different than most groups. So I knew from studying, I'm a v just by training.
What I just do.
I knew from. As a, that the virus mutates in a fairly predictable way that the virus has a part of its spike protein that the virus has a part of its spike protein that is what binds to the whole cell receptor, that is what binds to the whole cell receptor ACE 2.
And that's how it enters the cell. And this is this little blip right now. This is literally the sequence.
This is the amino acid sequence of that part of the protein. And what happens is because that's what binds to the cell if an antibody binds there it neutralizes it it prevents the virus from infecting and that's what you call that's what a neutralizing antibody is those are the good ones that can block an infection.
But what happens is then the virus will start to pick up mutations like this one, which is E 4, 4 K, which was a really popular one early on. It's in.
It's in a part of the spike where a lot of antibodies bind and what happens then if it picks up that.
Mutation the antibody can't. Bind anymore. And then this so this is called an escape mutation which means that it's escaped from certain antibodies.
And because this one part of the spike is where Most of the neutralizing antibodies buying this is where there's a really strong selective pressure to pick up these mutations to adapt.
And so this gives us an opportunity for identification because it basically is like facial recognition. If we can.
Figure out what the sequences of this part of the protein. We know what lineages are circulating.
And so. Our strategy was to try and not sequence the whole genome, but to focus on these little pieces where there are, that which are information rich and just sequence those.
So we do it in such a way that we sequence the whole area as once as one continuous string so that we not only know what mutations are there but we know which mutations went together.
Because if you have a hundred different samples, they're not all gonna be the same and you wanna know Which mutations go together?
Cause that's what will tell you what the lineages are. And it's been really successful.
This is this is our output from the state on, you know, what lineages we're circulating simply based on wastewater.
And it's basically you could in superimpose it on what you learn from patient sequencing.
It's a very, very good reflection. And so this is my cheat sheet or at least this was my cheat sheet.
We've gotten some new ones now, but so each one of these are the sort of where the major, is a concern up through 2022 and as you can see each one of them has a slightly different footprint.
Or fingerprint. These are the different mutations that each of them have in the receptor binding domain.
So I can just look through, it's like, oh yeah, Alpha beta gamma, just game of cataloging.
So. Now I was just gonna I showed this last time and I'll show it again this is this is sort of what happened with wastewater surveillance since the beginning.
So we got going. Our first sequences came out at the end of 2,020. And so by the beginning of 2021 we got this up and running statewide just in time for the first variant of concern to arrive which is in time for the first variant of concern to arrive, which at the time was called the UK variant and then later was renamed alpha.
And it first appeared in St. Louis and it was interesting watching it because we could watch it week to week and we could sort of see it spreading through the state and it spread in a very predictable sort of way.
It followed the population. So it sort of followed the. Interstates to the different parts of the state and made to the urban areas and then after why I was started fanning out into the world part.
It's kind of how you would expect it. And so this was in March. At this point in time, the, alpha variant is all of the, green crosses.
So we were seeing it all across the state. And if you had looked up at the CDC at that point in time, there had been a grand total of 5 sequences from the entire state.
When in fact it was already everywhere. So it just illustrates that. You know, patient sequencing has gotten so had got faster for a while, but now it's slow again.
So the waste wire really gives you a much faster picture of what's going on and it's a comprehensive one because it's showing you the entire sewer shed and just not.
What patients you might have sampled. So by the end of, of the, of, let's say this is April, 2021.
If you recall, this is the first time the pandemic was over. Everyone thought it was over. I thought it was over.
We were, the numbers were getting really low. There were actual sewer sheds that for the first time were non-detectable.
It was mostly alpha variant and a few others but. Things were getting really quiet. It was, yeah, it was the lowest we had ever seen it.
And then something happened. On May tenth, we saw a new lineage appearing in the Branson sewer shed, which is if you don't know it's a a tourist town has a lot of country music kind of stuff.
Air conditioning, indoor singing, really good conditions for a virus to spread. Yeah, so it appeared and, we looked it up.
It was B. One dot 6 1 7 dot 2. There was no alpha beta gamma yet at that point.
But World Health Organization, it said that this was the fastest growing of the, of the, sorry, of the India variances they were called at the time.
But there was no, nothing, we had seen this here and there in the US, but it really hadn't caught fire until until this time in May when in northern Arkansas in Missouri this lineage finally caught fire in the US.
By the next week, it had already sort of spread throughout the state. So it moved into both sewer sheds and Branson and it showed up and then started showing up in small towns.
It's spread in a very different way than the alpha variant had. And you probably don't remember this, but in May of 2021 there's this, Lynn County or Brookfield.
This was ground 0 in the entire US. If you looked at a map of COVID. This was ground 0 in the entire US.
If you looked at a map of COVID cases in the US, there was this big red spot in Missouri, if you looked at a map of COVID cases in the US, there was this big red spot in Missouri, which was this is something like 4% of the population got infected over one week period.
And we looked at it and it was all this new lineage, which later turned out to be Delta, but it didn't have the name yet.
But within a week it showed up just about everywhere in the state, but this one was almost The appearance was almost the reverse of the prior wages.
It was showing up in rural point parts of the town. And I really think this is probably because people were taking trips to Branson and bringing it home with them.
But eventually made it everywhere and then from that summer until Until Omicron, this is what the map looked like.
It was all Delta all the time and it reeks some
So here was an interesting thing that we could, and I'll comment on this more later, but we could we could look at total numbers from the sewers sheds and we could look at when new lineages first appeared.
And what was really interesting was like with Alpha, we would see it first appear in a sewer shed and it would displace the other wages but it never really caused any major spikes in the total virus, at least not in Missouri.
Whereas with DELTA, it was just so predictable. We'd see Delta in within 2 or 3 weeks, it popped and we would get these huge numbers and then the and then eventually the cases would follow and it was a mess.
And this was another way of depicting it. This is actually one of the really cool uses of our data that I never expected.
There was a data reporter from Time Magazine that reached out and she was trying to find a way to illustrate to the public.
What the Delta variant was really doing. And but she would try and get more detailed data about like how long it takes between when Delta arrives in a location and when you see a spike in cases, but you know, you can't really easily get below state level data in most places.
But, is all de-identified. So she could just come in. It's like, look at our data.
So she broke it up by like look at our data so she broke it up by county so what this is every line is a different county.
And she normalized it that point 0 was by waste water the first date where we detected Delta in that sewer shed.
And then the y-axis, the upper part of the line is showing how many cases were diagnosed in that county with COVID and without exception.
Delta arrived and within a certain number of days off it went. There was variability, but it did not track very well with vaccine status or anything else.
It seemed at least at that point in time that Delta was Having a similar output on almost every location.
And now moving on to. The Omicron lineage. So this is. It really stuck out like a sore thumb.
This was we were also doing surveillance at this point in time with from all the sewer sheds from New York City.
This is a sample that we collected on November 20 first. So this is the week before Thanksgiving.
So this is before we collected the sample before the world even knew about so we collected the sample.
This is about the time that there was that anime conference that you might have heard about, which was the very first cases of Omicron in the US.
The first detection from waste wire was the same time that the first patient was detected given that give it a day or 2 and those were cases that the first cases were people that they were targeting ones that they knew had come in from South Africa or places where Omicron was spreading, but there was in the wastewater.
Stuck out like a sore thumb and had 4 times more mutations than any of them prior circulating.
So it took a little while for it to get to Missouri and it took a different route in. I there had been a few cases in Nebraska, which is probably how it got in because we started seeing it in the northwest corner of the state.
It still is mostly Delta, but then Omicron showed up and it was Again, it spread more like Alpha though.
It kind of followed the population centers quickly showed up in. Spreading mostly in the cities and then eventually making its way out into the rural parts of the state.
And eventually, it was all, all the time. And then all of Omicron sub lineages, which were continuing to follow.
So this is my, last part about this is What can we do with this information?
When do we know that a lineage is going to be a problem? So this want to point out that for the most part, when you look at where we saw surges, Almost all of these have been variant driven.
So you see this, surge in the, summer of July, 20 first. Well, that very directly and clearly was a result of Delta emerging.
It was very clear. Ba one, same thing. It arrived in December, which led to this.
Massive surge. And then even in this, you know, spring about spring of last year, it was It wasn't a major surge, but there was a clear uptick which correlated with the arrival of BA 2, 12 one and BA 5.
And then again, even more minor was with BQ 1 one. But the one exception is Delta.
At least in Missouri, and this actually happened a lot of places. There was actually a second surge coming on.
Delta was actually surging when Omicron arrived and it probably would have caused quite a
It would have gone differently if it weren't for Omicron. I'll just put it that way.
So there are cases like with Delta where there is a second wave that was probably driven by weather where there was a second wave that was probably driven by weather and things like that.
But for the most part New waves of infection are driven by the emergence of new lineages.
So the question is, can we use wastewater is an unbiased readout that can warn us when some of these when a new wave is about ready to hit and we've looked at this and we kind of can.
So, this is all of those different lineages. One of the things we asked is how long does it take for between when we first detect the lineage and how long does it take to become dominant.
We can also look at how long it takes to spread across the state. But most informative is how, what happens when a lineage arrives?
Is there is there a correlation between The arrival of the lineage and an increase in the total virus.
That is actually the most valuable indicator. So Spreading for or across the state, this is interesting.
You would think, you know, with all of the lineages that were trouble, they did spread across the state really fast.
But that's actually not in and of itself a great indicator, believe it or not, because there have been several cases where a new lineage has moved in and it just appears everywhere, not literally everywhere, but we'll see it multiple watch of the state just really quickly and then it won't go anywhere.
Because I think there are some of these lineages that probably are somehow infecting a subset of the infection, but just seeing how broadly or quickly it spreads is not actually that helpful.
Slightly more helpful is how long does it take for a lineage when it arrives to become the dominant lineage in that sewer shed.
This is a little better, but this one also has a caveat, which is that when numbers are really low, when SARS Cov 2 levels are really low and we go to sequence, it becomes stochastic.
And what we're sequencing is probably actually the sequence from just one patient. Whoever happened to have a high level, the day we sampled.
And if it's only from one patient, whatever that patient has is going to be a hundred percent of what we detect.
So it when the levels are really low, we tend to, we don't tend to see a big breakdown.
So it could give you the false impression that a lineage has become dominant, which may or may not be the case.
But in terms of looking for The best indicator, I think it's that what happens once the lineage arrives?
Does the arrival of a lineage correspond with an increase in the total of viral level and that is what seems to be the best indicator.
So that's what I still do. This is what I was doing earlier today. There's some new lineages moving in.
So I look at what where the new, just arrived and then I go to the data and I say, okay, has arrived and then I go to the data and I say, okay, has there been any change in the RNA that's associated with the sewer sheds where this lineage arrived and that seems to be the best indicator of what's going to be trouble.
Okay, so now, the fun part. What's working beneath the surface. Can I go back?
Yeah, okay. So let me remind you that the way we do sequencing is slightly different than most places.
We're, the way I say it is Basically, we're doing facial recognition, whereas most places are doing whole body scans, but they aren't doing whole body scans of individual viruses.
They're by, they're doing it on all of the viruses and then averaging them together.
So they know like by mutation what is present, but they don't know what mutations go together.
So it's really hard. By the standard method to tell if there's something new and unless they already know about it.
So the way we designed it because there is no, I didn't know what was coming. I wanted to be able to tell if there was something new, which was why we designed our sequencing strategy the way we did.
And sure enough, shortly, shortly after starting our sequencing, just a few months in. We started seeing something that didn't make any sense at all.
So this is was in early 2021 and it was from there was a sewer shed from St.
Louis. Where most of what we were seeing at that point in time was the alpha variant or the UK very end it was as it was called in the time.
It only had 2 mutations in its receptor binding domain, but it was enough to fingerprint it to say, oh, that's what's circulating.
So this lower stuff that I've labeled cryptic lineages are the new lineages.
We started seeing. So each line is a combination of mutations that we are seeing together. And they were totally different than anything we'd ever seen or really had hardly ever even been seen in patients.
They accumulated at 9 different mutations. It appeared every week for 9 for about 2 months and then it disappeared.
And it actually was a large part of the total signal. So like fifth sometimes more than 50% of the signal from this sewer shed were these weird lineages that I didn't know where they were coming from.
They didn't match anything they had ever been seen in a patient. Then or since. So kind of drove me nuts and I started reaching out to lots of other groups that do waste water surveillance to see whether others were seeing this kind of thing.
And for the most part they said They don't know because they were doing whole genome sequencing.
They're not really geared up to see things that are new. But the one, the exception was in New York City where they were using a similar kind of strategy where we, we started working together.
And sure enough, so my first question was, is this lineage from St. Louis also in New York?
Is this like a lineage that's underlying, you know, it's just only infecting a certain population that never gets tested.
So we didn't know. But eventually we got a lot of data and we found a, but we found by the end of 2021 10 of these lineages most were in New York City there was one we found in California.
There was one we found in California and there were 2 in Missouri. And this is where I got into it.
I went down, there was a real red herring, which is a lot of these lineages have this one mutation called Q 4 9 8 Y, which at that point in time had never been seen in a patient in any background.
But one place we had seen it a lot is when they made rodent adapted versions of SARS Cov 2.
It that that mutation all by itself allows it the virus to be able to infect. Mouse based using mouse.
So I'm like, oh. This is coming from rats. It made total sense. And so I was totally convinced for the longest time that that's what the source of these wages were is from some kind of weird animal reservoir, most likely rats.
But there were a few other. My initial hypothesis is they was coming from an animal shelter. But then we would figure out that there's no animal shelters in the sewer sheds.
So that didn't really make sense. The next one is the most The one I like the most is coming from some kind of wild animal, presumably rats.
Another possibility is that this was actually like some isolated cohort that doesn't ever travel like in a nursing home if they like just kept infecting each other.
But the last thing I thought this was coming from is an individual shutter because A lot of these lineages we were detecting in in sewer sheds with half a million people.
There was just I couldn't believe that that much material could be shed by one person, but spoiler alert, I was wrong.
The answer is 4. So this is when I. I develop my favorite tool from wastewater, even more so than sequencing COVID.
My favorite tools, there's a group at Missouri that had developed this technique where they could amplify the ribosomal RNA from any water sample just to figure out what animals are pooping in this water.
And it works really well. So we This this was the first sample I collected. It was from the creek that's in my backyard.
This is Hankson Creek, which is, flows through, Boone County through Columbia.
And we did this assay and just looked to see what was there and it was there's so many critters whose poop I could find in there we could find red squirrels, gray squirrels, beavers, cows, dog sheep, a whole bunch of different fish and then a whole bunch of different birds.
It was, I'm like, wow, this assay really worked. So I thought this is going to be this is gonna sell it for me because we can go to our sewer sheds where we have cryptic lineages and I can actually take the same sample and we can see what poops there and we can figure out what the potential hosts are.
And so we did this with New York City and like within Y 3, this is one of the cryptic images we had there. This is published.
It made sense. There was. Actually, a kind of frightening amount of rat ribosomal RNA in that.
So I'm like, Oh, this makes sense. This really could be the source. But then there were other sewer sheds also from New York City also had cryptic lineages very regularly and we would sample them over and over and there weren't any rats there.
We always saw cat dog and, though, in rat were the 3 most prominent of the animals, but the other things we always detect into the things we eat.
So without exception, we would almost, we would find chicken, pork and beef. Which is because people eat it and it gets shed that way.
But, so this was where we were at the end of 2021. We didn't know where these were coming from and it was driving me crazy.
And. And that's when Omicron moved in. It was actually really frustrating at first because I was obsessed with figuring out where these, were coming from and then Omicron moved in and of course it was causing lots of problems but in addition to all the problems it was causing by you know infecting and killing people it was also causing people to shed so much fires into the sewers shed that all of our cryptical lineages
disappeared because they were just drown out by all of the Omicron signal. And in frustration I decided to design a new amplification strategy which explicitly does not amplify Omicron.
So it sits down on a place of the genome where Omicron has a bunch of mutations so that you can only amplify sequence that was from a lineage before Omicron.
And we tried it out and it worked so tam well. Like all like New York it was like a hundred percent Omicron and then we would try the new primers that and we amplify an Omicron disappeared and all we would see was our cryptic lineages, which were still there. They were just under the surface.
We couldn't detect them because they were being drown out. So once we had this, I'm like, we can actually make some, make some progress with this to figure out how prevalent these things are.
And maybe figure out where the hell they're coming from. And that's actually when I signed up.
For Twitter, my colleague in New York, John Dana, he had Twitter account. He's like, we should post this on Twitter and see if we can get people to send this way. I'm like, that's a stupid idea, but I'll do it anyway.
So I started my Twitter account and that's I chose my Twitter handle, which is solid evidence, which is just I'm very proud of that Twitter handle, but it was it So many people sent us their waste water samples from that one tweet.
I couldn't believe it. So we got a really good coverage of the United States. And learned a lot more about cryptic lineages and where they are.
But the one that was most, useful was one from Wisconsin that, my collaborator, Martin Schafer, who's, it, is in charge of the wastewater.
Testing facility. There and they're also a really great organization. They do great waste wire testing.
He sent me a bunch of samples and one of them had this really interesting lineage in it.
It had all of the it has many mutations as Omicron did, but it was totally different mutations.
And so he sent us more samples to see how prevalent it was and we could detect it every darn week.
And this is in a large sewer shed and I'm like. You know, we could maybe track this guy and figure out what animal was coming from.
Because remember I still believe that it was coming from an animal. And so we started to track it down.
We started to do our ribosomal RNA to figure out what the candidates were. One of the candidates was once again dogs were showing up in the wastewater and so we're like, oh dogs.
And so, this is a picture of some of my collaborators in Wisconsin going to the local dog park and then collecting water samples there as well as going to the occupants and collecting.
The feces from their dogs and sending them to me to look for COVID. That's in addition to I don't know how many hundreds of rat herds that were sent to me from New York that were all COVID negative.
So yeah, we're trying to find the source. It had to be coming from somewhere and then we're like, okay, let's try and find the source. It had to be coming from somewhere.
And then we're like, okay, well, let's try and track it This particular waste our treatment plant had 6 main lines that went into the main plant and so we tested them all and only one had the lineage.
And then that one was fed by multiple substations and we tested them all and once again they were all only one of them was positive for this weird lineage.
And then we worked our way up first through 17 man holes within the city and then we got to the village and we went through another 21 man holes again just figuring out okay where is this lineage coming from and we finally narrowed it down to a single manhole?
And we thought going into this, we were going to find an animal shelter or a nursing home. We get to this manhole, there's only one thing that services that contributes at this manhole, and it was a company.
Just a company, 30 employees, serves the public. Didn't make any sense. So we the Department of Health was leading everything at this point along with the CDC and they went to the company and said, okay, it seems somehow the signal is coming from here is probably someone in your in your company could we test them to see if any of them have a persistent COVID infection that maybe are not aware of.
And the company came back and said, Sure. You can do that, but first can we figure out which toilets it came from?
So they had 2 sets of toilets in their facility, one that was only used by employees and the other one was used by the general public sometimes people who are coming in to do business there and so we tested them both.
And it was only in the one that was used by their employees. But this is where everything turned around for me because they sent me this sample.
To see whether that it was there and oh my god I had never seen so much COVID in a waste water sample in all of the time I've been doing this.
It was a thousand times higher than anything I'd ever seen before. There was so much virus there that we could detect it with.
I mean, this is, I don't know how much it was a composite waste water sample over a 24 h period and that could take 2 drops into test detect the virus with a rapid antigen test.
It was insane. And this is when I realized that everything I had assumed was wrong. That people there are people with persistent infections.
That shed a thousand times more virus than a typical acute infection. And that is what's leading to these weird cryptic lineages that we're detecting.
So to wrap up the Wisconsin story, which unfortunately, well, It doesn't come with a satisfying end.
We never found the patient. We, they did communicate with the employees about the What was going on?
And offered free nasal testing about 2 thirds were tested by nasal pheringial swab and they were all negative.
So either they're not. Either the infection was not in the nasal cavity or the person that was infected did not get tested.
We don't know which, but that was sort of at that point the health department is like this is no longer public health this is research you need to get in the IRB.
So We got an IRB, but that took a long time and 4 months later, before we managed to go in to do patient testing, the signal disappeared.
I don't know whether the person took a different job. Or I don't think they died, but or maybe they went into remission.
I'm not sure, but you have IRB was eventually approved and we went ahead and I've actually now been to this company.
I've met with the employees. None of them looked obvious to me as the carrier. I got a selfie with the manhole that we tracked it down to, but all of the stool samples we've collected have so far been negative.
So I don't know if the story is over or not, but it did. It was very valuable because it taught me that these weird that there are very, very long persistent infections in patients that.
Are the source of these, we're doing, and I think these are things that we should be carrying about.
This is, an illustration of something we, keep trying to find a good way to illustrate it, but.
The mutations that we see in our cryptic lineages. They are forecasting the lineages in these persistent infections are basically evolving on the fast forward button.
They're picking up the same mutations that eventually are found by circulating. So this is just a few examples of some mutations like in 460 K was in the.
Wisconsin wage out of the starting gate. That mutation had never been really seen in patients at that point, least not in any circulating ages, but then by in the end of July of 2022 the Omicrons found it and now pretty much a hundred percent of sequences in the world have this very same mutation.
Same with a bunch more of them. I, here's another, I mean, now here's the rest of the story with the Omicron lineage.
When the Omicron was first announced, when they first mentioned it, it was just before Thanksgiving in 2021.
And I was with my family driving up to Chicago for Thanksgiving and my, colleagues in New York wrote to me, is like, did you hear about this?
And and they sent me the sequence and I was Daring at it. We were all staring at it and we were trying, we were going through mutation by mutation.
Every single one of these mutations we had seen in a cryptic lineage before, but we were trying to remember.
Is this one of ours? I mean, we knew our lineages at that point. They were very reproducible and we eventually figured out, no, this is not one of ours.
This is not one of our cryptic languages, but it has the exact same, it has the same mutations we had already seen, but just a new combination.
So that's led me on the search of lots of more of these. In addition to getting samples from all over the place.
We can also just go into public databases of other groups that have done waste water sequencing and upload it into, a public, server.
And once you know what to look for, you can find that these guys are all around. I need to update this slide because there's now 43 cryptical images. I found 3 this week.
It's crazy. They're still around and most of them are very old. So, here's an example of one that you might have heard about.
I took a slightly different tact with this one. So I was going through the public database and we found this really unique cryptic lineage from Ohio.
I'm like, that's really interesting. And so we made a specific search to look for other sewer sheds that might have this combination of mutation.
We went through all of the sewer sheds in the United States and we found that It was somewhere else.
It showed up in the second sewers all we knew initially is it was also in Ohio and we eventually figured out it was a small town 40 miles away and it was present exactly the same days in both locations.
So it's pretty clearly someone who either lives in Columbus, Ohio and commutes to Washington courthouse or vice versa or for some reason.
Zigzags between the 2. I forgot to mention this, but the Wisconsin lineage, we know now.
That it was derived from. A lineage that was circulating in late 2020.
So whoever that person was they were infected by about for about 2 years when we when we were detecting them.
Same thing with Columbus. It was this one, this person has been infected for over 2 years.
It is a highly divergent lineage. And I should mention that like in Washington courthouse, like in May of this year, They were seeing the highest levels of COVID and their waste water they have seen to date in the pandemic.
And when we when we did the sequencing, it was entirely from this one person. So there are cases where these lineages can really throw off the numbers.
So these one of the useful things we've gained from these lineages is that we, We can look at, like I said, that there are mutations that appeared in Omicron that we have seen before.
The SARS Cov 2 is highly convergent in terms of finding mutations that are of an advantage.
And we were we started going through all of our cryptic lineages to look for mutations in common and the most common one we found that is not generally circling is this 1 9 77 que and it actually isn't it's we it turns out a group already figured out what this mutation does.
It stood out because this is one of the amino acid changes that is different between SARS one and SARS 2.
So when you go from K to Q, you actually go back to the SARS one sequence. And so this domain of this protein is actually a protease.
It cleaves other protease. And if I can go into the weeds for just a second.
I answerropomorphize too much, but this is the virus has this really clever strategy.
So this is a protease that cleaves the poly protein at the first 3 sites. And those sites are different in the sequence where the protease cleaves is exactly the same sequences at the C-terminus of these little proteins called ubiquitin.
Which is this thing that the cell uses for signaling. And we know we now know that this mutation greatly enhances the the proteins proteins ability to cleave poly ubiquitin change.
So what this does for the virus is, often poly ubiquitin nation is how it triggers the innate immune system that there is something wrong that triggers the innate immune response.
So this is this mutation is part of a silencing mechanism. It helps the virus.
Hide the fact that the cell is infected. So you might wonder, why is this not in all the circulating lineages and I don't know.
It has appeared a few times and I'll talk more about that in a second, but I think this might be one of those cases where, what is an advantage in a chronic infection may be a disadvantage in a circulating lineage.
So my best guess is that if a virus is infecting you and it's not gonna make it.
I mean, your immune system is gonna kick its butt in 5 or 5 to 7 days. So it's got this short time window of which it can circulate and then spread to someone else.
And I'm guessing that there is a sweet spot in terms of how much of an immune response the virus wants.
It probably wants you to be at least partially symptomatic so your coughing sneezing all that stuff but That's my best explanation for why we see this mostly in persistent infections, but not in, those that are shedding.
So I'm not the only person that looks at chronic infections. There have been several papers, but here is a really elegant one that came out very recently from the Mount Sinai group in New York City.
They actually, had a really big data set on patients that were part of their whole, Mount Sinai hospital system.
And they found this set of lineages that it actually won that started out in one patient and ultimately led to 4 different patients, but the virus did the same kind of thing.
It went on. Evolutionarily, you know. Fast wire in terms of evolution and sure enough midway through this long infection it picks up this exact same mutation that I was just mentioning this for 79 77 Q.
But what's interesting about this one, I, remember these are persistent infections and although this did not become widespread, it was in facting new people.
It isn't, you know, Persistent infections are not necessarily non, non spreading.
This is an example of where it can start spreading again. So one of the things we could do then is we could start using this.
Information about what is probably a persistent infection to look at. How many persistent infections are there?
How many of the sequences in the database are people that were actually persistent infections and he might not have known it.
So this is really interesting. What I'm showing here is all of the sequences that were appeared in the database, which were BA one, the original Omicron lineage.
It was a very clean thing because it took over. It was absolutely everything and then it disappeared almost as fast as it was displaced.
So if you look in the database of whether there are any BA one lineages that have this 9 77 key mutation, what's really interesting is You hardly see any of them when .
One was circulating. But after it was circulating, you start seeing them pop up and they pop up every sort of regular.
Clip and they're continuing to pop up today. You'll still occasionally find VA one sequences from patients that were just sampled.
That the case I just mentioned, this was a BA one derivative that was, Yeah, they continued persisting in these patients for years after.
So you can tell that, okay, now this is actually in a good indicator because these are all presumably BA one persistent infections.
But there was one that stood out that didn't make any sense that there was this one, Omicron lineage, which was BS one, that had the same mutation.
But it was actually circulating there was like 600 patients and so I dug a little deeper into this and it's really quite interesting.
So the the BS one is also BA 2 3 2 one so it's derived from VA 2 3 2 And the first place that this BS one appeared was in Vietnam.
And so what I'm showing here is How much there was of these 2 lineages in Vietnam.
So. In blue, these are all the 2 3 2. These are all the parent sequences. The parent basically disappeared.
And then at the very end, this other one appeared. The BS one. And what was interesting is when it first appeared, it had already picked up 38 nucleotide changes.
This was not a virus that had been circulating. I guarantee you what happened was there was a patient that was infected with BS one or with the 2 3 2.
And it was a persistent infection for multiple months and then what happened later in the year is that it started circulating again.
This one it had several mutations that gave an advantage it ultimately was drowned out by the XPBs, which also had a lot of.
Advantageous changes, but it again shows that these persistent infections that start picking up a lot of mutations, they are sources of new lineages.
So what I've tried to do is, also the reverse. I wanted to ask how often do persistent infections have this mutation?
And so if we use, I've done a set with this for several ones. So if I look at sequences that I believe have to be persistent infections.
So I, if I look for BA one's that appeared after BA one was completely gone.
And I say how many of those have the K 97 or the 977 Q?
It's about 5%. Whereas when it was actually circulating, it was point 0 0 2%.
So there's clearly a thing. Is more commonly found in persistent infections, but it's not found in every percentage infection.
But I can use this to sort of do some reverse checking to look back at how often do we see this mutation?
And if we assume that it's 5%, you come up to the conclusion that about point 2% of the sequences in the database are actually persistent infections or about one in 500.
And here's the thing. We don't really know who these patients are. You usually can't track them down.
I've tried, believe me. We have no idea what their symptoms are and we have no idea what the long-term impact is.
I mean the question that really drives me is How much of long COVID is actually persistent infections in parts of the body where we're not checking.
We know from autos these studies that there are cases of circulation in the heart. In the GI tract and lots of other places, but it's hard to get a gauge on whether the virus is still replicating there and causing problems.
And I just like to mention here that there is a precedent for this kind of thing, which is with domestic cats.
There's another coronavirus called feline coronavirus. It's not a starbacco but it has a lot of things in common.
It also has a fear and cleavage site but it also has a fear in cleavage site but infects the GI tract.
And what infects cats, some of them clear it, but some of them have a persistent infection that lasts for years.
And this isn't necessarily an immune compromise cap. It can, the best indicator of whether a cat has feline coronaviruses, whether it's lived with a lot of other cats.
Most of the time it's asymptomatic, but about 5% of the time it it progresses to a new troopism called few line infectious peritonitis which is pretty much always lethal unless you treat them with COVID.
And so here's just some of the patients we found just going through databases. There are some pretty out there ones.
The most diverse ones we found are still from wastewater, but there is some pretty darn diverse ones we have found just like there was this one from Indonesia that was submitted last month.
It's a delta derivative. I tried reaching out to them to find out anything I could and they pulled their sequence off of DSA and won't respond to my emails.
It's kind of frustrating, but, there's sort of a catch 22,
It's hard to find out information about these patients when we don't have evidence whether this is hurting them or not.
But it's hard to find out whether it's hurting them or not unless you find out about the patient.
So that's my current circle of frustration. But we're making progress. There's a lot of groups that are starting to appreciate the persistent infections or something that deserve our attention, both for the because of the threat to the patient, but also to for the the broader population because this is where if there is a pie you know the Greek layer that comes after Omicon.
I guarantee you this is where it will come from is a persistent infection. So this is my summary.
Yeah, cryptic, persistent infections of people that are shedding a ton of virus.
They almost always have an incubation period between when we first So like when out there's always a lag between it when a lineage is circulating and when we start seeing cryptic lineages because it seems to have to go through certain things in the body before it can become these massive shares and I'm sure we are missing a lot.
We don't know what the symptoms are these patients are. I'm guessing their GI infections, but I don't know that.
And we don't know what they can. But I guarantee you what we're seeing is the tip of the iceberg.
We only find, so we're up to 43 cryptic lineages. These are only when there is a persistent infection, they have a lot of changes, they're shedding a ton of material and happens to be in a sewer shed where I have coverage and the data is publicly available.
I'm sure there are tons more that, will, this is part of the next wave.
It's no knowing what's happening with these patients. Enormous collaboration. I have a thousand people I think but I think my time is up so I'd be happy to take questions.
Thank you.
Thank you so much for that, Doctor Johnson. That was, you were actually right on time.
Oh good.
Right, so no problem there. Now what we're gonna do is we're gonna deal with the questions in the actual chat and I know that for us that you have your hand up so do you wanna intervene a little bit for us and Rob's gonna be also continues some questions.
Thank you so much for this presentation. Okay, nope, sorry, all right. Dr.
Yeah. Yeah. Oh.
Rock Wallace, 20, Give our friend here from Missouri some questions and I really appreciate your work and learn about you but your friends do tend to send you poop.
I'm a little worried about that Mark. Sure.
Yeah, yeah, this is not an open invitation everybody, okay? Don't just send a poop in the envelope.
Send me your shit! Yeah.
Yeah, a wonderful presentation and we have like, 35 questions. I don't think we'll be able to get them to all them.
But we did ball back out a half hour to throw some at you and there all over the place and we're gonna try to send them to you in a kind of order of the work that you're doing so that's I'm going to start for the first one because when you presented to us in house a few months ago, I think you did address this.
One attendee asked if there is time. Okay, I'd like to hear more detail about how wastewater analysis is conducted or if there are resources we could review independently that have a good explainer, that would be great.
Thanks. So how do you?
So, do you have, we have, so our, Source Jed surveillance project is actually a story map, which explains the whole process if they want to go there.
Do you have the website? I can grab it if you want.
Yes, yes, we will, that up in, in short order. So, oh.
So there's several sites now to get information, the news site and WSS. So if you Google NWSS CDC, national data.
It's not as fine detailed as a lot of the states. Biobot also has a really good dashboard.
Scan has a good dashboard and a lot of states have their own individual so Missouri has Missouri data is all transferred to CDC.
So you will see the news data on their website from Missouri, but there's a lot more detail in the Missouri site because we'll, drag it down to exactly what lineages are on each tourshed in the state and what's moving in and all that stuff.
Okay, and so those sites will explain the actual testing process of. Gathering the samples and how do you amplify the, RNA and all that.
Is that correct?
Yeah, if you look at the Missouri story map and if you still have questions, email me. I'm happy.
Okay, fantastic. So here's another question. I think maybe he has to do it's you know the graphs seeing over time the change will you please explain how to read and interpret waste water data graphs.
Well, let's see.
Let me share myself, where did you go? Just gonna share a screen again I lost you with Zoom.
Share screen.
I assume you mean the just the surveillance, the numbers.
Are you talking about the
I think, some sort of time series where you see, in a, yes.
Sorry. Like this one? So the Y access is just for this one. This is the state cumulative.
So, just pay attention to the orange line. This is the cumulative. A amount of SARS Cov 2 in the state.
So for each sewer shed, we measure how much virus is in each quarter cup. We multiply that by the total.
Sewer shed volume and then we add up all the sewer sheds from the state.
So this is the total. Copies of RNA that we detected for the whole state. So it.
The higher it goes, that means that's how much that means more virus was being shed during that time period.
So Y access is just amount of RNA x-axis is the date of collection. Does that help?
Okay. Yeah, I'm just gonna continue to throw as many questions as we can. We're up to 40 questions now.
And looking at, watershed data in my area. Someone asks, how can I read it to best assess current COVID risk?
What are the benchmarks to consider?
The best thing is to look at each sewer shed compared to itself. So the best thing is to look at that sewer shed over time and don't say how high is my number compared to Boston say how high is my number now compared to where it was this spring or last summer or compare it to when you know things were bad and if they're they're the same place then that's when you want to be
concerned if they're much lower than that you know it's corresponding less numbers nationwide are still on the low end now but not as low as they were a few months ago.
So it's a county by county or city by city. Here's another question. Post recently said that sewer only detect only detects a approximately half of total cases.
Okay.
What is your opinion and how should that issue if true impact interpretation of sewage data? I am asking for a link to the source but don't know if it will be obtained by the end of the conference.
Okay. Also this is gross, but I heard a long time ago that fecal can be a source for COVID testing, for example, in pets, which I think you covered.
Yeah, it, I've actually encourage people if they think they have well gone COVID to go ahead and try a rapidly engine test because Usually there's only one lab I know of in this in the States that will test stool and most doctors won't send the test there.
But if they find out for themselves, just don't use too much material. You just dip it in the in your toilet water and use it.
Okay, so the thing about 50%, I don't know that could mean one of 2 things.
It could mean either that only 50% of the population is covered, which is Probably about accurate because you can't get everyone.
There's a lot of really small sewer sheds and a lot of people on septic but you know the virus if I've learned anything is it does not stand still and what it's if it's happening.
In here is probably happening 10 miles down the road. I mean, Delta swept Missouri in 2 weeks.
It doesn't stay put. The other thing, but what they might be talking about is that Not everyone seems to shed in their stool.
The data is not entirely clear. And it's not even clear for sure whether what we're detecting is because of GI infections or because of nasal snot that makes it through your gut and we detect it.
So it's not every patient, but I can tell you it is. On a population scale, it is still very representative.
Yeah, I think a lot of questions here, speak to this issue of, whether or not COVID persists and everybody is it cleared from most people, it's fully cleared and some or in a what's the usual clearance time and it sounds like what you're doing is at the population level that allows you to make kind of certain generalities with even those conditional on what variant is around
and what watersheds you're looking at.
Yeah, I mean, there is variation, but it is generally very representative of what's going on in the population.
And so sometimes there will be lots of infections and not that much RNA. That probably means there's a lot of mild infections.
It's It's, it's not a one to one thing, but. It is reflective of the amount of virus circulating in the population.
Right. And for good reason, a lot of the questions are fascinated by the long haulers.
I mean the fact that how you got we're able to identify one's a magnificent detective work there.
One's a magnificent detective work there. So one question that's kind of representative of this is do you know if someone is infected for years with the cryptic work there.
So one question that's kind of representative of this is, do you know if someone is infected for years with the cryptic
I don't think they are. And the reason I say that is because If they were contagious, they would infect other people if they were infecting other people, it would not remain geographically constrained.
So, so far none of the cryptics that I have been following have escaped. But I gave you a few examples of where escape has occurred.
So it's not that they can't happen, but it's probably not easy. So my suspicion is that these really extreme cases are probably GI infections.
And for whatever reason so First of all, you, it's probably nearly impossible to get infected with COVID through the from waste water or from stool.
The virus we've tried culturing it even from even from that sample from Wisconsin that was just through the roof high we could not culture virus out of it.
It seems to not live very long in the GI. Environment. So by the time it's excreted, it's not infection.
So I don't think it's easy for it to spread. Because of that. That said, I think the virus, when if the patient is doing bad enough, the virus will become systemic and probably will receive parts where it can spread.
Right.
I mean, think of it like late term HIV infections where it just goes crazy. So I mean, they're all potentially gonna be contagious, but there's no evidence that any of the ones I've reported are currently contagious.
Right, so the person who was asking about the possible danger of environmental exposure from sewage can rest easy that that's not gonna be the infection.
Yes, it's. There's there was some weird reports from China about sewer, but I mean I can just say that from our own work it's It's pretty much dead.
Right.
What's in waste? And there's been lots of groups that also have done this with animal studies and in other studies and it's there's only a handful that we're ever able to recover even from fresh fresh school samples.
Right, right. Okay, so here's a, another methodological question. It says, at what, or even an ethical aspect to it, at what level catchment do you start to question anonymity of the sample?
What conversations were taking place when discussing how far upstream to move the sample collection.
Yeah, that's a great question and this is something that really needs to be decided by more than just me and my colleagues.
In general, we don't. So with Missouri, we don't report. Anything that's smaller than a thousand people.
I'm pretty sure that's correct. I mean, we, that's where we, that's where we start getting really cautious.
In terms of When we were tracking the lineage in Wisconsin, keep in mind when we were tracking, it wasn't until the very end that we even realized we were tracking a person, we thought we were tracking an animal.
So, at what point is, and that's a great question. When someone flushes the toilet, When does it become public?
Where you can no longer where it's no longer yours to claim. I mean, if it's like garbage, the moment you put it on.
The curve, the cops can legally come by and go through and see. I mean, in terms of like legality, there's a difference between, of course, legal and what's ethical.
And I guess the answer is I don't know and I think this is a conversation that needs to be had by more people than just me.
We need to include. Ethicist bioethicists. I will say with Ohio, I was public about that, but I did not narrow it down to a lot of people were saying I dox the person but you couldn't narrow it down to Less than 1,600 people because there's a lot of people that move between those 2 locations.
Right, there's the element of trust being an epidemiological variable that has to be included in all this and certainly we don't want people to become so distrustful that they refuse to use the bathroom anymore and decide, yeah, in the backyard.
Yeah.
So the public health, so speak don't grab onto it. But.
Hold on. It's a tough one because though at the same time, if If It I mean, I don't know what the outcome is, but if it really is something that could kill the person.
Alright.
And it's treatable and they don't even know they're infected. Most people would rather know.
Especially if they can, you know, get, you know, treatment and. Cur it's not like HIV.
It's not like something that is you can't do anything. There are treatments and there will be more treatments down the road.
Alright, so here's a question about where we are presently and, it kind of connects to, the Stanford University study that came out in February basically saying that the link between the wastewater and the cases were actually, the signal is best when your sample is at 50% or more, going back to December 2021 in terms of.
the samples and that link actually declined over time through 2022. There was a disconnect between wastewater and the caseloads there and, you know, everything from all the rapid tests being done and so the case loads aren't representing that any much but this one this question gets at perhaps another possibility given that you believe that less RNA is being expelled per case as
people are being vaccinated or getting more protection from natural infection has the method of calculating projected case counts changed to reflect that.
How much has the RNA been reduced per case? Is it half as much? 25% as much?
Yeah, I don't know. So in Missouri, we do not project a case numbers.
I had my formula that I would, you know, tell my friends if they asked me, but it's not something we said publicly because we knew that we didn't really know.
It's like saying how much does a person weigh? It depends. But in terms of how much is it reducing, that's a really hard one to get a handle on now because the testing is so bad.
The only way we could really know that is if we have situations where we do still have good testing and can do the correlation but
Yeah, I don't know. I can only say the disconnect for us started about the beginning of 2023 that's when the case RNA totally disconnected but before then it was It was just, you know, it wasn't like an all or nothing.
It was just a slow reduction. With each new wave in terms of how much our name is being
And there's an aspect of this doesn't necessarily have to be a zero-sum game.
It's not it's not that waste water. It's not it's not that wastewater. It has can replace caseloads.
It's that, you know, the fact that we've stopped collecting case loads is a damaging event and circumstance and that if we did have case loads at the various levels.
Then the wastewater could actually fold in together with that in a way that would benefit public health overall.
So, Yes.
Yeah. I mean, even if we can't. I mean, this will always be a shortcoming.
We can't say how many cases there were, but we can tell if things are going in the wrong direction.
We, I mean, when we see more RNA, we don't know whether it's a lot of asymptomatic people.
Or a few people, they're really sick, but we know that there are that someone's being infected somehow and is going, we can tell whether it's going in the wrong direction.
Alright, so we have some more technical questions. I think we'll circle back to them, but, with making sure, I mean, we do have some time.
We, we just about halfway through questions and then we've got plenty more for you.
But I do want to get to these 2 questions and they have the do with the, you know, given the applicability of wastewater surveillance.
They had questions about what can members of the public do to help support continued waste water surveillance. What would we, what would be effective?
What do you need? Thanks so much for your amazing work. And then the second question is, how are you currently funding the program how do you expect to expect to fund it for the next 2 years.
I guess there was also another question about perhaps that funding. Is in perhaps on chopping block as much as some of the other COVID surveillance methods.
Actually, I'm so There are there is some attrition. There are wastewater operators.
They're dropping out but the good thing is it's sort of reversed in the beginning it was easy to get waste water operators to sign up but it was hard to get the health officials to believe the data meant anything.
It's reversed now. So we've proven that this is a good tool for giving you a big picture of, you know, it's not a crystal ball, but it's a reality check of what's going on.
And The help the CDC and the health departments and the decision makers have totally bought in. It's the it's when groups are dropping out now is because the wastewater treatment operators are just sick of hand, you know.
You know, they feel like the pandemic's over and they're tired of sending us their samples every week.
But there's not that, so the news program has extended their funding. For 2 more years and they're adding a whole bunch of more things to what we can what we'll be surveying for one of the big ones that is a whole bunch of, antibiotic resistant bugs we hope to start being able to search for.
Right.
I feel like there was a part of this question I didn't answer.
Hello.
Government support, funding, I mean, you spoke to the reverse and that the public health department seemed to be in favor of it, but given that COVID money may be in decline.
Will that money be available or will it be repackaged as a kind of a more general method of infectious disease surveillance or
In the US, the wastewater monitoring is probably, it's a probably the cheapest part of COVID work and it's also the part that has the most support to keep going.
I think enough people have realized that you get a lot more bang for your buck with it and That way you're just that you don't stop everything but it's enough to keep your eye on it.
And then it is.
I'm pretty optimistic at least on that side of things.
Right, so there's also a lot of room to grow, right? So you've got the CDC reporting, 1,600, plants.
Every couple weeks in there as I understand it something like 16,000 public waste water surveillance plants so if this is expanded beyond COVID to other, pathogens this could be a you know a major national surveillance new surveillance method by which disease could be tracked.
Well, and you don't have to limit yourself to pathogens. We can also detect. We measure caffeine every week as a measure of whether the waste water has been diluted or not.
You can measure illicit drugs. You can measure opioid levels. So you can tell with a population.
How much opioids are, but also what kind is most the opioid consumption from prescription or is it from illegal import?
And then if you have a if you know it allows public health to potentially target their efforts where they're needed.
Most and have a readout for whether they're efforts are actually helping. But it's not just with pathogens.
But you know, once we get into those other things, there's a whole other conversation that needs to happen with.
You know, everyone's gotta buy into this. You know, there's gonna be a place where it's like, don't go that.
No, that's too much. Stop. And that's fine.
Alright, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, right, so there is, it's still the problem we had of the vaccination level, of, gaining, the people's trust enough to be able to buy into public
Good.
health. As a concept much less as a method and you know unfortunately coming out of our you know at least the view over here is that the coming out of a major pandemic, we would hope that would be a greater respect and understanding of public health and instead we have something going on in the reverse and so tracking down people's poop, even with all the public health applications as you were getting at earlier requires.
reframing and reset on the role of public health.
Yeah.
Alright, let, let me look some more some more questions here.
Meanwhile, let me just ask. Mark, so, those folks who are like, civilians, not scientists.
That's where I didn't answer.
What, do we need to do? Do we need to, you know, write to our Yeah, yeah, I mean, what do we need to write to people like let's say someone's in Missouri in your state and they like your work.
What do you tell them to do to keep it funded and to keep it out there in the public domain.
Well, you have, I mean. The all the testing is done by public, public servants that respond to the desires of the public.
If you want this, you have to let them know that. If your, you know, community stops doing wastewater testing, go to city council and say, This is stupid.
We want this back. They tend to be very responsive to that. I mean, II mean, the There's a there's a So often when places do drop office because there's a disconnect between the people that are collecting the samples, the ones that are digesting and utilizing the data.
And if you let them know that this is important, then usually they're perfectly happy to keep doing it.
As long as there's funding to pay for it.
That's great. And I,'t think somebody really, there's many things I'm gonna take away, but one of them is this notion of the 2 things we need to watch now given the dearth of some data.
It's been sort of, you know, not done anymore, hospitalization and race border, right?
Those are the 2 things we need to watch out. And also I was looking at a newspaper. Where they talked about the fg variant and they were sort of worrying about it.
EJ.
What's your, it's FG, I think it was like, You, I'm ahead.
Oh, so yeah, each E 5 is, yeah, it's. It's making some headway.
Thank you.
It might be part of the reason we're seeing increases, but it's not a game changer.
There's already some EG derivatives that I'm watching more closely or. There's.
Yeah, FL and. There's a few.
I mean, it's hard to know which are going to be trouble until they are, but there's there's already some EG sub derivatives that I'm pretty sure will overtake it.
But none of them are game changers at this point that I've seen. It might take a combination of waning immunity and changes in environment before we see another wave.
Unless we see, unless there's something entirely new and then all bets are off. I mean, I think Pi is still out there.
I think we will see another major wave at some point. But All the time, so don't take it to the bank.
And so you Alright, so your, adhering to more of, your swaying more optimistic, at least for the short term, that, But then there's also the issue of that.
Any new variant that shows up in the wastewater doesn't necessarily mean you know whether or not it's going to be virulent.
Yeah, we watch it every week. We look to see whether when there's a spike, whether it correlates with some new variant and You know, we like with BA 4 5 wave last summer.
It wasn't as obvious as it was with the earlier ones, but I mean like with Delta and VA one, I mean, It's not hard.
You know in a week that this is trouble. I haven't seen anything like that since.
In a year and a half.
Yeah, but I would take that as good news. Fingers crossed.
You can you can die even if it's not a major wave though. I mean there's still infections.
Right.
I mean I will say that I mean this is amazing but there's basically no sewer shed in our state that's negative.
They all have some. It's it's it's low but it's It's all it's still there.
Right, and of course, there's the disconnect between the damage in the acute, phase of the infection, the early, the first infected.
To the long COVID stuff. Which seems to be still, on, track. So let's do some more questions.
That's right. How can LHD, Epidemiologists into my embarrassment?
I don't know what LHD means. How can LHD epidemiologists or clinical hospital data analysts help with these efforts?
You know, they if they want the data, we'll keep providing it. That's the best I can say.
I, you know, I can't, I think it's probably the best source of, I mean, along with hospitalizations, like I mentioned those or, I mean, along with hospitalizations, like I mentioned, those are in my opinion or the best metrics of what's going on.
Those are in my opinion or the best metrics of what's going on. It's, you know, user lose it.
If you use the data, it will continue to be there.
So I think your example of what happened with, with sequencing, as a Is a good example of that.
I mean, genomic US was a major center in genomic sequencing at least what to do with it.
And Holding all the analyses and but as it is applied to public health, it kind of went by the wayside, which was unfortunate.
So one can see the kind of combo of. You know, wastewater, surveillance.
Hospital surveillance with COVID cases and with genomic sequence. Having those 3 things talk to each other so that each one can fail, in what the other ones can't do.
Yeah.
And then we start moving into a world of a 20 first century public health. Rather than stripping those things back.
Yeah, I mean, wastewater is never gonna replace patient diagnostics and sort of what it can do is it can give you the big picture and it can give it to you pretty fast.
I mean, I think this will also will eventually become more of a thing with the influenza that we can give a rapid readout of whether the vaccine works is going to work this year.
Right, right. So this gets into another question here and that speaks along these lines. Would more comprehensive general testing and contact tracing have helped you identify individual patients.
Probably not actually, because They were infected 2 years ago.
Right.
With a lot of other things, it would still be useful, but for, specifically for the persistent infection, probably not.
Oh, it's suppose you had a new, variant that emerged that had signs and signals of a, amino acid replacement that was dangerous.
Could you then go to that wastewater and with the public local public health department? Do some contact tracing enough.
To maybe find that person or that small group before they that it went
Oh, that would be actually if there were like a persistent infection that then started spreading it would be interesting if you could go back and figure out for sure what was the source.
Then gets into ethical quagmire, so I'm not sure you would do that or not.
Yeah. Right.
It, it would be from a scientific point of view, it'd be very interesting. I'm, I mean, most of us think Omicron came from a chronic infection, but.
Right, right, right.
I doubt the person would want it to be known that they were the source of If there's
Well, nobody wants, yeah, you don't want them have be known as patient 0 or anything.
Yeah.
So the ethical aspects are critical here. See.
So, you know, but they it does link to something that was, I think, unfortunately, some of our colleagues at the CDC may have missed on this is that the focus was on say.
You know, keeping, people, quarantined for 5 days instead of 10 days, right?
Even though the molecular kinetics are showing that people are infectious or at least a goodly proportion of people infectious, you know, even 14 days out.
So at the population level here, you have a folk with chronic infections. Don't know if they're infectious.
I think you said that they Probably not. But, ostensibly, if you still have, people, walking around still generating infection.
And if we've basically You know, very much limited our capacity to. Engage in quarantine and such then the it's the tail end folk that are capable of keeping the the lineage or lines of infection continuing.
Yeah, although the stuff you're talking about goes beyond what I, is not my expertise.
Okay.
You have Michael Mina on sometime to talk about this stuff. He's you know, when are people infectious and what is the, if you're really using the data, what should the recommendations be?
There are a lot of smart people who can answer that question a lot better than I can.
So I guess in this. That line and I don't mean to follow up within a question that may not speak to it but yeah.
Another one from our YouTube channel is I'd still like to know how he knows these people aren't immuno compromised.
If he doesn't know who these patients are and can't test them or know their medical history.
Oh, I don't know that they're not immuno compromised. I'm just not assuming it.
I'm not taking it for granted. Actually there's a very good. I think it's very likely that they are somehow a.
Compromise, but it might not be the obvious things that you think of. It could be some.
Defect in some gene in the innate immune response that you don't even know you have unless something like this happens.
I think there's something about these people that allows the percent infection. I just I'm not because especially because of the stuff with the cast.
I'm just I'm not just assuming that they're gonna be your caricature, your obvious example of an immune compromise.
I don't think there's any reason to limit ourself to that.
Perfect. So we're getting down to it, but, here's a question that, often ends a show so I thought this is a good way and it just popped up now is someone asked what keeps you up at night?
And I think they're referring to COVID. We don't need to know your personal business, sir.
Okay, so not too much coffee. You know, I lost a lot of sleep in 2021.
I sleep pretty well now. I think I think we're going to get through this. The thing that scares me most is the backlash.
It's not actually the virus, but it's the. This stuff you're talking about the backlash against public health against it's over now and now we distrust the people that are trying to help us.
That's the part that scares me the most because it could get really bad and You know. You know, it's always, I hate it when it's one step up and 2 steps back and I hope it doesn't come to that but that's the thing I worry about the most I think.
But in the in the short term there is to just if I may summarize what you said, in terms of your, recent surveillance, there's nothing that that's arriving that is.
Worrisome about in terms of a new variant that might lead to a new spike.
EG 5 is seems to be within the boundaries of what you've seen before does that is that a fair summary?
It might be. It could be a 4 or 5 level spike like what we had last summer. But I don't see anything that's like in the VA one original or the Delta.
Those are the 2 really big ones in Missouri. There are a few other places where other one you just had major impact, but you know, you know what a major hit is when you have it because your hospitals are full.
I haven't seen anything like that.
Yeah, but would you, it'd be fair to say as we wrap up, that the pandemic though is still ongoing.
Oh yeah, this virus is never going away. Whether we call it a pandemic or endemic is just nomenclature.
But the virus is gonna be here forever. And learn to deal with it. It'd be nice, you know.
We're better equipped to deal with these kind of things than we've ever been in the past, but getting back to your question is like, will we have the common sense to actually utilize the tools we now have or not.
Okay, thank you very much. Okay.
You got some playing? Speaking, that's some, azor plates. We did there at the end.
Thank you.
That's it. First of all, thank you so much. Our team, of course, Rob and, and Kinsey, but thank you, Mark, for sharing your time with us and just keep on doing the science, brother, because we need it and you're right.
We need to keep on doing the signs, brother, because we need it and you're right. We need to be very aware of the backlash. And folks, you can join us.
You can annoy the people CDC. You can go on to Dr. Johnson's website. You can be part of the solution as well.
And I'm gonna end today because we're gonna be ending and doing some music soon. Rob, I'm gonna give you the last word and then we're gonna do a little vote and then do some music.
I just, I'll have to say is thank you, Dr. Johnson for your work. Really, really appreciate it.
You've been very open with the public about the work you're doing, your website, surveillance project.
If we don't post it here, we'll certainly post it in the video description. It's fantastic.
I think, if only all the states across the US had what Missouri has now. We'd be in a much better position.
So that's all I have to say. My, deep appreciation.
Thank you.
And I'm gonna pull from this book to speak at the VI word, which is the, oh, they're writing to someone named Charlie Murray who was way ahead of her times, Dr.
Reverend Dr. Pauling Murray was also schooled both, Vader Ginsburg.
Taught her how to do some of the law and she wrote. I have never been able to accept what I believe to be an injustice.
Perhaps it is because of this. I am America's problem child and will continue to be. Let's continue to be the Cdc's problem child and doing the thing we need to do.
Thank you, Mark. Thank you, everybody. For us, a little music as we go out and take a conference for coming.
We had a lot of people up in here and that's a good sign. Keep the faith.
Thanks.
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