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The reopening metric we should be heeding

From Twitter:

Here’s that link:

Abstract

We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples and, when adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99). SARS-CoV-2 RNA concentrations were a seven-day leading indicator ahead of compiled COVID-19 testing data and led local hospital admissions data by three days. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community.

Introduction

The most common metric followed to track the progression of the COVID-19 epidemic within communities is derived from testing symptomatic cases and evaluating the number of positive tests over time.1 However, tracking positive tests is a lagging indicator for the epidemic progression.2, 3 Testing is largely prompted by symptoms, which may take up to five days to present4, and individuals can shed virus prior to exhibiting symptoms. There is a pressing need for additional methods for early sentinel surveillance and real-time estimations of community disease burden so that public health authorities may modulate and plan epidemic responses accordingly.

SARS-CoV-2 RNA is present in the stool of COVID-19 patients5-7 and has recently been documented in raw wastewater.8-10 Thus, monitoring raw wastewater (sewage) within a community’s collection system can potentially provide information on the prevalence and dynamics of infection for entire populations.11 When municipal raw wastewater discharges into treatment facilities, solids are settled and collected into a matrix called (primary) sewage sludge, which has been shown to contain a broad diversity of human viruses including commonly circulating coronavirus strains.12 Primary sludge provides a well-mixed and concentrated sample that may be advantageous for monitoring SARS-CoV-2. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant.

So in plain English, if you know what the level of SARS-CoV-2 is in your municipal wastewater, you will have a very accurate predictor of the new COVID-19 case rate in your community. And guess what? The city of Houston is tracking this very data. I don’t know if it’s being published anywhere, but it sure could shed some light on how things are really going around here. Other cities should be doing this as well – if they aren’t doing it already, they need to start – and that information should be collected and published at the state level as well. What are we waiting for?

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20 Comments

  1. C.L. says:

    Thought For The Day:

    Someone in this town has a job that involves them testing our effluent for evidence of Covid-19 infection(s). I’m never going to complain about my job again.

    Whoever is paying him/her for this week, isn’t paying him/her near enough.

  2. David Fagan says:

    I wonder if there’s been people doing this for several different viruses and illnesses?

  3. Jason Hochman says:

    OK, I take the whole pandemic with a grain of salt. All of our leaders, who have inside information about the true state of affairs were leading a gathering of 60,000, and no mention of the risk. Was it a calculated risk to placate the potential rioters? If LGBT activists got worked up enough about PRIDE being cancelled, threatened to loot Target, would Mayor Turner and SJL lead a PRIDE parade?

    Meanwhile I see that the tests are very inaccurate. So why is more testing so important? when the test is as accurate as a coin toss. I read on Medscape about a patient who arrived at UC San Diego with pneumonia and needed to be intubated. He tested negative for corona virus twice. The doctor is quoted as saying, “those two negative tests didn’t convince anybody.” Well, doctor, there are many causes for pneumonia, these exact signs and symptoms can come from other pathogens. Of course any symptom you name is attributed to novel corona virus, from sore throat, cough, shortness of breath, all the way to rashes, heart inflammation….it’s so variable that every sickness is being labeled COVD19. And hey, then again, if you’re infected there is a 50-50 chance that you will never have any symptoms at all, that’s why you have to wear your mask to protect everyone. I have trouble taking this seriously anymore.

  4. Bill Daniels says:

    C.L.:

    I laughed out loud. That’s probably your best post of all time on OTK. Definitely top 10 material.

    10/10 would laugh again! 🙂

  5. Jen says:

    Dear Jason H.– please we are all done with your meaningless drivel. Meanwhile, it would sure be nice if Rice U would publish the results of their testing.

  6. Jason Hochman says:

    Hi Jen, very nice to see how someone who criticizes meaningless drivel is unable to engage in a real way, can only post personal insults, and can’t offer any alternatives or critique of the information. The tests are inaccurate, go ahead and read about it. Please put on your mask, stay locked inside forever, and make sure that you get everything delivered by a person who leaves it outside and scurries away, and make sure to leave that stuff on your porch for at least a week in case it is contaminated.

  7. Jen says:

    Whoops! Rice Poop Group Scooped!

  8. Bill Daniels says:

    Jason has a very good point that no one, including Jen, in her eloquent response, has been able to refute. If we’re all gonna die of the Wu flu, especially non whites, because the virus is racist, how do we reconcile 60,000 people in close space, led by the majority of our city’s leaders? Either it’s OK to gather in groups of 60,000, or it is not. It’s either OK to have a state level funeral in a packed church, with all our favorite activists and race baiters, or it’s not. This is one of the very few it’s either black or it’s white moments we’re going to have here on a political discussion board.

    So Jen, are you going to pick a side? Jen? Jen?

  9. Jen says:

    Well all right dear I will take the bait. Of course you misstate the situations, to try to make your point. For the large outdoor march, I think the Mayor decided it would be better to have a controlled rather than uncontrolled situation, it was going to happen anyway. All were advised to distance and wear masks. This was the best that could be managed under the circumstances, and it did bring an end to the protests. BTW outdoors is not a “closed space”. The memorial service has yet to occur, so you cannot know it will be “packed”, or what.
    Jason’s point seemed to be that the city leaders knew the c-virus is a hoax, so they allowed the march. He knew this because he read somewhere that some tests were inaccurate. So he decided the whole global epidemic thing, which has killed 340,000 people or so, is really just nothing to worry about. Drivel.

  10. Jason Hochman says:

    Jen, right, I kind of alluded to what you are saying–I wrote a calculated risk to placate those who might riot–so if the baseball fans demonstrate enough and get rowdy enough–will the Astros get to play.

    As for the tests being inaccurate, I get updates from something called Medscape. It had a piece about a patient in UC San Diego medical center, who tested negative twice, but they weren’t fooled by that. They knew that this patient had COVID. They did a bronchial wash and it was positive. The article went on to mention that the tests are 38% are incorrect on the first day of symptoms, 20% incorrect a few days later, and up to 66% incorrect after two days.

    Now, we are being told that we must test, test, test. With tests that accurate, you might as well flip a coin. They are labeling everything COVID. Even Dr. Birx stated that the death count may be inflated as much as 25%.

    Our local leaders must be in the know more than we are. What I said is the I take the pandemic panic with a grain of salt…not that the entire thing is a hoax…but it is being exploited to benefit some. The billionaires have collectively increased their wealth by tens of billions…regular people are struggling. Our president goes golfing, nervous Nancy eats her $20 a pint ice cream. But they say we’re all in this together.

  11. Jason Hochman says:

    Oh, and Jen, I am questioning my sanity, for sure. I saw Gov. Cuomo saying he was shocked that 66% of admissions came from people staying at home. Literally retired, or nonessential workers, made up the biggest percentage of admissions, and he kept going on about it, and then his next slide said: “Stay Home Stop the Spread Stay Safe” across the bottom! You just gave us the stats that show staying home doesn’t equate with staying safe, but you still say that? What is the truth?
    https://www.cnbc.com/2020/05/06/ny-gov-cuomo-says-its-shocking-most-new-coronavirus-hospitalizations-are-people-staying-home.html

  12. Manny says:

    Jason for Cuomo’s unscientific remark is probably because of people like you, visit people that stay home or maybe retired.

    Did you lose your job, Jason? Is that why you are complaining?

    What ever Turner and all the 60,000 people did is one event, if you want to include all those events then include them. The number of cases are going up as the number of virus related deaths, over 1000 in one day. It had been much lower.

    I know you don’t care if people die, maybe some people do.

    I am aware that you don’t care about people dying, I at get it.

    https://www.click2houston.com/health/2020/06/05/med-center-sees-uptick-in-covid-19-patients-in-icus-warns-if-trend-continues-capacity-could-be-exceeded-in-2-weeks/

    Oh, Jason I am so glad Edison did not give up so quickly we could still be reading by candle light.

  13. Bill Daniels says:

    Hey Jen,

    Here’s the video of just one of St. Floyd’s many, many funeral services:

    https://www.youtube.com/watch?v=gr5ftH86tIk

    Do you see any ‘social distancing’ there? This was broadcast as a state funeral, on all the major networks, by the way. Are you saying that at his other funerals here and in other states (the St. Floyd tour?) they will be imposing crowd limits and social distancing?

    Just admit it……the Wu flu attack on Trump has failed, jobs are coming back, so we no longer even pretend to give a shit about it, and just move on to the next play in the playbook: “race war.”

    Pro-tip: Biden is going to lose. Decent people that you never hear from or about aren’t down with insurrection, especially over a screw up multiple felon who was speedballing on meth and fentanyl at the time he died. Is this your idea of “he wuz a good boy just tryna to turn his life around? I mean, if I was turning my life around, maybe I’d lay off the meth and fentanyl…..but that’s just me.

  14. Bill Daniels says:

    And just so y’all can say you heard it here first, the cops are going to be found not guilty of murder or manslaughter, but probably some lower charge like failing to render aid. Dude had enough fentanyl in his system to kill anyone.

    Medical examiner’s report:

    https://interactive.kare11.com/pdfs/Autopsy_2020-3700_Floyd.pdf

  15. Bill Daniels says:

    Article showing the level Floyd had was lethal, and not even Narcan could reverse that:

    https://www.acsh.org/news/2017/02/02/fentanyl-overdose-dont-count-naloxone-save-you-10822

    St. Floyd was higher than a mofo on that fateful day. Fatally high.

  16. Manny says:

    Typical racist bs by Bill Daniels, he was high therefore he deserved to die.

    Bill Daniels like most racists like him, uses false logic to try to convince people that day is night.

    The fact that people are protesting has nothing to do with what should be safe practices to stop people from dying from the virus.

    4 million people in Harris County, 60,000 attended, most chose not to attend.

    Actual unemployment was 16% but an error gave us the wrong number. Black unemployment went up.

    Asian unemployment went up. Trump and his cronies are all the same, lies, lies, and more lies.

    I guess protestor are tired of seeing police kill Black Americans.

  17. Jason Hochman says:

    Manny, not sure why I bother to respond to you. You will simply say “racist” or “don’t care about deaths.”

    For what it’s worth, I would agree with Bill in that a murder conviction is not a slam dunk. If Floyd couldn’t breathe, he wouldn’t be able to talk would he? He had so many drugs in him, and other health conditions. We still haven’t heard from the officers; at trial they may have some explanation as to why the use of force was needed. Now Manny, this is not racism. Convincing a jury beyond a reasonable doubt is not gonna be that easy. I agree that what happened was wrong, and he didn’t deserve it. Having a knee on his neck didn’t help him in any way.

    Love Field took down its statue of a Texas Ranger, I guess the baseball team is next to join the Redskins and will have to change its name…The move to take down Robert E. Lee statues is back. They keep saying that the Civil War history we’ve heard all these years is one big lie…conventional wisdom is that the victors write history….who won the Civil War?

    Manny, I didn’t lose my job. If you’d been tuned in to my drivel, you would have seen that I was almost crunched to death on my way home from work. I’m grateful for my good fortune, to still have a job, where I can go in to work, or work from home. I am lucky that if I get the corona virus, I have the means to work at home until I recover, and able to get necessities delivered for a week or two no problem. If I get really sick, I have good insurance. Now, you seem quite insensitive to those who lost their jobs. If they lost their insurance, what to do if they get COVID? Just let them die? Cuomo was telling a reporter that if people are tired of waiting for their unemployment, if they need more money then let them get an essential job, tomorrow morning, go out and get one. He went on to say, that losing a job, getting depressed, domestic violence, all are bad, but death is permanent. Does he not know that in a normal year 50,000 people in the US permanently die of suicide? That domestic violence quite often ends in the death of the victim? Murder/suicides have increased. Are we going to be successful if we have 300,000 deaths due to domestic violence and suicide, but COVID deaths kept to 110,000?

  18. Jason Hochman says:

    Manny, and I forgot to mention I did look at your link. The truth is that hospital admissions for COVID have gone up, over all, though, cases have remained stable. There may be reasons why hospitals are admitting more. For example, it is a fact that with the CARES act, the hospital gets paid more for treating a COVID patient. Of course, the hospital makes this diagnosis, and the hospital decides whether or not admission is the recommended course of treatment. Just thinking here. I have been going in the hospital throughout this. The hospital is still mostly empty. Corridors and floors are dark and blocked. staff hours are cut or they are furloughed. Maybe the hospitals are just concerned about the bottom line and admitting more? I don’t know. I thought that the whole point of “flattening the curve” was to give us time to understand the virus and for the medical system to be prepared for any surge, to have plenty of ventilators, ICU capacity, PPE, and everything else on hand, ready to go for the huge run of pneumonia patients.
    Your link says that “capacity could be exceeded in two weeks.” Just two weeks, for only a moderate increase in patients? Why the hell did the TMC not take the last two months of stay at home curve flattening to be prepared for a tidal wave of COVID patients? That was the whole point.

    Also, is it racist to ask, was the killing of Floyd completely racially motivated? I don’t know, just thinking. Officer Chauvin seems to have been a rogue officer with several incidents in his history. He can trace his lineage to Nicholas Chauvin, from whose name we derive the word chauvinism.

  19. Jason Hochman says:

    I do still feel that I’m losing my mind and will need to talk to someone. The contradictions and confusion of the so called pandemic. Since the George Floyd protests and ceremonies, the news doesn’t even give me a daily corona death count any more. Where are we? 100,000? 150,000? This number used to lead the news daily before the BLM events started now I’m forced to seek it out. There have been many events, and then I read that Houston activists had a Friday June 5th event for Breonna Taylor. So we can have these big rallies daily, but my church can’t be full for Mass? My local bar can’t be full with 80 people? Pride can’t go on?

    I took the John Hopkins course on contact tracing, and a contact is defined as “close contact (less than 6′), longer than 15 minutes, w/o face covering.” So why do you need a mask in Kroger? If I am looking at frozen peas and someone walks by for just a second, that’s not a contact, mask or no. If’n I’m in line at Home Depot, 6′ or more, and hopefully not there for 15 minutes, that’s not a contact, mask or no. Same thing with checkout. The transaction with the cashier is not 15 minutes and most cashiers now have a Plexiglass shield. Mask not needed.

    I also read that the study in the Lancet about the risks of hydroxycholorquine to cause death was retracted. Now it is safe to take it again, just like Trump does.

    Then I read about COVI PASS. https://www.covipass.com/
    It is a “digital health passport” that facilitates “safe return to work and LIFE.” (emphasis mine). They are planning an autocratic no privacy society that will make Trump look like the Little Old Lady who Lived in a Shoe. The COVI PASS will expand to check your government required vaccines, and then check your vitals, and move on to genetics. A day will come when you hear: “Your COVI PASS does not qualify you for life, please step this way.”

    I hope that you readers can understand my real confusion and feelings of derealization. The messages are so contradictory, but also, so certain of their importance and truth, but then changing from day to day.

  20. Manny says:

    As of two days ago, Jason the official count was at 107,000, with deaths now at 1,000 a day again.

    Not sure why hospitals being empty has any thing to do with the corona virus. But, I have read that people are scared to go to the hospital. I for one would not choose it unless I believe it was a life or death matter.

    Do what you have to do, wear a mask, preferably made from microfiber cloth, unless you want an official medical mask. We do what we must do to survive. Do I like masks, no, but I wear one because one of my family members is scared and no sense in doing things that would upset them. I, also, have a brother whose health condition would put him at the top of those most vulnerable. If you don’t have anyone to worry about, then don’t worry and do whatever makes you the most comfortable.

    Wearing a mask does not make you less manly, real man don’t give a sh*t what other people think about them. “I yam what I yam, and that is what I yam”, Popeye.

    https://www.armytimes.com/news/your-army/2020/04/24/army-researchers-say-this-is-the-best-material-for-a-homemade-face-mask-theyve-found-so-far/