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Amount of Covid found in the wastewater in Boston
- hardtke 5y agoBe careful interpreting this. Delta and now Omicron are more contagious than the original virus precisely because they have higher peak viral loads and shed more virus from infected patients. Hence, the virus in wastewater per infected individual has been changing along with the number of infected individuals.
- ripper1138 5y agoGood point. Also keep in mind this is just one location. Would be really cool to see this measured by most cities.
- jvmiert 5y agoWe do this in The Netherlands: https://coronadashboard.government.nl/landelijk/rioolwater https://coronadashboard.government.nl/landelijk/rioolwater
- systemBuilder 5y agoWow that is SICK! I think if I had to read viral particles in wastewater for many different diseases at a sewage treatment plant I would go crazy and move to the countryside!
- yread 5y agoThere is no "countryside" in the Netherlands
- OneTimePetes 5y agoYou can move water-sides though, buy a houseboat and camp out on the lakes..
- twofornone 5y agoHas that been proven or are you just speculating? I don't think increased viral load/shedding is the only mechanism by which a virus becomes more contagious.
- mlyle 5y agoDelta has been documented to result in higher viral loads and this is thought to be a factor behind the increased transmissibility. I don't think anyone knows about the kinetics of Omicron yet. I think the increasing prevalence of Omicron may have a lot more to do with its ability to escape immunity from past infection and increased probability of vaccine breakthrough than any inherent higher transmissibility to those who are immunologically naive.
- anonuser123456 5y ago>Delta has been documented to result in higher viral loads and this is thought to be a factor behind the increased transmissibility. has it ? I've seen this claim made over and over, w/out documentation. I've seen documentation of higher nasal swab loads, but not higher systemic circulating virus. Higher upper respiratory loads (e.g. mucosal) would also lead to increased transmissibility, but not higher waste water levels.
- mlyle 5y ago> has it ? I've seen this claim made over and over, w/out documentation. Very early report on Delta, describing higher loads in oropharyngeal swabs: https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v2.full.pdf https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v... > I've seen documentation of higher nasal swab loads, but not higher systemic circulating virus. You'll have almost no reports of "systemic circulating virus" load, because there's not really an accepted definition for how this measurement would be taken. Plasma concentrations don't appear to be particularly meaningful except in late stages of critical disease. > higher waste water levels. My understanding of the evidence is that fecal loads of Delta are higher than other variants, but not as elevated in comparison to how much throat and nose swabs are elevated. I.e. both statements appear true (higher loading overall, and even higher loading in upper respiratory tissue).
- itamarst 5y agoMA sequences 30% of PCR tests, and has so far found only a single Omicron case...
- incongruity 5y agoCouldn’t that potentially be explained by the lag between infection and symptoms with many people being asymptomatic early on while still shedding virus at significant levels? If that’s theory is true, we should see many more tests and identifications of omicron in the coming week.
- seoaeu 5y agoMA does massive amounts of surveillance testing of people who don’t have symptoms. So infections should be picked up by both wastewater testing and PCR tests at about the same time
- fragmede 5y agoSpecifically, Boston has a large number of biotech firms and colleges who have the equipment to do PCR testing, as well as the know how to run them.
- Robotbeat 5y agoStill, I think it means we’re likely in the early/mid stages of the exponential curve. I saw estimate of ~5 day doubling time. Meaning that even if 3 weeks ago there were 100 people with Omicron in Boston, there are still only like 800 now. Takes another month or three for it to explode to a large case load.
- jointpdf 5y agoBut Delta has been the only game in town for a while now (>99% of cases since late August), so this recent rise in the wastewater viral levels shouldn’t be attributable to a change in the proportion of variants (TBD on Omicron?). https://covid.cdc.gov/covid-data-tracker/#variant-proportions https://covid.cdc.gov/covid-data-tracker/#variant-proportion...
- tyrfing 5y agoThe current situation is a handful of confirmed Omicron cases in the US, and a (useless) travel ban to prevent additional cases. Either this data is noise, or that genie isn't just out of the bottle, but ransacked the house while we're arguing over the cork. With a doubling time around 3-5 days and very effective spread to both previously infected and vaccinated, the exact position on that curve is a difference of days. If we're lucky, it's a mild strain - this doesn't have strong evidence yet. If we're unlucky, and it's similar to other strains, we have around a month before things get very bad indeed.
- mmatus 5y agoLots of good points here! Viral loads and variants are important to keep in mind when interpreting wastewater data. That said, our current best guess is that the rising SARS-CoV-2 concentration in Boston wastewater reflects a real increase in cases. Delta has higher nasal shedding than other variants, but not necessarily higher fecal shedding--the ratio of wastewater concentrations to clinical cases seems pretty constant in our data over time (see our blog post on this topic here: https://biobotanalytics.medium.com/mass-vaccination-delta-and-wastewater-covid-19-data-1c143e3d96a3 https://biobotanalytics.medium.com/mass-vaccination-delta-an...) We know much less about omicron, but it's probably still only a small minority of cases. We're currently sequencing samples of Boston wastewater, so we'll know more about omicron levels in wastewater very soon!
- deleted 5y ago[deleted]
- glial 5y agoSimilar work in MN shows that wastewater rates are a leading indicator of positive tests: https://www.kare11.com/article/news/local/breaking-the-news/minnesota-wastewater-predicted-each-covid-wave-including-this-one/89-8cadce74-65f7-4445-8705-15149ff29ec1 https://www.kare11.com/article/news/local/breaking-the-news/...
- epakai 5y agohttps://biobot.io/biobots-wastewater-monitoring-the-omicron-variant/ https://biobot.io/biobots-wastewater-monitoring-the-omicron-... indicates they use PCR. How does PCR testing return a quantitative result? I thought the purpose was to amplify (reproduce) proteins to enable detection, and this precludes finding original concentrations.
- jhj 5y agoThe cycle threshold (Ct) is the quantitative value from PCR. This is mapped to counts per volume based on results in https://pubmed.ncbi.nlm.nih.gov/32607521/ https://pubmed.ncbi.nlm.nih.gov/32607521/ I believe.
- dsizzle 5y agoYes. I think the device used is a bit more sophisticated than simply obtaining the cycle number where it crosses the threshold. There's a variation of PCR called quantitative PCR (qPCR) that measures a fluorescence signal more or less continuously and the growth rate allows one to work backwards to the initial count. Here's a basic description from the maker of the device they used (Taqman) https://www.thermofisher.com/blog/ask-a-scientist/what-is-qpcr/ https://www.thermofisher.com/blog/ask-a-scientist/what-is-qp...
- mlyle 5y agoThere's a lot of ways you can get fancier and more precise quantitative results, sure. The basics is the cycle threshold. The next step further is just to try and come up with a fractional cycle number through interpolation-- e.g. if cycle 20 was not-quite-positive-but-very-close and cycle 21 was strongly positive, that implies a value close to 20, versus if cycle 20 was very far from positive and 21 was just barely over the threshold, that implies the real value is just under 21. And there's further, but diminishing gains from fitting the fluorescence curves.
- jonas21 5y agohttps://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction https://en.wikipedia.org/wiki/Real-time_polymerase_chain_rea...
- philoph1122 5y agoIt looks like the amount simply varies by season (high in winter, low in summer), unless I'm missing something...
- dragontamer 5y agoIts well known that COVID19 spreads more easily in the winter. Because more people are getting sick with COVID19 at this time... it makes sense that more COVID19 samples will be found in wastewater.
- chiefalchemist 5y agoNot to nitpick but I don't think that's what's well known. The virus' "behavior" doesn't change in the Winter. What changes is human behavior. We're inside less and inside more, and that typically means we end up in closer (enclosed) quarters with others. Perhaps that's what you meant?
- sterlind 5y agoThe humidity inside buildings changes with the outdoor temperature, since cold air carries less water and heaters don't add that back unless you use a humidifier. Isn't that one of the theories behind transmission changing with the seasons?
- dragontamer 5y agoI think you have a valid theory, but... its not 100% clear if that's the only case. Viruses could literally be affected by the lesser amounts of sun and shorter days. UV-rays kill the virus for instance, and we get less of them in the winter than during the summer. Without knowing any more details on "why" there's a relationship between COVID and the winter (whether its human behavior that changes, or if its physically something associated with the virus / sun... like day length + UV rays or heat vs humidity), we just have to say the most generic thing possible to remain correct. In this case: we know that COVID19 seems to spread more in the winter. We have lots of theories why this happens, but I personally haven't seen any "Mythbusters" style study that goes over all the theories and actually proves any of them.
- a45a33s 5y agoits unfortunate that we'll never know what this data looked like in 2019 or before
- ceejayoz 5y agoSeems like it’d be a pretty flat, unremarkable chart.
- jdavis703 5y agoPerhaps, but there have been reports of varying veracity hinting that COVID-19 was already in Western sewage, blood and autopsy samples in 2019. Who knows if that was contamination, flawed equipment, geopolitical shenanigans or legitimate data though.
- patall 5y agoThe reason why these are mostly believed to be false positive is that all current covid-19 lineages (sequences) can be traced back to a single clone that (based on mutation rate estimates) appeared somewhere in late 2019. There may have been other lineages before that, but we seem to have no RNA sequence of those lineages, so we cannot put them in relation to any existing strain. One has to wonder, where are those 'alternative' lineages now, if they existed in the first place? Sure, they may have gone extinct in the great lockdown. But then one has to ask why did those went extinct while so many other virusses didn't. An a simple (occams razor) explaination is: they never existed.
- teeray 5y agoHopefully, otherwise we have other problems
- a45a33s 5y agothats an assumption that we have no way of confirming
- ceejayoz 5y ago
- deleted 5y ago[deleted]
- usr1106 5y agoNot sure what copies / mL means. Milliliter? The standardized abbreviation would be a small l. Here in Finland they use a N2 PCR test published by the CDC (don't ask me how that works, I am a software developer...). However, the results are presented in millions of RNA copies per 1000 inhabitants per 24 hours. I guess that leads to results unaffected by water consumption habits or rainfall (if the rains drains to the same system as household sewers, some location have dual systems). https://www.thl.fi/episeuranta/jatevesi/jatevesiseuranta_viikkoraportti.html https://www.thl.fi/episeuranta/jatevesi/jatevesiseuranta_vii...
- 1over137 5y agoThe standard abbreviation for litre is uppercase L.
- usr1106 5y agoActually ISO mentions both. (Of course they don't define it because the standard unit would for volume would be m³.) So maybe usage really depends on country, I have lived and worked in several European countries, all of them use a small letter. https://web.archive.org/web/20170814094625/http://www.bipm.org/utils/common/pdf/si_brochure_8_en.pdf https://web.archive.org/web/20170814094625/http://www.bipm.o... The first random picture seems to confirm that in the US a capital L is used. https://murraybrand.com/wp-content/uploads/2015/07/crystal_organic_milk_lineup.jpg https://murraybrand.com/wp-content/uploads/2015/07/crystal_o...
- schoen 5y agoWikipedia says > Since 1979, the litre may exceptionally be written using either an uppercase "L" or a lowercase "l", a decision prompted by the similarity of the lowercase letter "l" to the numeral "1", especially with certain typefaces or English-style handwriting. The American NIST recommends that within the United States "L" be used rather than "l". In European measurement contexts I've sometimes seen ℓ (with a script l), but I'm not sure I've seen plain l. (However, I live in the U.S. and might not have as much exposure to European references to liters.)
- jasonhansel 5y agoWould be interesting if they could also tell apart different variants--I'd be interested to see if any of the recent increase was Omicron-related.
- reaperducer 5y agoThey can. I've seen on the news that at least two southwest cities that are currently using wastewater specifically for omicron surveillance.
- gentleman11 5y agoOmicron is not a significant spreader yet, this is still Delta. Omicron hasn’t had enough time, it’s only just arrived Eg, in the uk there’s less than 300 cases of it
- aardvark92 5y agoWe found Omicron genomes in my county's wastewater. Give it like, two days and it'll hit the news. SOURCE: I work in a leading U.S. wastewater testing lab.
- aardvark92 5y agoWe're working on it! Demultiplexing the signal is tricky though. Currently, labs have two main tools available - RT-qPCR and tiled amplicon sequencing. RT-qPCR provides cycle threshold (Ct) values which quantify the amount of virus RNA in a sample. RT-qPCR is not practical for finding and quantifying de novo variants as it relies on standard primer sets. Sequencing based approaches are less quantitative but provide more insight into the diversity of RNAs and mutations present in a sample - and thus which variants are present. https://www.gisaid.org/hcov19-variants/ https://www.gisaid.org/hcov19-variants/ has a variant dashboard based on sequencing data, including Omicron. It's not as quantitative qPCR, but still may be of interest.
- yread 5y agoCouldn't you run RT-qPCR twice with two different sets of primers? Does RT-qPCR give you the spike gene target failure rate?
- Ifkaluva 5y agoIt looks like the spike this December is already bigger than last year at the same time?
- smalley 5y agoInteresting, looks like the South Bay has some similar numbers: https://covid19.sccgov.org/dashboard-wastewater https://covid19.sccgov.org/dashboard-wastewater but I suppose having milder weather hasn't seen as serious an uptick as Massachusetts?
- jrmg 5y agoI think you’re looking at the ‘last six weeks’ charts? The ‘since tracking started in Oct / Nov 2020’ charts show current levels being way, way below last year, or even the July peaks. Although, to be fair, last October didn’t look bad, and then there was a massive spike…
- smalley 5y agoNo I agree with that, I was looking at the 2020 peak to 2021 peak magnitude on the Boston Area plots and the same relative magnitude on the SCC plots and being somewhat surprised at how much of a difference there was between the two locations. As far as I understand we have roughly similar levels of vaccination although santa clara county is probably less dense so I would have guessed we'd have similar magnitude changes in positivity rate. (A good reminder I am in no way an epidemiologist)
- rossdavidh 5y agoWell I don't have positive PCR data for Boston specifically, but the data from Massachusetts generally has peaks at basically the same times over the last year and a half, so I'd say it's a valid measure.
- jghn 5y agoI followed it pretty close until the spring. My recollection was that the data were noisy but over time seemed to have a strong correlation with what we saw in terms of case counts. Where it was less useful was when people would cite it day by day. All kinds of examples where it'd contradict what we were seeing in the actual COVID data when using it that way.
- dustintrex 5y agoBy "actual COVID data", do you mean positive tests? All things considered, I would assume that wastewater data to be a lot less suspectible to biases (eg who gets tested) and random fluctuations (testing on weekends, holidays, etc).
- jghn 5y agoYes. r/coronavirusma had a daily dashboard with numbers on positive tests, hospitalizations, and deaths.
- rossdavidh 5y agoShould have mentioned that the data I was referring to I found here, at John Hopkins' Univ. github, which they are pulling from a variety of sources: https://github.com/CSSEGISandData/COVID-19 https://github.com/CSSEGISandData/COVID-19
- throwanem 5y agoStepping up for the pedants of my adopted hometown, I note the proper name of that institution is The Johns Hopkins University, named for its likewise plurally christened founder. Around here we mostly just call it Hopkins or JHU.
- benrapscallion 5y agoCOVID is the disease, coronavirus is the pathogen.
- aftbit 5y agoCOVID-19 is the disease, SARS-COV-2 is the pathogen, coronavirus is a large group of viruses.
- AtlasBarfed 5y agoThat curve matches generally the "Daily New Cases" graph in https://www.worldometers.info/coronavirus/country/us/ https://www.worldometers.info/coronavirus/country/us/ I definitely think there was going to be a major fourth surge that propelled the US death count to 1 million people from the holidays. Who knows what omicron will do.
- alex-korr 5y agoIn LA County the correlation between the amount of covid in the sewage was very clear in 2020 but seems to have diverged in 2021 - https://www.lacsd.org/home/showdocument?id=4318 https://www.lacsd.org/home/showdocument?id=4318
- jollybean 5y agoWould be nice to see that overlaid with the test positive data. I wonder if this could be an effective way of determining COVID prevalence in areas where they are not doing enough testing?
- mmatus 5y agoYou can see our data overlaid with clinical testing data here: https://biobot.io/data/ https://biobot.io/data/ And yes! Our testing represents every individual in the community that has used a toilet connected to a sewer, independent of where they live, whether they experience symptoms, or whether they have the time, money or access to clinical testing. It's helped public officials stay informed and make decisions even with limited or inconsistent individual testing data.
- chaps 5y agoDoesn't look like there's anything like this for where I live, so I submitted a FOIA request to my local water agency to get that data. If anyone's curious about submitting one for their own city, here's the kinda sloppy language I used for Chicago (IANAL): Pursuant to IL FOIA, please provide me with records sufficient to show all non-exempt fields of information from the COVID-19 water sampling that's described at: https://mwrd.org/sites/default/files/documents/Sewage%20Surveillance_FS_210119.pdf. The document mentions that MWRD already shares this surveillance information with academic partners, so I believe it should be relatively easy to collect these records. As the statute allows a requester to specify a file format, please provide me the records in excel format. Please reach out to me if you have any questions about this request.
- deleted 5y ago[deleted]
- chiefalchemist 5y agoSlighly off topic, but it would be interesting to see what other activities have increased or decreased as well. For example, what's happened with legal and illegal pharmaceuticals? What about foods (e.g., sugar)? What else can our waste tell us?
- aardvark92 5y agoFolks have been testing wastewater for legal and illegal drugs for years (https://score-cost.eu https://score-cost.eu has an interesting report if you're interested). There's been talk amongst Police Departments in whether investing in wide scale wastewater monitoring could help locate drug dealers/labs. Personally, I think this is a huge invasion of privacy, but since wastewater is a "public good" police currently can do whatever they want with it (source: I work in a wastewater testing facility).
- onecommentman 5y agoPrudence might be as big a concern. If the public gets used to reports on waste streams, it would be an easy target for those who wish to create fear and panic among the populace. As easy as one bad actor flushing the wrong/right stuff a few times (stuff that is known to be monitored, say a specific infectious agent) in a few public toilets across a city, and waiting for the reports to trickle in. More of a fanning the flames rather than starting a panic, since the threat would have been well-known enough to have been monitored in the first place. So maybe keep those waste reports on a need-to-know basis, rather than broadcasting a public “daily waste report”.
- chiefalchemist 5y agoYes. I'm aware of that. The arc of mmy point is collateral damage. Are we saving some lives and ruining others?
- abc_lisper 5y agoCould this be from animals? Like cats or rats
- rdevsrex 5y agoTIL that even my poop can get analyzed by the government.
- newsbinator 5y agoOnly if you use the government's infrastructure to transport it.
- tpoacher 5y agoIt's so refreshing to click on a page and just see the answer to the question in the url. I've gotten very conditioned when urls contain a question, to expect a bloated, ad-ridden , 5-page editorial, focusing on a tangentially related long sob story of a guy and their dog, with the answer to the question barely hinted at, buried inconspicuously somewhere around page 4.
- mmatus 5y agoHi everyone, I’m the CEO of Biobot. I’m a computational biologist, passionate about leveraging wastewater data and analytics to improve human health. I’d be happy to answer any questions you have about the COVID-19 data that we’re generating at MWRA, what we’re up to at Biobot, or wastewater epidemiology generally.