Amount of Covid found in the wastewater in Boston

https://www.mwra.com/biobot/biobotdata.htm

by simonebrunozzi • 5 years ago

185 103 5 years ago

mwra.com

glial• 5 years ago

Similar work in MN shows that wastewater rates are a leading indicator of positive tests:

https://www.kare11.com/article/news/local/breaking-the-news/...

epakai• 5 years ago

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• 5 years ago

The 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/ I believe.

dsizzle• 5 years ago

Yes. 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-qp...

jonas21• 5 years ago

https://en.wikipedia.org/wiki/Real-time_polymerase_chain_rea...

ImaCake• 5 years ago

You can measure how efficient a PCR is by how long it takes to get a positive result. PCR requires a loop of different temperatures to cause different steps in the reaction to occur. This loop is usually repeated 30-40 times. You measure if its positive by looking for a (continuous) light signal. The light signal increases each time you loop through the temperatures. When the light signal passes a pre-determined threshold, that cycle is said to be the one where you got the positive result. The more virus DNA/RNA in the sample, the less loops you need for a positive result.

a45a33s2• 5 years ago

its unfortunate that we'll never know what this data looked like in 2019 or before

ceejayoz2• 5 years ago

Seems like it’d be a pretty flat, unremarkable chart.

jdavis703• 5 years ago

Perhaps, 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.

teeray• 5 years ago

Hopefully, otherwise we have other problems

a45a33s2• 5 years ago

thats an assumption that we have no way of confirming

tbihl• 5 years ago

Or in 1889-1890.

orblivion• 5 years ago

Maybe they have old samples?

muzani• 5 years ago

I'm entertained by the idea that somewhere out there, the CCP sent Chinese James Bond to swipe archived wastewater with covid infected ones to prove that it wasn't in Wuhan, but nobody has tested it yet.

TechBro8615• 5 years ago

That makes me wonder… where does the Covid in the wastewater go? Do we successfully filter it out of the wastewater before recycling it back into the ecosystem? Where specifically does filtered wastewater go, and how confident are we in the filtering process?

revicon• 5 years ago

I am not at all an authority on this but I think they use UV light to kill it during one of the treatment steps.

dredmorbius2• 5 years ago

A significant goal of wastewater treatment is reducing or eliminating pathogenic load. For a methods overview, see: https://www.filtsep.com/water-and-wastewater/features/pathog...

This paper discusses treatment and emergent pathogens:

"The Role of Wastewater Treatment in Protecting Water Supplies Against Emerging Pathogens"

https://www.jstor.org/stable/23803199

I thought direct chlorination played a larger role, it seems it doesn't.

(Heavy chlorination of water does result in post-treatment chlorine compounds being present, these are themselves an environmental concern. The bulk of the chlorine evaporates or is reacted relatively quickly. Chlorine also negatively impacts "digestors" which process residual organic matter in wastewater.)

UV, oxygenation, sunlight, filtration, and dilution are all utilised as well.

Viruses tend not to survive long periods of environmental exposure outside a host in most circumstances, though I'm not knowledgeable on specifics or exceptions.

aardvark925• 5 years ago

Not sure what the water treatment plant steps are downstream, but I can tell you I've been processing SARS-CoV-2 positive wastewater samples for ages and managed not to catch COVID. Most of the gene fragments tested for in these studies are just that, fragments. The virus itself degrades pretty quickly under environmental stress (UV, heat, evaporation, etc).

I wouldn't be too worried about catching COVID from the water.

elihu• 5 years ago

If memory serves, there was a city in Italy I think where they were able to verify that Covid was present in the city some time before the first reported case because they keep samples of the sewer water for awhile, and that allowed them to retroactively test for it.

philoph1122• 5 years ago

It looks like the amount simply varies by season (high in winter, low in summer), unless I'm missing something...

dragontamer3• 5 years ago

Its 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.

chiefalchemist3• 5 years ago

Not 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?

m0llusk• 5 years ago

Coronavirus typically has a spike that starts in December and lasts until February. There are many theories about why this happens, but reduced Vitamin D levels has substantial proof behind it.

dragontamer3• 5 years ago

There's nothing "typical" about COVID19 yet.

But yes, there was a spike in December 2019, and another spike in December 2020. So we all are expecting a spike in December 2021.

bellyfullofbac• 5 years ago

In the northern hemisphere? My theory is in spring/summer/fall people are hanging out outside, and as winter comes they think "I've been fine socializing the last few months, hanging out inside will be safe." and socialize indoors, where the lack of fresh air means the virus will spread...

Enginerrrd2• 5 years ago

First, in case it's not clear, these are (indirect measurements of) concentrations not volumes. There is a strong seasonal effect here, but it also tells other stories based on variations outside of that. Still, the seasonal bit is not unexpected, but hugely significant.

Most respiratory viruses, like influenza and colds have greater prevalence during the local winter. We'd expect COVID to behave similarly. The reasons for that are still debated.

In wastewater collection system, I&I (Inflow & Infiltration) is a constant problem where excess water from the environment enters the waste treatment pipeline. It's costly because all that otherwise clean water has to get the full treatment. So, it's interesting to me, that, unless they have normalized for I&I somehow which is not apparent in their raw data, the true seasonal variation in concentration is actually understated.

mlyle7• 5 years ago

So, it's interesting to me, that, unless they have normalized for I&I somehow which is not apparent in their raw data, the true seasonal variation in concentration is actually understated.

Biobot says:

"We normalize the SARS-CoV-2 viral concentration to a fecal indicator, to account for differences in dilution. We use PMMoV as this fecal indicator, which is an RNA virus that is commonly excreted in stool."

So they're effectively reporting on the ratio between SARS-CoV-2 and PMMoV concentration, which should be normalized for seasonal changes in dilution.

scotty79• 5 years ago

In some countries like Poland, covid looks like solely seasonal disease with nearly zero cases throughout the whole summer, and ramp up during autumn to peaks in winter and spring only broken with lockdowns, dropping back to near zero cases in the summer.

usr11063• 5 years ago

Not 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_vii...

1over137• 5 years ago

The standard abbreviation for litre is uppercase L.

usr11063• 5 years ago

Actually 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.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_o...

mlyle7• 5 years ago

Re normalization: see this comment https://news.ycombinator.com/item?id=29468598

jasonhansel• 5 years ago

Would 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• 5 years ago

They can. I've seen on the news that at least two southwest cities that are currently using wastewater specifically for omicron surveillance.

gentleman11• 5 years ago

Omicron 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

aardvark925• 5 years ago

We 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.

aardvark925• 5 years ago

We'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/ has a variant dashboard based on sequencing data, including Omicron. It's not as quantitative qPCR, but still may be of interest.

yread2• 5 years ago

Couldn't you run RT-qPCR twice with two different sets of primers? Does RT-qPCR give you the spike gene target failure rate?

Ifkaluva• 5 years ago

It looks like the spike this December is already bigger than last year at the same time?

smalley2• 5 years ago

Interesting, looks like the South Bay has some similar numbers: https://covid19.sccgov.org/dashboard-wastewater but I suppose having milder weather hasn't seen as serious an uptick as Massachusetts?

jrmg• 5 years ago

I 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…

smalley2• 5 years ago

No 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)

rossdavidh3• 5 years ago

Well 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.

jghn2• 5 years ago

I 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• 5 years ago

By "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).

rossdavidh3• 5 years ago

Should 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

throwanem• 5 years ago

Stepping 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• 5 years ago

COVID is the disease, coronavirus is the pathogen.

aftbit• 5 years ago

COVID-19 is the disease, SARS-COV-2 is the pathogen, coronavirus is a large group of viruses.

hardtke• 5 years ago

Be 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• 5 years ago

Good point. Also keep in mind this is just one location. Would be really cool to see this measured by most cities.

jvmiert• 5 years ago

We do this in The Netherlands: https://coronadashboard.government.nl/landelijk/rioolwater

twofornone• 5 years ago

Has 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.

mlyle7• 5 years ago

Delta 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.

itamarst• 5 years ago

MA sequences 30% of PCR tests, and has so far found only a single Omicron case...

incongruity• 5 years ago

Couldn’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.

jointpdf• 5 years ago

But 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-proportion...

tyrfing• 5 years ago

The 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.

mmatus3• 5 years ago

Lots 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-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!

AtlasBarfed• 5 years ago

That curve matches generally the "Daily New Cases" graph in

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• 5 years ago

In 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

jollybean• 5 years ago

Would 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?

mmatus3• 5 years ago

You can see our data overlaid with clinical testing data here: 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• 5 years ago

Doesn'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.

chiefalchemist3• 5 years ago

Slighly 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?

aardvark925• 5 years ago

Folks have been testing wastewater for legal and illegal drugs for years (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• 5 years ago

Prudence 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”.

chiefalchemist3• 5 years ago

Yes. I'm aware of that. The arc of mmy point is collateral damage. Are we saving some lives and ruining others?

abc_lisper• 5 years ago

Could this be from animals? Like cats or rats

rdevsrex• 5 years ago

TIL that even my poop can get analyzed by the government.

newsbinator• 5 years ago

Only if you use the government's infrastructure to transport it.

tpoacher• 5 years ago

It'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.

mmatus3• 5 years ago

Hi 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.

Amount of Covid found in the wastewater in Boston

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