Thread by @ZiadFazel

Over the weekend, smart & caring people like this ⤵️ have been raising alarms about #COVID19AB virus measurable in Alberta wastewater.

So I'm here to explain:
• where to find the results for your city or town
• how to interact with the graph
• how to interpret the results

https://twitter.com/JMeddings/status/1477390862095032321

First, let me take you exactly to where to find these results:
• for now, it is the only graph on the "Wastewater" tab
• hosted at @ucalgaryCHI, the results are province-wide including years of innovative work by @UAlberta, @UCalgary, @ACWAWater et al

covid-tracker.chi-csm.ca

Now, although the CMOH said on 7 Dec 2021 it was just about here, after that I could find no information from CMOH, AB Health, or GoA about where to find the website, or how to use it.

It is as if the Gov had been suppressing this information for so long, it sorta squeezed out.

And it fell on @UofC_Science and @BabychStephanie at @calgaryherald to provide an explanation and a link to the site then.

https://twitter.com/UofC_Science/status/1470857206639824901?s=20

Last week, @sarahoffin at @GlobalCalgary also explained how important wastewater sampling is.

Because AB Health is cutting back even further on PCR swab testing, we need other ways to see how fast #COVID19AB is spreading.

Spoiler Alert: WAY TOO FAST!

globalnews.ca/news/8479988/w…

In May when I built my #BalancedScorecard, I included @ucalgaryCHI wastewater sampling:
• it remains independent of government reporting
• not completely reliant on GoA funding
• everyone poops; not everyone gets swabbed
• wastewater sampling was a few days ahead of PCR

During Aug long weekend, I focussed on independent, daily R from @imgrund + wastewater sampling from @ucalgaryCHI, because:
• GoA's 28 July 2021 decimation of Test/Trace/Isolate would understate cases
• GoA was suppressing Alberta-wide results eg. UofA

https://twitter.com/TheBreakdownAB/status/1422625011484045315

In September, when we finally saw disinformation to cabinet in June to launch 4th wave:
• more empty promises about making wastewater results available
• which took until Dec to shart publicly
• did we ever see any local response, rather than top-down?

alberta.ca/assets/documen…

With above screenshot, I may have subtweeted @jvipondmd @PopAlberta @GosiaGasperoPhD with CMOH's notorious "SHIFTING FROM PANDEMIC TO ENDEMIC" document that:
• over-relied on highly-vaxed UK to predict AB Hospital
• cherry-picked worst to become worst

alberta.ca/assets/documen…

But I digress. Now that we have Alberta-wide wastewater sampling results:
• in a vacuum of information from PCR testing suppressed
• and rapid-testing results unavailable
• let's use it while we got it.

Lemme show you how...

covid-tracker.chi-csm.ca

1. Click on the name of your town or city on the map of Alberta on the right.

This will give you the graph for eg. Edmonton, which has been in just as much trouble as Calgary, and for which there are results since June 2020.

Why didn't we see that before, you may ask? Me too.

2. "Comparing sites is also problematic because different communities have different proportions of residential and industrial water use contributing to their municipal wastewater. The most important signals to compare are within a given community by following trends over time."

That's what most of us are looking for anyway:
• how is my town or city doing?
• how is the town or city of my loved ones, or my workplace, doing?
• oh ya, I remember we had it pretty bad around here before - you can see that confirmed in the wastewater sampling too, eh

"What the heck is this?" you may ask.
• Starting Date - eg. you can look since 1 July, for launch of the 4th Wave, or from 25 Nov, for neglect of the Omicron Wave
• Raw v Normalized - See Dr Parker explanation ⤵️
• I'll try to be your PhD whisperer

3. Raw v Normalized?

Raw = count of virus independent of whether lots of rainwater got into sewer, or industrial/residential mix

Normalized = uses fecal microbiota marker like Pepper Mild Mottle Virus* to focus on human poop in the wastewater.

* resists making jalapeño joke

4. N1, N2 or Average?

N1, N2, etc. are target sites on the virus that the wastewater sampling lab looks for.

If you want to know way more than me on this, read:

facetsjournal.com/doi/10.1139/fa…

@COVIDPoops19 is an awesome account to follow.

@threadreaderapp unroll

Thank you!
💩💩

Heavy media coverage yesterday about Alberta's wastewater sampling project, because:

Co-lead Dr Hubert: "There might be fewer people getting PCR tests, but what we do is a PCR test for the entire community."

@drdagly: ⤵️

AB Health: MonitoringClosely™

edmonton.ctvnews.ca/alberta-doctor…

Funding for the UofC and UofA projects has evolved, but AB Health is now funding the joint province-wide project with $3.4m (of Albertans' money).

As I explained throughout this thread, it is crucial these results remain publicly visible in realtime.

calgaryherald.com/news/wastewate…

True picture (therefore control) of #COVID19AB has been suppressed by 28 July 2021 Public Health Order that decimated Test/Trace/Isolate during 4th Wave.

Therefore we have to look at other signals like Wastewater Sampling, independent Daily R, and help from @bcCOVID19group...

@mentions@bcCOVID19group Dr Karlen had to switch from Cases to Hospital Admissions, and then analyze the lower testing volumes and higher test %, to explain Alberta's Urban/Rural Delta Wave.

pypm.github.io/home/docs/stud…

Impressive work from an experienced modeller to adapt to gaps in Alberta's information.

@mentions@bcCOVID19group @GosiaGasperoPhD @jvipondmd @PopAlberta @LeylaDAsadi @drdagly @noelgibney @RajBhardwajMD @dupuisj @demandsbetter @politicalham It will be interesting to see how Dr Karlan adapts to even more severe cuts in Testing, Tracing, Isolation, and the switch to unrecorded Rapid Testing, for Omicron now.

[Extremely unsubtle hint to read these].

pypm.github.io/home/docs/stud…

More on his work in a separate thread tbd.

@mentions@bcCOVID19group @GosiaGasperoPhD @jvipondmd @PopAlberta @LeylaDAsadi @drdagly @noelgibney @RajBhardwajMD @dupuisj @demandsbetter @politicalham We're fortunate that:
• despite Xmas reporting gaps
• 2-3 week lag of Albertans hitting hospitals from exponentially growing, unmeasured cases through Dec
• that Alberta-wide wastewater sampling became public
• so we can break down these graphs

Let's look at each one individually. Here:
• Virus measures N1 & N2 compared to new PCR swab test cases, and to test positivity
• As Dr Parkins explains (not Parker as I misstated above), wastewater virus sampling predicts both PCR swab test cases & positivity by about 6 days

Here, we see just how good the correlation between wastewater sampling results, and the 5-day moving average of daily new cases from swab tests.

Just as Dr Karlen at UVic infers underreported Cases from Hospital Admissions, we'll be able to infer them from Wastewater Sampling.

We see that here:
• Waves 2 & 3, qty of actual cases predicted 6 days earlier from wastewater sampling model was close.
• actual cases dropped off as swab testing capacity saturated ~ 20K tests/day
• in Wave 4, actual cases were below model, similar to what Dr Karlen saw.

Since we're here, let's look at Dr Karlen's 29 Dec model.

pypm.github.io/home/docs/stud…

He predicts severe outcomes at:
D: Hospital probability 10% of previous, Death 1%, Hospital Duration 10%
E: 30%, 9%, 30%
F: Same as previous

6-mo view ↙️ 2-mo view ↘️

pypm.github.io/home/docs/stud…

What's even scarier, is that Dr Karlen modelled these outcomes on 29 Dec, before AB Health had updated Hospital Admissions since 22 Dec (3.5/day/million people).

His next update will have the latest (currently 9.1).

2.6x higher, and climbing Omicron-fast.

I wish there were a simple formula like:

Cases = a x Wastewater + b

But we have to work more from trends than data points.

Dr Karlen has explained that pandemics have trends with the same slope for a while, than a switch to a new one. @GosiaGasperoPhD shows this too.

@mentions@GosiaGasperoPhD In the fall, I attempted to correlate @imgrund R with @ucalgaryCHI Wastewater project, who are inferring Cases from wastewater.

A different approach than @bcCOVID19group use of Hospital Admissions.

Or @KanjiJamil retrospective use of serosurveys.

Hoping there are connections.

@mentions@GosiaGasperoPhD @imgrund @ucalgaryCHI @bcCOVID19group @KanjiJamil For those of you new to Dr Karlen's work, there is this 54-min video, accessible to someone comfortable with first-year university-level math & science.



and this scientific paper, which is somewhat deeper.

pypm.github.io/home/docs/stud…

@mentions@GosiaGasperoPhD @imgrund @ucalgaryCHI @bcCOVID19group @KanjiJamil In retrospect, I won't be doing a separate thread on Dr Karlen's work.

I know I lost some of you moving from wastewater into his modelling, but may have picked up some ID docs, epidemiologists, engineers, etc along the way who are able to see the connections better than me.