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Post Archive 2021

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Ontario is screening all positive COVID cases for the N501Y mutation present in B.1.1.7 and the trend does not look good. Total case counts (and so deaths) will certainly be on the rise again soon as B.1.1.7 begins to dominate. 😢

In computer science we make off by one errors. In microbiology I apparently make off by 10,000x errors! 😂

I diluted my DNA control by 100,000x when it should have been 1,000,000,000x to get down to a “reasonable” 6,000 copies of DNA per μl.

I think I’m starting to feel what punch card programming must of felt like.

Each iteration takes me 30 min of careful planning, 20 min to carefully formulate the instructions in the bizarre way the machine understands, an hour for the machine to follow my instructions, and…

then I spend hours pouring over the output trying to understand what the heck was going on inside the machine and how I’ll tweak my program next time.

But in this case, the machinery is biology (eg. Taq DNA Polymerase enzyme doing PCR experiments).
It’s super tedious but hella gratifying when stuff works! Makes me wish I was either coding computers in the 70s or hacking life in 2040 😁

I’m so grateful to @ianklugman, @communitech and the government of Canada for making this happen!

@VicLeungIDdoc Self-screening is what we’re doing with https://staysafescreen.ca and initial indications are that it’s working well! Essential business owners are overjoyed to be able to have their staff self-screen onsite.

@VicLeungIDdoc “In the UK, screening showed lower sensitivity when tests were performed by testers who were not health care workers than when they were performed by health care workers;however,”…

@VicLeungIDdoc “the discrepancy disappeared over a 2-week period, which suggests that workers who are not trained in health care can be taught with experience to adequately perform swabs.”

@VicLeungIDdoc The claim that COVID testing can’t be done by regular people will go down with “masks aren’t needed or only protect others” and “transmissions isn’t airborne” as the most deadly ideas of this pandemic.

AZ Dose #1 - last Tuesday when it first became available in Ontario to 40+.

To keep from spamming my web followers with COVID tweets and my COVID followers with web tweets, I’m splitting my account. Follow @RickByersLab for COVID (but I’ll retweet for a couple weeks).

This is what a negative rapid COVID antigen test looks like at 20x speed.
”C” for Control (test works)
“T” for Test (virus detected).

By the way, this video is taken on my kitchen table. Why don’t you have these at home in your kitchen yet?

If millions of English high-school students and government employees are using them at home twice a week, surely you could too?

One business owner, nearly in tears, picking up their free #StaySafeScreen kits: “Every day I’ve woken up wondering if today would be they day I have an outbreak among my staff. Now I finally have a powerful tool to help avoid that.”

@cat10086338 @RegionofHalton @HaltonHlthcare @OakvilleChamber @Communitech Here’s a photo of my Grade 9 son instructing someone on the #StaySafeScreen bus to self-swab. If millions of high-school students in England can self-swab at home, then I’m pretty sure Ontarians are up for it too! https://www.bbc.com/news/health-56750460

Yes 2 is better than 1. But 2×1 looks pretty clearly better than 1×2 in most cases!

Similarly many people getting frequent lower-sensitivity antigen tests is better for containment then a few people occasionally getting highly-sensitive PCR tests.

Hard for many to reason about! https://x.com/jkwan_md/status/1389407379352137728

Comparison of negative and positive rapid COVID screen results. Note real positive human samples often generate a much fainter line (depending on how much virus is captured).

I love the detective analogy. PCR is like checking everyone’s fingerprints, while antigen screening is having people be on the lookout for the description of a suspect (who can later have their fingerprints checked).

“The root of the CDC’s behavior was simple: fear. They didn’t want to take any action for which they might later be blamed”.

From the book “The premonition”. Pretty much sums up much of the pandemic response. 😥 Fear of taking the wrong action is greater than fear of inaction.

In tech we know this mental disease well and how it breeds mediocrity if left unchecked. To combat it we have a “bias to action” and “blame-free post mortem culture”. Nobody is punished for making mistakes, only for failing to learn from them.

But then, in tech we aren’t charged with keeping millions of people
alive and healthy. I can’t imagine what that burden of responsibility does to one’s confidence or risk tolerance.

“Justin Trudeau gave credit to the StaySafe project in announcing the rapid testing expansion Friday. ‘Cases have been found in asymptomatic people who had no idea they were positive, but because of the test result, were then able to isolate to prevent transmission’ Trudeau said” https://x.com/btaplatt/status/1391114568831840261

Received my Lucira Check-it home PCR-quality COVID test today for $75. I’ll be using this (instead of my $12,000 PCR machine) to check any positive antigen test results I get.

Antigen tests are awesome! But at 2 in 1,000 false positives, you need a pragmatic plan to validate!

Every high school student in England has been testing themselves for COVID at home twice a week for the past couple months.
Big surprise, it appears to work in Canada too! 🙂 https://t.co/XHEanbRxiA

Two positive antigen tests from the #StaySafeScreen bus (one so faint it’s almost invisible here), alongside synthetic positive tests at 1x, 10x and 100x dilutions for reference.

This is what catching sneaky asymptomatic COVID looks like in practice!

I’m no conspiracy theorist, just a follower of Occam’s razor.

Imagine, this whole pandemic may be due to one lab tech or field researcher getting sloppy in their use of PPE and accidentally exposing themself to a bat virus!

I need to update my analogies.

I’ve been saying rapid antigen testing can feel as normal as flossing your teeth. I just realized I’ve done an antigen test 6 times in the past week and only flossed 4 times. It’s starting to feel more like brushing my teeth than flossing them!

Hopefully regular wastewater surveillance of respiratory pathogens becomes common practice in the future. We have complicated surveillance to help us answer “should I wear a raincoat today”, why not also “should I wear a mask”?

The history of public health is full of frustration getting people to accept new ideas, which in retrospect appear so obvious. Thank you @michaelmina_lab, to my family and other fellow #StaySafeScreen volunteers, you are our John Snow 🙏😁.

Hey @michaelmina_lab, widescale deployment of antigen testing is still being held back in part due to the real costs of false positives. I’ve heard you say to use rapid nucleic acid for confirmation, but those aren’t always available in all settings (eg. UK home use). 1/

A RAT manufacturer has told me they expect false positives to be random events, generally not correlated with anything in the sample. In practice I’ve seen this - people retest 2 or 3 times and get negative every time (then negative PCR). 2/

So why not just suggest confirmation by 2 or 3 repeated antigen tests, where any one is interpreted to mean a true positive? 3/

Some quick and dirty math suggests this turns a 99.8% specific and 80% sensitive test into a 99.9992% specific and 76% sensitive one. Or, for 3x, a 99.9988% specific and 79.2% sensitive one. 4/4

Apparently Twitter believes the FDA logo is “sensitive content”. Either it’s being REALLY smart about what I find objectionable, or really dumb 😂.
@michaelmina_lab, you too?

Hey @ResortsOntario, my family is having a great regenerative time at one of your member resorts this weekend. As someone with an unvaccinated child and concerned with COVID protocols, I feel quite safe. Thank you for your support of a safe reopening of the industry!

That said, I’ve seen unmasked staff talking closely with guests outdoors, and lots of staff mingling closely without masks indoors. With delta having an R0 of 5-8 and full vaccination being a couple months out for many young employees, some staff outbreaks seem sadly inevitable.

If you’d have any interest in helping your members leverage free rapid tests to reduce this risk with a minimum of hassle and cost, I’d be happy to advise. I’m a volunteer strategic advisor for COVID testing at Communitech, working with Health Canada.

I know we’re all anxious to put this thing behind us, but it seems a wakeup call is in order. Around the world we’re loosing the equivalent of 50 jetliners full of humans every SINGLE day, and its not clearly slowing down yet! History will judge the level of concern we show!

“It’s like you’re in the wrong job there, buddy” 😂 Right on.

If your job is to help guide us with our health and you aren’t willing to be vaccinated, then you aren’t qualified to guide us (rare medical exemptions aside). It’s not “forced”, it’s having the skills for the job. https://x.com/DanielGriffinMD/status/1407652109911302147

It’s as if in software, someone complained about being “forced” to use e-mail because they were baselessly afraid they might get carpal tunnel syndrome despite training. Sorry buddy, your beliefs preclude you from doing your job effectively, please find a different one.

I’m now an AstraZeneca Pfizer hybrid 🎉. Very impressed by the mass vaccination clinic and what that volume of doses will mean for our community in the next months 😁.

Of course, as impressive as the mass clinic was, it’s hard to beat the experience of my first dose: in and out of a small family pharmacy with few other people around.

Yes, PCR is better at detecting the virus before contagiousness, but not incredibly so: 70% the day before vs 40% for antigen. Once again, if your goal is to prevent spread, frequency and turnaround time of testing matters MUCH more than analytical sensitivity.

In Waterloo region, one of Ontario’s last COVID hotspots, it’s now possible to sign up to run your own rapid testing pop-up or to be a raid testing community ambassador: https://staysafescreen.ca/

3.4% of Canadian Children had COVID before April. Sure most will be fine, but some will have lifelong effects and others will have contributed to spread reaching vulnerable populations.

Unvaccinated kids using rapid tests in the fall could be key to avoiding another surge. https://x.com/DGBassani/status/1412546197231968256

Rather than all the “we’ll have to live with COVID like we live with Flu” talk, I’m excited for the reverse: Let’s crush Flu (and RSV, and all Coronaviruses) with vaccines like we’re learning to crush COVID!

We’ve been so complacent in assuming that colds are a fact of life. https://x.com/DanielGriffinMD/status/1413210011065520128

Bravo! All health workers (and high school students) in the UK have been doing home testing for months, why is this so controversial? You can’t go to a bar or restaurant in Germany without proving you’re fully vaccinated or have a negative rapid test that day. Get with it Canada! https://x.com/bradwouters/status/1412781484151279616

I got vaccinated because I consider it an ethical responsibility to society to ensure I don’t contribute to the spread of a disease that has already caused 4 million deaths and immeasurable suffering. #WhatsYourWhyWR

And please let’s not forget - fully 1 in 500 people (0.2%) in the US have died of COVID already, for a disease that’s was predicted to have an infection fatality rate of <0.5%.

The OST report on schools argues against serial rapid testing (https://covid19-sciencetable.ca/sciencebrief/school-operation-for-the-2021-2022-academic-year-in-the-context-of-the-covid-19-pandemic/#:~:text=Asymptomatic%20screen%20testing%20(i.e.%2C%20asymptomatic%20testing%20in%20the%20absence%20of%20documented%20exposure)%2C%20is%20not%20routinely%20recommended%2C%20especially%20in%20the%20low%20to%20moderate%20COVID-19%20risk%20scenarios.). It cites one short letter which claims antigen testing is “low-yield”: https://www.cambridge.org/core/journals/infection-control-and-hospital-epidemiology/article/low-yield-of-severe-acute-respiratory-coronavirus-virus-2-sarscov2-asymptomatic-routine-screen-testing-despite-high-community-incidence/176BA478C1D529E0DACCE0D6FA8DADC0

This conclusion comes from serial antigen screening having a positivity rate of “only” 0.36% at a time when the weekly case rate in Ontario was 0.1% and public health test positivity rate was 5%. Comparing positivity rates like this is flawed logic.

If you take the high risk people out of the pool (symptomatic / close-contact) then of course those remaining will have a lower risk of being infected. But rapid testing STILL caught cases at 3x the presumed prevalence, suggesting public health containment was completely failing!

The important comparison is not positivity rates but cost of interrupting one transmission chain. If you give antigen tests to people to do at home and have rapid molecular testing handy to confirm any positives, they can be about 1/10th the cost of PCR tests.

The question is: how much value is there to society in each COVID transmission that gets interrupted (that case and all downstream cases)? I don’t know how to calculate that, but in the cited study, if done efficiently it would have cost about $2000.

I don’t know how the authors of this paper would compute a value for human suffering, but calling $2,000 (or even $20k, assuming 10x admin overhead) to prevent a nursing home outbreak “low yield” and “not cost effective” seems pretty callous and inhumane to me.🤷

The situation today is that pro sports players, many politicians, employees of Canada’s biggest companies (Air Canada, Rogers, etc.) and rich white dudes with the educational privilege like me are all keep our families safe by regular rapid testing.

My daughter’s private school makes regular use of rapid COVID tests. I took her out of public school due to very poor COVID protocols.

How on earth can keeping these tests out of public schools possibly be an equity “improvement”?

Why is there so much concern over the 1 in 500 risk of false positive with antigen tests but nobody is asking “what’s the false positive rate of COVID symptom screens”? Surely having an unusual headache, stuffy nose, cough or fever that isn’t COVID is more common than 1 in 500!

We weren’t sure we’d get sterilizing immunity, then we did, now it looks like we’re losing it. The important response is not “this is what we always said”, it’s “crap, what can we do NOW to get this awesome protection back?”

To be clear, yes of course the MOST important role of the vaccine is to prevent serious disease (and yay, we still have that). But preventing serious disease in those who can’t or won’t get vaccinated was a pretty damn valuable property too.

Hey 🇨🇦Canada🇨🇦, we could effectively end this pandemic now by:
➡️ Making rapid tests available to everyone for free (~$1B/month)
➡️ Requiring a rapid test within 48 hours to enter any building outside your home

Is the alternative of a 4th wave really the choice you prefer?

In the https://staysafescreen.ca/ community testing program we’ve been using a new type of screening test with amazing properties:
78% sensitivity
99.996% specificity
<$7/test (90% gov’t subsidized)
Avg. 15 minutes for negative, 45 min for positive
Best of all: already HC approved!

It’s simply an Abbott Panbio antigen test, with presumptive positives followed up with a Lucira check-it rapid molecular test.
Fast, cheap and sensitive enough to be a highly effective screening tool but with almost zero false positives.

And in case it’s not clear, this is still just a “screening test”, not a medical diagnostic. We always encourage presumptive positives (even with a positive rapid molecular test) to go to public health for confirmatory PCR testing.

👎Bad news: waning immunity 6 months after getting vaxxed is likely a big deal.
👍Good news: dosing intervals around 8 weeks likely offer more durable protections (yay Canada!)
∴ It’s time to plan boosters for all! https://t.co/qwSZjNb22R

@uhwuhna, I’ve personally observed many folks in the liberal Health Canada administration bend over backwards trying to give away rapid tests and expand access. Obviously I wish they could/would do more still. This report sums it up: https://www.canada.ca/en/health-canada/services/drugs-health-products/covid19-industry/medical-devices/testing-outreach-collaboration/industry-advisory-roundtable/reports/taking-stock-looking-forward.html
[Replies were locked] https://x.com/uhwuhna/status/1428814495053451269

The hospitalization risk of the vaccinated is a key trend to watch. It, more than anything else I think, will predict how and when this pandemic ends. Will it hold in Canada (perhaps due to our extended dosing) or rise significantly 6+ months post vaccination like in Israel? https://t.co/mh7qkT6pL8

If we can make rapid testing an easy part of everyday normal life (like brushing your teeth) then we may never need to lockdown to contain a pandemic again!

Sadly, the direction we’re headed in Ontario I think means that by the end of the year we’ll either be dependant on heavy lockdowns again or there will be a lot of suffering. Vaccines mandates are great, but insufficient on their own now. 😢

This is a Check-It (https://www.lucirahealth.com/) RT-LAMP device. Looks like 8 wells (only 6 illuminated), 2 positive controls and a CCD sensor for taking a photo of the colorimetric reaction. Seems so wasteful to be disposable but super cool!

Rapid tests do a damn good job showing where COVID transmission is likely to come from. Let’s require their use broadly to avoid the need for another lockdown and further avoidable suffering.
@michaelmina_lab @TestandTraceCa @cdlscreening @LisaBarrettID @DFisman

Correction: despite unclear wording on the page, I have it on good authority that the tests are only provided to people who are unvaccinated. That’s a shame - vaccinated people can still get infected and transmit (but at perhaps 1/8th the rate in Ontario right now).

“I salute all hardworking journalists who put science and facts at the heart of what they do, and ask me tough questions every day, but make sure they’re educating and informing Canadians from a broad range of perspectives”.
Now THAT’S how a real leader addresses “fake news”! https://x.com/Ben_Parsons__/status/1435799898071310337

Tonight my family put together a bunch of 2-test rapid testing kits for my Daughter’s school to hand out to participating kids tomorrow!

Hey @DFisman, if rapid tests were in limited supply, how would you prioritize distributing them for maximum society benefit? I’m assuming it takes at least a month to spin up in any given group (education, logistics, etc.).

“All we needed was access. We didn’t really ask for permission for the rest of it… If you’ve got the kits you can take the initiative. Right now it’s time to beg forgiveness later I think” @LisaBarrettID
#StaySafeAmbassador
https://youtu.be/3rB5SzCgn4A?t=605

This study tells us what to expect from COVID in Canada this winter: lots of infections but relatively low hospitalization rate. But 10% of a big number is still a big number 😥. Hopefully longer dosing interval, boosters and rapid tests will save us from a terrible winter. https://x.com/VincentRK/status/1445164155712032770

Its also interesting to see that all the noise about delta evading vaccine immunity a couple months back indeed seems overblown - minor compared to the effect of waning immunity for all variants.

The mention of “at home” testing is absolutely key. This isn’t about healthcare workers / teachers having new responsibilities in classrooms or about take-home swabs that have to be sent to labs, it’s about distributing tools to parents. That’s key for real scale and impact.👍 2/

Empowering local medical officers is also great news IMHO. It means we’ll see some diversity of approach that will enable us to learn and build consensus rather than everyone following the same dictated opinion. Tradeoffs are hard. Experimentation is key. 3/

Lots of emphasis on the true solution being vaccination. This confirms signals I’d been getting elsewhere - that some hesitation to embracing testing was due to the crowd looking for an alternative to vaccination. Lets all be clear: tests aren’t an alternative to vaccination. 4/

Lots of emphasis on being “targeted”. This makes sense when there is supply constraints, which is certainly the case. I am optimistic that strictness of targeting will diminish as comfort grows and supply increases. But this is probably the greatest risk to maximizing impact. 5/

All in all, I think there’s a lot more to do to get rapid tests used at the level that’s likely the sweet spot of Canada-wide cost/benefit tradeoff. But this seems likely to become a very good step in the right direction for Ontario. 6/6

@co2detective, you don’t know what you’re talking about. Rapid tests were never allocated by health unit. Do you really think StaySafe would have been able to give out >400,000 tests if tests were proportioned equally by health unit?

I’ve just had the first cold go through my house since I built my home microbiology lab. qPCR test results are in and it’s definitely Rhinovirus (green line at cycle 25, earlier green line is external control “B2M”). This is a big day for my long-time dream of home virus testing!

I’m sure most of you are thinking “who cares, it’s not COVID so it’s a cold - what difference does it make if it’s Rhinovirus or Parainfluenzavirus or whatever?”. That’s true, I’m just geeking out on something totally impractical (as the first computer hobbyists did).

Hey @michaelmina_lab it looks like the FDA updated their antigen test approval guidelines on Oct 6th: https://www.fda.gov/media/137907/download. There’s a new clause in the asymptomatic evaluation section avoid avoiding participants with recent +PCR. Should help fix the post-infectiousness bias?

Direct comparison to PCR, which is well-known for being positive for weeks or months post contagiousness, has led to a dramatic under-appreciation of the effectiveness of antigen tests for reducing transmission risk. 2/3

Also, is it weird that this paper was accepted in May but only published now, 10 days after Biden announced the new US rapid testing plan and, on the same day, the FDA updated their guidelines potentially addressing the flaw in their approval process? https://www.fda.gov/media/137907/download 3/3

I realized I was sloppy with my wording here. So correction: ”… Resulted in cutting infection risk IN HALF”. VE 80%->90% means infection risk 20%->10%. “Doubling protection” isn’t mathematically accurate. I’m happy to admit when I’m wrong (even without being called out). 😁

Of course I know all to well that this isn’t up to the chambers to decide. We should all be lobbying our provincial government to expand the distribution channel we know has worked for small businesses. Its simple, pragmatic and easily actionable.

This seems to be why good tests like Abbott Panbio are available in Canada for asymptomatic use only “off-label” in a few provinces.

With waning immunity (protection from infection only 6x, not 7x anymore), more time being spent indoors and lowering humidity, I fear we’ll have to do a lot more than “pause” to keep from having a disaster on our hands.

Unfortunately the data lags by a few weeks, so it’ll be at least a couple weeks before we have a clear idea of how much omicron we have. And we’re still under-testing, so maybe our sequencing coverage is somewhere around 10% of ALL cases.

However, they explicitly use a conservative specificity of 99.1%. StaySafe’s experience with Panbio was consistent with the licensed specificity of 99.8%. I suspect using that number would result in guidance with a much lower threshold (perhaps 75 cases per M instead of 250). 2/

That’s to say: If we use a realistic instead of conservative specificity estimate, then the advice would likely be that most Ontarians should be screening with rapid tests 2 - 3 times per week at today’s case loads!

Millions of rapid tests have been given to businesses to help keep their workers safe. For this omicron Christmas, governments should allow those workplaces to distribute any tests they have sitting around to employees to use with their friends and families. #FreeTheRATs

We’re NOT going into isolation all winter again! The sense of duty was strong last winter, but this winter is very different. Individuals have had every opportunity to get vaccinated and public health leaders have had plenty of time to prepare.

Public health leaders, don’t you DARE ask us to suffer in isolation and educate our kids at home again this winter unless you’re going to show us some basic respect by empowering us with the education and tools needed to gather safely in small groups. #FreeTheRATs

Any students of public health history?

When public health departments in different jurisdictions are fiercely split on the value of a new tool (like self-screening with RATs), which does history suggest is the most probable explanation?

Many public health leaders are:

I agree the “I heard ..
from a random person” comments are unhelpful. But I also don’t think “discouraging” this behavior will have any positive effect other than helping our tribe feel more self-righteous. What does research say on how to actually change minds and behaviour?

In particular, note: “Nova Scotia Public Health has said they see their rapid testing program as a way of normalizing testing for residents so that they have the tool available to deploy at scale quickly should it become necessary. ” 1/

“All too often we wait to act decisively until hospitals are almost overloaded, and then are left with no options other than long and strict lockdowns. Hope is not a strategy.” 2/2

We weren’t better equipped, we just had the foresight to prepare and build an awesome volunteer army over a period of months so that we could scale. This is the same reason NS is succeeding while ON is floundering.

Credit where credit is due: Thank you @fordnation for buying 10+ million rapid tests (on top of those from the feds) in time to distribute them for the holidays. That must have been a contentious decision before omicron. I genuinely appreciate the act of leadership. 🙂

I’m grateful for the tests that have been distributed. But 50M over ~6 months is one test per person every 2 months! Think bigger! ⬆️⬆️

I’ve kept my family of 4 safe by purchasing and using over 200 rapid tests in that time. So let’s aim for at least 20x the volume, shall we? https://x.com/fordnation/status/1473436983297032201

I’ve updated http://StaySafeScreen.ca with a list of all the HC-approved COVID antigen tests I can find available for sale in Ontario with a link to the shop with the lowest price. Let me know if I’ve missed any!
Of course everybody is out of stock until January at this point 😢.

Wow, look at the massive increase in COVID alert keys being generated for Ontario! I’ve plotted both the absolute value (>300 keys/day) and relative to the number of 7-day cases (>10%).
Keep using the COVID alert app. With contact tracing failing it may be your only notice!

Of course COVID alert is only as good as our testing system and that’s failing too.
I know a high school student who was just contacted by public health to say they were exposed 7 days ago, and that they needed to isolate for the remaining 3 days!

Whoa, look what just showed up on the list of Health Canada approved rapid COVID tests. Finally a company capable of producing hundreds of millions of tests has a license in Canada for a product for consumer use!

Note “PanBio self-test” is distinct from “PanBio”. Cost? 💵😐