On Rapid Tests

[citation needed] Parte Deux

Like the first part of my Covid citations, this issue of And Another Thing is free for all Letters readers. Also, it was kind of glitchy on the settings front, so if you got more than one version of this email, I apologize!

Those of you who’ve been following my Pandemic Thoughts for the past year have probably heard me complaining about testing policies as alternatives for vaccination policies, which means it may have seemed like a dramatic shift when, a week or so ago, I posted this:

Because it’s true! Testing alone is inadequate, especially when done infrequently and with a gap of time between test and event. You simply can’t take the information from a PCR test done on Monday and use it to determine if it’s safe to gather with a group on Friday. That’s not how this works, and we’ve known that since very early on.

But I have come around to the idea of day-of rapid screening as a means of providing an extra layer of protection on top of vaccine compliance against the spread of infection, and here’s why:

Our rapid screening tests are less effective than PCR at telling us if we’re infected, but they are very effective at telling us if we’re currently infectious.

This is because rapid antigen screening doesn’t necessarily tell us if we have any Covid in our systems. They have a threshold viral load before they’ll detect the virus in the test sample. But what we know is that the viral load threshold they can detect is a transmissible viral load.1 That means that if we have crossed the viral load threshold that can be detected by rapid screening, we’re probably contagious, and if we haven’t crossed that threshold, we probably aren’t.2 And because currently infectious is sometimes a more important piece of information than whether you have any virus in your body at all, it’s a useful tool for us to make day-to-day decisions about things like dinner parties and holiday gatherings.

Michael Mina, an epidemiologist, immunologist, and physician at Harvard Public Health/Medical School adapted the data collected by the UK’s Lateral Flow Oversight Team to this chart3 showing each of their tests’ sensitivity at detecting contagious viral loads:

The chart is summarized in a thread on Twitter,4 in which Mina says that the issue we have is that we’ve been considering rapid tests as medical devices, which means we’re always comparing them to PCR. As medical devices, rapid tests aren’t going to measure up to PCR, because the point of a PCR test is to find out whether you have any Covid at all. PCR tests are much better than rapid tests at detecting trace viral loads as well as post-infectious viral loads. The study’s researchers, in the discussion section of the article, say the same. But what I’m arguing here is that any virus at all isn’t a useful metric for making daily decisions, because that’s not the metric that determines whether we’re going to contract or spread the virus. By shifting our focus to treat rapid tests as public health devices, we can consider their efficacy and sensitivity in their own right and start utilizing them in that way.

The current trend in North America is to skip over rapid testing in favour of the more sensitive PCR, and in Ontario, where I live, they’ve very strictly limited home use of rapid antigen tests because despite successful programs in countries like the UK, Ontario says they can’t trust individuals to perform or report the test correctly. There is legitimate debate about this measure among experts, some of whom argue that accessible home testing will encourage people to abandon other protective measures, or that people will under-report positive tests and fail to seek appropriate verification and care. And those things are probably true, for some people. It’s not a fail-proof measure and can’t effectively stand-alone, and we definitely need to be planning for user error and test failure in the strategy.

Overall, though, my rebuttal to the imperfect use argument is very similar to the discussion on safer sex vs. abstinence in pregnancy and STI prevention. Even though we know condoms are 98% effective against STI and unwanted pregnancy with perfect use but only 86% effective under normal use, we don’t require people to seek professional help and supervision for their use, because we understand that 86% protection is better than 0% protection. Ideally, if your condom fails, you’re getting post-exposure care, like PlanB or pregnancy and STI testing, because none of these things is a perfect measure on its own, but each layer adds to the safer sex equation. In a similar vein, harm reduction measures for drug use like naloxone programs don’t stop people from using drugs (and some people think that should be the goal), but they do help reduce overdose deaths, one of the most risky parts of using.

Rapid antigen tests, like condoms and naloxone programs, are a harm reduction strategy that allows people to make less-risky decisions with as much information as possible. It made sense to ask people to skip gathering for quite a while, but we’re social creatures, and it’s very, very hard for us to never gather. Realistically, even I’m not willing to do that forever. Long-term abstinence expectations will almost always fail, and we know from other versions of this story that when people don’t have the information they need to make a safe choice, they’ll often make a dangerous one. We need to empower people to make safer, informed choices. Mina and the study authors argue, and I agree, that a public health rapid testing strategy requires education campaigns to ensure correct usage within a minimized margin of error, but that’s super possible. Roll the condom on the banana, demonstrate the dental dam, offer naloxone training, show how to collect enough saliva for a spit test. We could do this. And while it wouldn’t mean zero Covid, it would probably mean we could have Christmas without worrying that we’re going to kill Grandma, and that’s a benchmark I’m extremely eager to reach.

1

Peto, Tim, and UK COVID-19 Lateral Flow Oversight Team. “COVID-19: Rapid Antigen Detection for SARS-CoV-2 by Lateral Flow Assay: A National Systematic Evaluation for Mass-Testing,” January 26, 2021. https://doi.org/10.1101/2021.01.13.21249563.

2

Harmon, Alexander, Celina Chang, Nol Salcedo, Brena Sena, Bobby Brooke Herrera, Irene Bosch, and Laura E. Holberger. “Validation of an At-Home Direct Antigen Rapid Test for COVID-19.” JAMA Network Open 4, no. 8 (August 27, 2021): e2126931. https://doi.org/10.1001/jamanetworkopen.2021.26931.

3

From Michael Mina, adapted from Peto et al. COVID-19: Rapid Antigen detection for SARS-CoV-2 by lateral flow assay: a national systematic evaluation for mass-testing.

4

Michael Mina. “Rapid Tests Work Very Well to Answer 🧵 AM I INFECTIOUS and a RISK TO OTHERS This Is THE Public Health ? We Care about I Made a BIG Chart of Rapid Tests - Overall Sensitivity vs Any PCR Pos - What FDA Judges - Sensitivity If Infectious (97%!) - What We Actually Care about 1/ Https://T.Co/Or0L2R7Y4D.” Tweet. @michaelmina_lab (blog), September 15, 2021.

The Things I Know About Covid-19

A bibliography in early October, 2021

And Another Thing is a sub-category of the Letters usually reserved for paid subscribers. I’m making this issue free for alla y’all.

Having been on the “Covid beat” in whatever unofficial capacity I can claim since the earliest whispers of the pandemic started in the waning days of 2019, I’ve spent a lot of time reading and learning from experts about Covid itself, about vaccines and virology, about public health and science communication, and about our communities of health. A lot of my information comes to me initially through my list of experts and professionals on twitter and through daily check-ins with Nature, The Lancet, Science-Based Medicine, JAMA, and digging down on press releases from the relevant pharmacology companies. It’s because of a year of tracking both publications and retractions that I know to take publications from the UK with an eye to potential retraction or debate, and to watch for the times when the CDC and FDA can’t agree, or when approvals in the US vary from those of other countries. I see when “my experts” disagree or take time to come to agreement on a question (like whether rapid testing is worthwhile, whether kids need priority vaccination, whether mandates make sense) and I actively follow those conversations as they evolve.

It’s time-consuming, usually a couple of hours a day at minimum, and it makes use of every information skill I’ve got. I generally don’t expect that everybody’s keeping up with the latest publications (and retractions) as much as I am, because it’s exhausting. I do it primarily because I know that there’s a not-small number of people who trust me to have relatively accurate and up-to-date information on what the heck is going on out there, and while I take that responsibility very seriously, it also strikes me as a symptom of a more complicated problem, which is that it’s hard for people to find a trusted source of good, accessible information and guidance. We’re all so freaking tired.

So anyway. What follows is a list of things I currently believe to be true about Covid-19, and some sources to back up why I believe those things.

Covid-19 is serious and has a higher IFR (infection to fatality ratio) than most strains of influenza.

Additionally, the death toll both from Covid itself and from the strain on healthcare systems (also known as “excess deaths”) is much higher than official estimates.

Vaccines are very effective, even against the Delta variant.

Getting vaccinated isn’t an impenetrable wall, but it means you’re much less likely to contract the illness in the first place (and if you haven’t gotten it, you can’t spread it). If you get a breakthrough infection, you’re infectious for fewer days than an unvaccinated person on average, and you’re much less likely to have complications up to and including death than an unvaccinated person.

  • Lederer, Katlyn, Kalpana Parvathaneni, Mark M. Painter, Emily Bettini, Divyansh Agarwal, Kendall A. Lundgreen, Madison Weirick, et al. “Germinal Center Responses to SARS-CoV-2 MRNA Vaccines in Healthy and Immunocompromised Individuals,” September 21, 2021. https://www.medrxiv.org/content/10.1101/2021.09.16.21263686v1.

  • Pilishvili, Tamara, Ryan Gierke, Katherine E. Fleming-Dutra, Jennifer L. Farrar, Nicholas M. Mohr, David A. Talan, Anusha Krishnadasan, et al. “Effectiveness of MRNA Covid-19 Vaccine among U.S. Health Care Personnel.” New England Journal of Medicine 0, no. 0 (September 22, 2021): null. https://doi.org/10.1056/NEJMoa2106599.

The following items in this group are pre-prints, which means they are not yet reviewed by other scientists in the field for accuracy or reliability. Because the science of Covid is moving extremely quickly (because pretty much all of our best minds are focused on some angle of the pandemic), pre-prints are a valuable source, but it’s important to follow up with information gathered from pre-prints to ensure the information wasn’t retracted after further consideration from the field. With that said:

  • Chia, Po Ying, Sean Wei Xiang Ong, Calvin J. Chiew, Li Wei Ang, Jean-Marc Chavatte, Tze-Minn Mak, Lin Cui, et al. “Virological and Serological Kinetics of SARS-CoV-2 Delta Variant Vaccine-Breakthrough Infections: A Multi-Center Cohort Study,” July 31, 2021. https://doi.org/10.1101/2021.07.28.21261295.

  • Ke, Ruian, Pamela P. Martinez, Rebecca L. Smith, Laura L. Gibson, Chad J. Achenbach, Sally McFall, Chao Qi, et al. “Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveal Limited Infectious Virus Shedding and Restricted Tissue Distribution,” September 2, 2021. https://doi.org/10.1101/2021.08.30.21262701.

  • Kissler, Stephen M., Joseph R. Fauver, Christina Mack, Caroline G. Tai, Mallery I. Breban, Anne E. Watkins, Radhika M. Samant, et al. “Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Individuals,” August 25, 2021. https://doi.org/10.1101/2021.02.16.21251535.

  • Shamier, Marc C., Alma Tostmann, Susanne Bogers, Janet de Wilde, Jeroen IJpelaar, Willemijn A. van der Kleij, Herbert de Jager, et al. “Virological Characteristics of SARS-CoV-2 Vaccine Breakthrough Infections in Health Care Workers,” August 21, 2021. https://doi.org/10.1101/2021.08.20.21262158.

Several of these pre-prints were covered in this piece:

Vaccines are safe for almost everyone, including kids and pregnant people.

We are still very dependent on keeping community spread down to reduce the frequency of exposures most people will encounter. Even vaccinated people are more likely to eventually be infected if they are exposed frequently in their daily lives. With that in mind:

Mitigation matters.

Because the first-round vaccination campaign hasn’t reached as many people as we’d like for a lot of reasons, many in countries with good vaccine access but lower-than-ideal vaccination rates are looking to third doses and boosters as one of these mitigation measures. For some people, a third dose is helpful, but for most of the population, the science says:

Boosters are sometimes, but not always, useful.

Now, one of the things that was very reassuring in the early days of the pandemic was that kids didn’t seem to be contracting the illness as often as adults, and that the younger you were, the less likely you were to have a serious case. This meant that even when schools were closed to all but remote learning, it was with the intention of protecting vulnerable adults, rather than out of fear for kids themselves. And while it’s still true to an extent that kids are lower risk than the elderly, we’re learning more all the time about the potential long-term effects of Covid, even when the initial infection was asymptomatic. And when it comes to the protection granted by age, things have changed dramatically with the Delta variant.

In the Delta era, kids get Covid at similar rates to other age cohorts. They are also experiencing adverse outcomes, including “long covid,” permanent disability, and death.

Further, because kids under 12 are the only cohort that remains entirely unvaccinated, they’re currently at the lead of several major regional case surges in the past six weeks, and the capacity of the healthcare system to handle both the Covid cases and all the other pediatric emergencies is under extreme strain. Spread among kids, and how to slow it while they wait for vaccines, is at the front of mind for most of my sources. But because Delta and the pediatric surges are relatively new (most case counts only started to climb in August), the majority of our knowledge is limited to case numbers and epidemiological projections.

Because of these statistics compared to the current relative safety data on vaccines, I believe kids of all ages should be vaccinated as soon as appropriate dosages are established and approved.

Mandates and “passporting” are legal in the US and Canada.

With legal challenges largely defeated, the tide of mandates and passporting seems to be growing across the US, UK, and Canada, and the good news is:

Mandates and passporting are working to improve vaccination rates and protect our communities.

All that said, concerted efforts have been and continue to be underway to undermine all this evidence, and we need to be on the alert for those who are willfully and deliberately misleading people in ways that are leading to thousands of deaths. If someone is telling you a mitigation strategy does more harm than good, they’re usually either lying or sharing something they believe, but that is untrue. Mitigation matters. Keep it up. Because:

Disinformation is causing harm.

Don’t die, I say

Letters #159

How can
you not fear humanity, want to lick the creek
bottom dry, to suck the deadly water up into
your own lungs, like venom? Reader, I want to
say: Don’t die. Even when silvery fish after fish
comes back belly up, and the country plummets
into a crepitating crater of hatred, isn’t there still
something singing? The truth is: I don’t know.
But sometimes, I swear I hear it

-The Leash | Ada Limon

Because we are, maybe, hopefully, moving in the next half-a-year, I’ve been doing an inventory of all our stuff, sorting through the pack-store-sell-donate piles and shifting things around. Today’s project was the backlog of R’s clothes that have been sitting in storage waiting to be donated since she was wearing 18-month-old sizes; she’s into 4T now. There are a lot of clothes, haphazardly stuffed into boxes and bags in her closet. None of our usual options have been taking donations, and, in large part because of the pandemic, I don’t have the kind of network of moms in our current corner of the city that I had where we lived before. Our connections to this neighborhood are fragile, silvery filaments of near-nothingness. I know almost no one by name, have no phone numbers or email addresses for my neighbours. In our old part of town, I had all of those things and a community centre besides. I always knew where the outgrown clothes were needed. The fact that I currently don’t is a symptom of something so much bigger and overwhelming that I struggle even to name it.

I think, though, that a lot of what I’ve been experiencing in the past two years is something very like a crisis of faith. I’ve built myself pretty solidly around a foundation of caring about people, of people caring about each other, and while things since 2016 have made that foundation pretty shaky, the pandemic has definitely crumbled it to something nearly impossible to stand on with any sense that I’m not going to fall from it. As with most crises of faith, this one came because the thing I believed in—that people are mostly doing their best—was failing me, and because I’m disconnected from my community it’s hard to find exceptions to those failures. It’s been a brutal couple of years, and while my work with VaxHunters definitely offered a moment of respite, I’ve been so exhausted and so overloaded with other people’s anger and fear that it’s been really, really difficult to translate that experience into the world as a whole.

Still, however loud and relentless the non-carers are, they’re a minority: in Canada, as a specific measurable example, fewer than 20% appear to be actively refusing vaccination, and while it’s hard to get an accurate count in the US, it’s still significantly less than “most.” Still too many, insofar as we’re trying to get a pandemic under control, but mostly, people want to be doing the right thing. They’re taking care of themselves and their communities. Politically, the anti-carers are a minority, too, even in the US, and we have several rounds of election data to back that up. Most of us want to be doing better for each other, even when it’s not working, even when it feels like pushing back against a wave with our hands. Even when it’s nearly impossible to see the hands that surround ours.

I think, to some extent, the only way forward is to forgive that failure and do the next thing. To believe, willfully and with force, that the faith is worth it. And I do. In the face of fear and grief and loss, I still believe in you. Bird by bird, my friends, and onward.

stepping gently, looking two times north and south

Letters #158 (in which I implore you to immediately take the Delta variant seriously)

We're not going to be able
to live in this world
if we're not willing to do what he's doing
with one another.

The road will only be wide.
The rain will never stop falling.

-Naomi Shihab Nye, Shoulders

R is three-and-three-quarters this month, a fact she carries around like a badge of honor, and one that in our lives has signified a very thorough entrenchment in The Why Phase. Over the last six weeks or so she's gone from accepting our first answers to digging deep into the details of her questions until she gets to a point where we can't find answers. When we suggest she should do something, her response is an innocent (but nevertheless instinctively frustrating) "why should I?" The emphasis changes according to the situation: "why should I" means something clearly different from "why should I" or "why should I." She wants so deeply to understand everything in her world, and that’s starting to include a real curiosity about other people. She wants to talk to neighbors, and play with other kids at the park, and it’s hard to explain that we could do those things earlier in the summer, but things are different and we can’t anymore. 

I know you and most people in my life are sick of the way I can't get my teeth out of this subject, but if you haven't already noticed that things are getting bad again, please check in. I'm not exaggerating when I say I'm convinced that, even though death rates will likely be relatively low, in terms of infections and long-term disabling outcomes, I really believe this fall will be the worst part of the pandemic so far in North America. In terms of disease, it's going to be hardest on the unvaccinated, which includes all the kids under 12 on the planet, along with the refusers and the hesitant and the unable among adults. In terms of social consequences, the burden is going to continue to be carried overwhelmingly by children and their parents, especially their mothers, and by marginalized people.

If you're not yet vaccinated and can be, I trust that you waited for a reason that mattered to you, but now is the time. The vaccines are working, and they're protecting both the vaccinated, by drastically reducing the risk of infection, severe disease, and death, and those who aren't, by reducing the number of potential exposure points. The headlines have been extremely discouraging, but the actual numbers in terms of whether and to what extent vaccinated people can transmit Covid, even with Delta, are miraculously good. They're not perfect, but they're very, very good. 

If you are vaccinated, or if you can't be, adding additional layers of protection like masks, only gathering outdoors, and keeping safe distancing help further protect you from both illness and acting as a vector by reducing your number of exposures. The fewer virus particles we can all encounter, the better any given measure works. We can keep our vulnerable community members safer by combining protective measures. And whether those are people who are willfully unvaccinated by choice who frustrate you, or people who want to be vaccinated but can't be, or who are vaccinated but whose bodies don't retain immunity, it doesn't really matter. Protecting ourselves and each other is the only way through. 

I'm including below a few very readable resources from recent coverage. These are not scientific papers (if you want those, let me know), but they're good summaries from sources I trust. If you've been on the fence, please take a minute with them, and if you're still not convinced, well, let me know why. I can't promise I won't be frustrated, but I'll try to hear you out.

And finally:

today, I'll wake up better

Letters #157

I’m not awake enough to understand
but will be, soon, my son, and then we’ll go
to blaze the day, to stomp each puddle left
by the rain you never notice as you pull

me into the world, all leap and bowl, all grab
and fall. Today I’ll wake up better, call
the distance order, order it to be
a smaller thing. I’ll stand to make it so.

-Dan Rosenberg, Order

Well.

Today, I had to pull up my pumpkins, their vines having seemingly overnight established a nasty case of powder mildew that I didn’t want to spread to the rest of the garden. It happened last year, too, but I wasn’t quick enough at pulling it up, trying instead a dozen food-safe methods for battling the stuff only to have it spread to the grass and other plants. This year, I just pulled it. It’s kind of disappointing, honestly, because the vines were lush and abundant and filled in a large patch of our garden that doesn’t tend to thrive, and the birds and squirrels liked to hunt for bugs and seeds under there in ways I found entrancing.

In a similar vein, the neighbourhood coyote I mentioned briefly last time has become a local pariah, with a couple of small dog “attacks” under its belt. This is extremely frustrating for me, having actually encountered the animal, because it’s extremely clear that the reason it’s behaving this way is a combination of poor treatment of its habitat and people feeding it so it’s been needlessly desensitized. Now that they’re denning, their lack of fear combined with territory protection is making them “aggressive” and people want them gone, yesterday if possible. It makes me really sad.

Shortly after my last letter, I grabbed a couple of photos of the overgrown patch where the coyote has been living, including its small and inobtrusive entry point in the construction fencing:

The simple fact of the matter is that if this construction site were being cared for appropriately, they’d have likely denned safely in the ravine, where escape from people is simple. Instead, they’re forced into near-daily encounters. Hardly the animals’ fault, and yet now that they’ve been pushed into these interactions, it won’t be the people who pay the price for it.

It’s not the pumpkin’s fault it got a fungus, either. More likely than not the fault lies with me, and something I should’ve done last fall or this spring to prevent a recurrence. But now that it’s happened, it’s either pesticides that would limit the garden’s usefulness to both us and other creatures, or taking the plant away. So the plant goes, and the birds will have to go seed-hunting in the berry brambles and rosebush for a while.

Today an old friend invited R and I to a playdate with her son, and I could only respond with “I’ll have to think about it; I’m still pretty nervous.” All the caregivers involved are fully vaccinated, there are no schools or daycare settings involved in either group, both kids are comfortable with masks, and we’d be outside. All in all, it’s as safe as we can be around other Toronto kids until the kids themselves can also be vaccinated, a moment that remains hovering on the horizon but never seems to get any closer. At the same time, though, Delta continues to be a growing problem, and frankly I am in no hurry to get back to normal for normal’s sake if the calculus doesn’t work out. The thing here is: I don’t know if it works out. I do not know where there’s a pumpkin to pull in this metaphor; I’m unclear which bit needs to give to let the other parts thrive. Does the situation need to change, or do I? It’s a question I’ve been struggling with since this all started, and although I’ve so far consistently come down on the side of the situation, eventually there’s going to be a tipping point. I just don’t know where that is, yet, and I hope I am able to see it coming in time to figure out how to navigate it in a way that makes sense for all of us.

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