(🧵It's the Сονіd, ѕtυріd!): Viewing the US election through the lens of the ongoing ЅАRЅ-Соν-2 раndеmіc.

(My hot take on what happened, and where things are headed. Prelude to the final 🧵in the "How does it end" series)

(1/) The post-mortem season for the elections is in full swing, and commentators on the left & right have lots of theories about why the Dems lost.

US elections are part of a global trend- incumbent parties in developing countries have lost vote share in every election this year(2/)

(🧵, CAN WE TALK ABOUT IT?):Over the last 5yrs, we as a society have developed a set of norms about 𝐂𝑂𝑉𝐈𝐃. As someone who's been actively publishing on the subject, I notice it very strongly. People will ask "why are you still masking", then wince when they hear my reply(1/) I find it almost amusing, because our friends & famly know I work on the subject, & they're usually the ones that bring it up first. But my reply is obviously not what they want to hear, so I often get the "that was too much" look from my wife & kids in these situations (2/)

(🧵NO ONE COULD HAVE PREDICTED THIS): To answer the question "What does the future hold for 𝑆𝐀𝑅𝑆-𝐂𝑂𝑉-𝟐?" it's worth examining how predictable its evolutionary trajectory has been so far. Evolution is stochastic, but stochastic processes can still yield predictions. (1/) Paradoxically, while evolution is highly unpredictable at a molecular level, predicting its consequences and anticipating its risks is actually quite easy. We'll dive a lot deeper into this idea in a later TT, as it's a crucial one for understanding our current situation. (2/)

(🧵2/5, HISTORY): What does history teach us about pandemics?

This is a topic that's been covered by others, but much of what's been said is worth taking a closer look at, in context.

Let's look at some historical pandemics/epidemics & see what we can learn. (1/) It's worth starting by defining what a pandemic is- and isn't. To quote Michael Osterholm (in '09): “(A) pandemic is basically a…novel agent emerging with worldwide transmission.”

It's an epidemiological, not a social, construct. Pandemics don't go away if you ignore them. (2/)

(🧵1/5, EMERGENCE): What happens to virulence after a new pathogen emerges? Popular thinking on the subject is that pathogens evolve become less virulent over time when they co-exist with their host species, based on the logic that virulent pathogens don't spread effectively.(1/) This perception is occasionally echoed by experts as well, for example in this Science article: “𝑆𝐀𝑅𝑆-𝐂𝑂𝑉-𝟐 is going to become a common cold. At least that’s what we want.” (If wishes were horses, then zoonotic spillover would be nothing to worry about, I guess?) (2/)

(🧵 0/5, Foreword):

It's been ~5yrs since 𝑆𝐀𝑅𝑆-𝐂𝑂𝑉-𝟐, the virus that causes 𝐂𝑂𝑉𝐈𝐃, made its fateful jump into humans. Now seems as good a time as any to ask "is it over yet?" (For the 10th time, but who's counting?)

Let's talk about how this ends, shall we? (1/) Every few months over the past 5 yrs, we've been reminded that the pandemic is over now, or perhaps it ended a long time ago, no one really knows.

The important thing is that it'll never go away, so we have to learn to live with it.

But not to worry, it's all very mild. (2/)

Been doing some thinking about how the pandemic will end (@TRyanGregory & @madistod have been great sounding boards).

In particular, focusing on two questions relevant for sc2:

1. What does biology teach us about emergent pathogens?
2. What can past pandemics teach us?

(1/) TL; DR is we’re all gonna die.

Just kidding. (Actually true if you wait long enough, but that thought is not an original one).

Some interesting titbits, details to follow): (2/)

This is exciting, right?

The CDC found zero cases of onward transmission of monkeypox on flights.

So, either monkeypox doesn’t transmit on flights, or the CDC’s approach to contact tracing is broken. Which is it? (1/)

https://twitter.com/ashishkjha/status/1832061219853025358

In a recent paper, my colleagues and I assessed the effectiveness of contact tracing during the early stages of the Covid pandemic. We found that contact tracing identified 1-2% of all transmission events. (2/)

bmcpublichealth.biomedcentral.com/articles/10.11…

@KonLontos @GidMK Talk of a “plateau” of risk comes from a fundamental misunderstanding about the underlying math.

The statcan data is consistent with a fixed probability of LC per infection. Such a fixed probability will give you a curved line asymptotically approaching a plateau (1/) @KonLontos @GidMK Unfortunately, that “plateau” is not useful, because such a risk function plateaus at 100%.

@gckirchoff and I explain the math in this blog post (with an interactive tool that you can play with) (2/): thedataquill.com/posts/understa…

This has been a concern of mine for a while.

We now know that some fraction of LC patients (and sc2 infections generally) feature viral persistence. Some fraction of LC also features autoantibodies that drive symptoms.

We also know that most people will get sc2 1-2x/yr (1/)

https://twitter.com/mileswgriffis/status/1803529332578771422

An increasing fraction of the population will likely be harboring sc2 virus directly or autoantibodies. We know that viremia (virus in the bloodstream) for sc2 can be a huge issue. (2/)

Thread 5/5: You can't learn to live with a potential carcinogen by pretending the risk doesn't exist. In a recent 🧵 I showed that a mechanistic basis exists to suspect that Sc2 is a carcinogen & it'll be hard to prove this with epidemiological studies(1/)

https://x.com/arijitchakrav/status/1799685306414993755

Okay, so what do we do with that info, given that we can't run our own genotoxicity assays at home. Just ignore it? Can't live our lives in fear, right?

In this 🧵, let's discuss the practical implications of learning to live with a ubiquitous potential airborne carcinogen.(2/)

Thread #4 of 5: Suppose the 𝐂0𝕍𝕚𝖉 virus is carcinogenic. Why not wait for "real world" (epi) data to "prove" that the before we do anything? In this 🧵, let's discuss why such "calm-mongering" is a reckless choice & can lead to devastating consequences for public health. (1/) A recurrent theme during the ongoing pandemic has been the panic about public panic. @Heavyredaction & I tackled this issue last year, in an article for The Nation, making the point that Public Health spends a lot of time providing reassurances. (2/): thenation.com/article/societ…

Thread #3 of 5:

Is Sc2, the 𝐂0𝕍𝕚𝖉 virus, carcinogenic?

(If you've been scrolling through my threads on cancer the past couple of days, waiting for the other shoe to drop, here it is.) (1/) We started this conversation with what causes cancer- the TL; DR of that 🧵is - chromosomal instability (CIN) is a driving force in carcinogenesis. Events that put CIN into motion kick off a process of unbridled somatic evolution- tumor progression. (2/)

https://x.com/arijitchakrav/status/1799685306414993755

How do viruses cause cancer? (Thread #2 of a 5 part series).

There's been a fair bit of twitter-chatter about this topic lately, so let's talk about it. Understanding the process of viral carcinogenesis is key to managing the risk of viral infections. (1/) Disclosure: I'm not a viral carcinogenesis expert. I've published on cancer as part of my day job for 25+ yrs (& on The Virus That Cannot Be Named as a 'night job' for (ugh) 4+ yrs now. This experience provides me with a unique perspective on the topic. (2/)

Bit of a change of topic, but let's talk about cancer.

What causes cancer? We learned in high school that it's mutations in oncogenes- "cancer is not one disease, it's many different diseases, each driven by a different oncogenic mutation." (1/) It's an attractive paradigm, because it makes it all very simple. All you have to do is find the driver mutation for any given cancer & target it to make the cancer disappear.

Someday, the vision goes, every cancer will have a personalized cure. (2/)

@hallinen_diane @pan_accindex I think if someone’s going to make a claim like “Covid doesn’t harm your immune system”, that’s a bold claim.

If they’re wrong, the consequences will be much more severe than the unnecessary concern that would result from a false alarm. (1/) @hallinen_diane @pan_accindex The claim itself is contrarian, as it flies in the face of the established science. It’s beyond meaningful debate at this point that *some* cases of Covid -even mild ones- lead to depletion of immune system components for months (2/)

1/ Powerful testimony by @zalaly today in the Senate Hearing on Long COVID.

He makes a lot of really great points- well worth a watch!

There is no treatment for Long COVID. Recovery rates are low. (🧵👇)

https://twitter.com/luckytran/status/1748037164913267006

2/ "The best way to prevent Long COVID is to prevent COVID in the first place". He makes a compelling case that this is something that requires government action.

In the meantime, we still have some agency as individuals, too. Check out:

typingmonkeys.substack.com/p/you-dont-nee…

@sunsweptforest Exactly. The big-name journals have a huge optimism bias.

In 2020&21, we predicted the virus would quickly evolve to evade immunity, that vaccines alone wouldn’t bring the pandemic to an end, that schools would seed disease, that appeals to altruism from PH would backfire. (1/) @sunsweptforest For the first 2-3 papers, we tried our luck at the big name journals. They would sit on the manuscript for a month and then send a form-letter rejection. Meanwhile, they were fast tracking review and publication of “good news” papers on the exact same topics (2/)

This point has been before, but if you want to know what the future holds for long Covid, look to high-contact-rate professions.

In the UK, the Guardian noted the shortage of workers specifically in this category (1/)

https://twitter.com/1goodtern/status/1723966195701801101

If you think of high-contact-rate professions in the US, ones where people are likely to come in contact with Covid, what are they? Childcare workers, bus drivers, nurses, pharmacists, prison guards, for example? (2/)

Grimly fascinating thread on the way in which the murderous Tory response to covid was shaped by advisors who believe in (surprise, surprise!) eugenics (1/)

https://twitter.com/0bj3ctivity/status/1720765016998113521

“Covid is just nature’s way of dealing with old people”. Can’t make this shit up. It explains why, as groups like ours were warning about the negative consequences of a negligent covid policy, governments such as UK were actively pursuing such policies (2/)

Taking Paxlovid in this study was associated with a minuscule reduction in risk of long Covid. Note that the article is written in a way to make that less obvious. (1/) cidrap.umn.edu/covid-19/resea… While the article is focused on inequity, the magnitude of the effect size (reduction in LC risk upon taking Paxlovid) is so small that you have to squint to see it (2/)