Rich and Strange Aeons

Possibly you haven't heard about covid much recently. Is it over? Nah. Going by wastewater models, as described in the various reports here, 1 in 96 Americans is estimated as infected with covid-19 as of April 8. Different groups estimated 1 in 139 for Canada (wastewater, March 31) and 1 in 143 for UK (surveillance testing, March 14, project discontinued then). And the forecast based on past years is to go up again, before another trough in June-July, and then going back up again a lot.

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As for bird flu, I dunno. This article is more comprehensive than most, talking about genetics, and why the probable cow-to-cow transmission going on may not mean it's airborne between mammals (yet). Infections don't seem that bad for cows, but have been devastating for sea mammals.

Survey of vaccine plans. Republicans are turning away not just from covid vaccines but flu and RSV vaccines.

https://www.usnews.com/news/health-news/articles/2023-09-27/just-23-of-u-s-adults-definitely-plan-to-get-new-covid-shot

I have a longer thing in my head but I am Busy so want to get the core ideas out so they stop bouncing around.

There are more complex approaches, but a simple one is that you're safe if there's no one infected in the room with you.

Say you dine out in a small place, exposure to 10 people. Also that you want to be safe as a medium-term habit, say over 100 meals, so 1000 people. "Safe" meaning 90% chance of no exposure to infected people, so you want community infectiousness to be 1 in 10,000 people. Nobody measures that, so assume an infected person is infectious for 10 days on average, so you want daily new infections to be 1 in 100,000, or 10 per million.

A few countries kept such levels before omicron or at least delta. Now, though, I infer case rates on the order of 1000 per million per day. Or maybe 10,000.

Some dining areas like cafeterias or dim sum palaces can seat 200 people at at time; poor ventilation could mean that by dinner time 1000 people had been breathing the air before you; eating out for life could mean 10,000 meals in your future.

Bon appetit!

I was amused to realize that technically, I've been one of the people with respiratory symptoms but blowing it off as allergies without a test.

But, I feel justified. None of the episodes lasted more than a few hours, let alone a day; they all happened during times of high reported pollen that I'm known to be allergic to (tree, then later grass, both in Vancouver this year); and I could basically turn them on and off by breathing unfiltered outdoor air or not. (Or, for grass, breathing unfiltered air while walking through big parks with lots of unmowed grass -- walking in the urban area seemed harmless. 20 minutes into the park walk I'd be sneezing or blotting my runny nose, then some time after masking again I wouldn't be.)

If I actually had symptoms lasting for a couple days I'd turn to a test, but that hasn't happened since Feb 2020. (Or if the symptoms involved more than sneeze/sniffle during allergy season, like the hacking coughs people report being surrounded by.)

https://travel.state.gov/content/travel/en/international-travel/before-you-go/covid-19_testing_required_US_Entry.html

"Effective December 6, the  Centers for Disease Control and Prevention (CDC) will require all air passengers two years of age and over entering the United States (including U.S. citizens and Legal Permanent Residents) to present a negative COVID-19 test result a negative taken no more than 1 day before departure"

Bad writing aside ("result a negative"?), what is the point of this requirement? It's not like the US has ever been a low-covid fortress that was usefully keeping out outside cases, like Japan/Taiwan/AU/NZ/Korea. It's not to protect the air passengers, or we would be requiring this of domestic flights. To try to keep out new strains that we don't already have circulating? ...I guess I don't have a simple refutation for that. Except that they allow antigen tests, not just PCR, and you can be early-stage infectious and still negative on antigen. Hell, from a covid-19 challenge trial, you can be infected and still negative on PCR. So it's certainly not bulletproof... whether reduction is worth the hassle is another matter.

Only 3 week delay, haha.

Still in the 'north' place of my last post. The first week felt very busy, like I couldn't believe it was only a week. The last two weeks have been faster. Not sure why, I did a bunch of walks but nothing that seems all that novel in my diary. Maybe just local shopping, checking Chinese markets, trying a Vietnamese restaurant, I dunno. Walking enough to find the big Japanese market... huh, didn't realize that was so far back.

Job hunt continues.

BC has gone back to Normal. Masking no longer required even on public transit, though "recommended". At least one big pharmacy, London Drugs, has also collapsed, with a "masks strongly recommended" sign. I am wondering if returning to the US would make sense for covid safety reasons.

Airbnb one week out was looking rather horrible, but I found a cheap 2-week place in Richmond BC, a suburb to the south of Vancouver, which holds the airport and a lot of Chinese people. Then looking for 30 day places after that has good options again, though I wonder if I want to keep staying here. OTOH I don't want to juggle disruption and job hunt that much, and have some medical concerns that might call for staying still -- or for going somewhere where I have more friends to help out if I need it.

Yeah, not a lot of exciting 'Vancouver' things recently, been more internal stuff. Reading the new Liaden book, reading Niven Warlock stories, 'being there' for a friend trying to escape Russia (they made it), reading a book on *early* Roman history, immune system stuff I've already posted about, couple new-to-me filk groups (thefaithfulsidekicks.com, viabellaband.com). And some computer stuff, that can be its own post.

Paper 1: https://twitter.com/ENirenberg/status/1496294352594915328 (summary, but also has direct link to PDF.)

bad news: antibodies decline a lot after 3 months.

good? news: that's not a covid vaccine thing, it's an immune system thing. Infection antibodies come from short-lived plasmablasts, that pump out a flood of antibodies, then die on schedule. Then you have long-lived plasma cells that trickle out antibodies, and memory B cells that will spawn more short-lived cells 4-6 days after a new infection, which is a lot better than the 2-3 weeks to get antibodies to a novel antigen.

good news: memory B cells increase over time -- 10x as many 9 months later, compared to right after the second covid dose.

bad news not in this paper: omicron can propagate in 2-3 days. By the time your B cells respond, you've infected people and *they've* infected more people. I've mentioned this before.

other news: unvacced, 28 +/- 15 days from first positive swab to first negative PCR test; 20 +- 9 days for vacc.


Paper 2: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009509
I've linked to this before, but it deserves a second pass. The key table is replicated here https://twitter.com/jmcrookston/status/1498877041105674240

The author says that all the viral diseases we develop lasting immunity against infection to, need to pass through our blood/lymph to transmit. I don't remember him spelling out exactly why, and I see two possibilities: one is that passing through the blood in itself exposes viruses to more of our immune system; the other is that passing through blood intrinsically takes longer than being able to transmit from respiratory cells alone. If I knew of any fast blood diseases or slow respiratory-only diseases, that would help differentiate the mechanisms. (Measles has a 12 day generation time; influenza may have 2 days, though other sources say 3.6. Wiki says typically 1-2 days.)

[Edit 2022-04-12: couple of money quotes:

"even natural respiratory infections with measles or variola (smallpox) viruses, famous for inducing life-long immunity to disease, do not prevent respiratory reinfection,"

"What polio-, variola, and measles virus share is dissemination from the initial infection site via lymph and (secondarily) blood as an obligate step in pathogenesis or transmission." ]

At any rate, since covid-19 has a generation time of just a few days, down to 2 for omicron, and does not need to pass through blood to transmit, we get the same result: lasting immunity to covid-19 infections is impossible. And people have done challenges with less alarming coronaviruses: "Human challenge studies established that seasonal CoV [coronavirus] reinfection with the identical strain can occur within a year after initial exposure, though typically with reduced shedding and milder symptoms."

Put another way, if the only thing between a virus and transmission is mucosal antibody levels, the virus will eventually transmit. As opposed to diseases like measles or polio where B and T cells must be crossed before transmission.


Seems to me that covid-19 is a "worst of both worlds" virus. It doesn't need the rest of our bodies to propagate, so it can transmit quickly and repeatedly, uncurbed by memory B cell responses. But thanks to the cell receptor it uses, it *can* randomly wander off to infect any organ of our bodies (vs. some cold virus that infected our noses but *stayed there*.) Influenza may also be such a virus (family)... and hey, influenza can be pretty deadly too.

On top of that, covid-19 has the killer app of suppressing initial innate immune response (something about blocking or inhibiting interferon production), which is why it has such a long pre-symptomatic infectious period, and probably part of why even partial NPIs (non-pharmaceutical intervention, masking and staying home and such) that failed to contain covid were able to crush flu and cold transmission.


And that's the virus that world leaders have decided we can just let rip, trusting entirely to our vaccines, despite not having a clear view of how much vaccines protect against long covid/blood clots/organ damage.

Dunno about you, but I'm still wearing respirators and not dining out.

Simplistically, you get 3 main benefits from infection or vaccination: antibodies which circulate in your body, and can respond right away to invaders; memory B cells, which make more antibodies ("secondary response") but take a few days to activate (I found various claims, from 4-7 days to 24-48 hours, so I can't be more precise); and killer T cells, which will purge infected cells, and I've got nothing about their response time except obviously *after* infection.

Ideally, the circulating antibodies stop re-infection cold. But antibody levels drop naturally, and we particularly don't seem to keep high levels in our mucus membranes, so there's a high chance that a respiratory disease is *not* stopped cold. What happens next?

In the case of measles, its generation time (from you being infected to you infecting someone else) is maybe 11-12 days. So even if an 'immune' person is breached, that infection will have to face a fully mobilized immune system, secondary response and killer T and all, so it probably gets clobbered before it can propagate. One breakthrough infection doesn't lead to more.

But in the case of covid, the generation time is just a few days, maybe only 2 days for Omicron. So it's possible that by the time your memory B cells get to work, not only have you infected more people, but those people have infected another wave of people in turn. Your T cells and any new antibodies will probably beat down the rest of the illness and keep it from killing you, but for infection-control purposes it's too late.

Is covid uniquely fast? Probably not: this says "The generation time is the doubling time, or the time required for the number of infections to double in size. Epidemiologic field studies of novel H1N1 flu infections in several states indicate that the generation time for acute respiratory illness (ARI) was 2.0-3.1 days and 2.4-3.1 days for influenza like illness (ILI)."

Flu, of course, is another disease that's been hard to contain via vaccination, for various reasons. But I would now guess that the main hope of a flu shot protecting you is from the initial wave of antibodies; if you were exposed to the exact same virus a year later, you would be counting on memory B cell protection, and likely get (mildly) sick.

With the onset of the omicron strain, various people who are just done and eager to just trust their vaccines and who make fun of "zero covid" people, gleefully announced that getting covid was inevitable, that omicron was going make its way to everyone no matter what we did.

Well, out of all the people I'm in frequent contact with, I'd say the vast majority have not yet gotten covid. The first wave of omicron has peaked and declined while claiming only two households.

And it's not like we're all super hermits. One is a doctor who is face to face with covid patients every day, and has two kids in physical school. Another goes into a lab to work, and has a kid in school and dance classes (edit: and goes to a gym that requires masked workouts). Others have flown (in December) from Philadelphia to Honolulu and back, from San Francisco to DC and back (for an SF convention of 2300 people, that avoided being a superspreader event), from Toronto to Vancouver (me!), and other travels. Another teaches in schools -- she did get Original covid back in Jan 2021, thanks to her husband's workplace, but has so far avoided a rematch.

The one common element is a commitment to avoiding unmasked mingling. Somehow, the people I become friends or even online acquaintances with, agree that dining out and partying in a respiratory pandemic should be avoided.

As for community control, please compare Denmark with Shimane, Japan.

Why is omicron spreading so fast and well? We don't know the whole story, and the Hong Kong report of "70x more bronchial virus" raises the possibility it spamming way more. But other studies are suggesting it's not intrinsically more infectious than Delta, it "just" bypasses old school antibodies. Most people don't seem to have internalized that, so... imagine March 2020, but without anyone changing behavior at all, and how fast covid have ripped through a population. Then crank that up because Delta is more infectious than the original strain, and *speed* it up since omicron's generation time is shorter. Voila!

Some places still have some mitigation measures, including masking. The parts of Canada I've been in have been pretty good about that. So why are their curves just as bad? Well, I also know people have been filling restaurants and bars, where people eat and *talk* unmasked. It's like wearing a condom whenever you have sex... except for orgies at the anonymous sex club. Wearing a mask 23 hours a day doesn't protect you if you if you take it off while infected people talk at you.

That makes sense. But where I get worried is, there are a few places -- too few IMO -- that have been going further. Portugal closed bars Dec 25. Quebec closed restaurants Dec 31. The Netherlands have closed restaurants from Dec 19. So we should be seeing a difference in such places, right? Well, maybe not Portugal, closing bars but not restaurants may not do much.

Graphs of Quebec, and Netherlands. Quebec does have a sharp spike down, but what looks like the beginning of a bounce up. Netherlands does have a late December decline -- though when Delta was maybe still dominant -- but is bouncing back up.

Granted, the holidays just happened, and lots of people were probably mingling all on their own. But still, the data isn't supporting my model well.

Ontario closed indoor dining too, but only Jan 5, so it's too soon for my data sources to see effect there.

On the flip side is this thread suggesting that covid can spread between apartments, like through dried drains, or poor ducts, or gaps in apartment envelopes, or just through the hallway. (Not to mention breathing hallway and elevator air.) So as someone who could have rented a laneway ADU but is in a downtown condo, that's terrifying. (I have taken some measures: blocking the bottom gap of the door, though I can't when I leave; having windows open (and checking that air is blowing in, not out), and running water on the lesser-used drains to make sure the trap stays full.)