Coronavirus

[AlanSubie4Life]

This is from the discussion conclusions in a recent paper from a well-regarded researcher in South Africa. The paper itself is fairly technical (link below):

“While higher titres of neutralizing antibodies are common in hospitalized individuals, however most SARS- CoV-2 infected people [with no or mild/moderate symptoms] develop moderate neutralization titres. >>>>Therefore, the data herein suggest that most individuals infected with previous SARS-CoV-2 lineages will have minimal or no detectable neutralization activity against 501Y.V2 [AKA B.1.351 AKA South African variant]. <<<<”

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

I guess that is somewhat promising. Maybe the vaccines will work well enough on these variants to keep them from spreading, with much higher antibody levels present after vaccination than there is after a minor infection.

I came across this long but useful Twitter thread tonight. It makes me feel a little sad. But at least the vaccines seem to work against B.1.1.7, which is the only one that is *confirmed* to be more contagious, at the moment. Other variants may be, but I haven’t seen the data.

Summary: With what we currently understand...Expect B.1.1.7 to dominate in areas of the US that have not been hit hard yet (assuming vaccination is too slow). And for the P.1 Brazil and B.1.351 South African strains expect that they may only flourish where there is a lot of population immunity (think the Dakotas).

https://twitter.com/k_g_andersen/status/1355689990487896065?s=21

What makes me sad is the speculation about other reasons these strains may be escaping B-cell mediated immunity. If there is some other reason, other than a key epitope change, that it is evading immunity, that is bad.

An excerpt:

We’ll know more in the coming weeks, as there is detailed study of these strains and how they interact with induced immunity.

What seems the most important is the effect of vaccination and (less important) prior infection on the risk of severe disease upon reinfection (and the effect of vaccination on transmissibility of the variant during any illness). Not a lot of detail on that yet.

 

[AlanSubie4Life]

This is from the discussion conclusions in a recent paper from a well-regarded researcher in South Africa. The paper itself is fairly technical (link below):

“While higher titres of neutralizing antibodies are common in hospitalized individuals, however most SARS- CoV-2 infected people [with no or mild/moderate symptoms] develop moderate neutralization titres. >>>>Therefore, the data herein suggest that most individuals infected with previous SARS-CoV-2 lineages will have minimal or no detectable neutralization activity against 501Y.V2 [AKA B.1.351 AKA South African variant]. <<<<”

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

Had a chance to read it through, rather than the summary:

This is where we pin our short-term hopes, in combination with an extremely strong antibody immune response to the vaccine:

“Despite neutralization escape, we show here that a significant proportion of non-neutralizing, RBD binding antibodies remain active against 501Y.V2. While antibody effector functions elicited by infection and vaccination have been implicated in protecting from reinfection and disease, the role of non-neutralizing antibodies and the efficacy of T cell responses to 501Y.V2 remain to be elucidated.”

Yes, that’s right, we have to pin our hopes on the freakin’ T cells, which have let the “we’ve reached herd immunity at 10% infected” crowd down so many times in the past. Sad!

This Great Barrington Declaration is not looking great, I have to say. What a bunch of hacks.

 

[EVNow]

Be careful there. I once suggested that the Tesla UI was better for younger people, and got chewed out by some 80+ers who said that it is a stereotype to suggest they would have trouble learning new UIs. Those "sharp as as a tack" late seniors don't like being pigeonholed.

That’s why I said some might be savvy. But when you design processes and UI you design for 80%, not the 10% who might be the exceptions.

 

[EVNow]

Meanwhile, at least two months ago, this guy over at chevybolt.org who isn't a doctor and says he was previously infected by COVID-19 asserted that he's invulnerable. Then he went onto cite 11 years (I've never heard his comparison before) to which someone else replies, that's wrong.
Corona virus and oil crash
Corona virus and oil crash

I wonder how many other people out there who've recovered from COVID-19 infection have similar thinking: they're invulnerable or will be so for 11+ years? Sigh...

My brother, a doc, got mild Covid but is super careful about PPE etc. He also got vaccine at the earliest opportunity. He still doesn’t think he is invulnerable.

OTOH, there are never infected people walking around without masks thinking thinking Covid is like a common cold. You can’t convince people who are in a cult.

 

[AlanSubie4Life]

This is old, but even after six months, still not aware of good additional research on benefits of eye protection (though Fauci strongly recommends it). But this letter to the editor provides background info:

Examining the need for eye protection for coronavirus disease 2019 (COVID-19) prevention in the community | Infection Control & Hospital Epidemiology | Cambridge Core

For true aerosols you’d want something like sealed goggles. But most of the time I’d guess that safety glasses (or even regular glasses) or a face shield (or both) would be sufficient.

 

[uujjj2]

This South African variant seems to be quite a concern. It is different enough from the original Wuhan strain to be considered almost a new virus, and immunity to the Wuhan virus only gives partial immunity to the South African virus.

 

[AlanSubie4Life]

It really differs very little from the original virus. Large portions of the spike protein are nearly unchanged. For sure it is concerning, however:

virus, and immunity to the Wuhan virus only gives partial immunity to the South African virus.

1) In tests so far, vaccines appear to be quite protective against severe disease with this variant.

2) Vaccines seem to consistently result in much stronger antibody response than natural infections. (Or at least, there is a lot less variability, and the general level is around or above the “high level” of a natural immune response.)

3) T-cell mediated response is based on a broader range of virus (and vaccine) protein epitopes (and thus triggered by a wider range of antibodies), and at least some of these vaccines seem that they may be effective at generating a strong T-cell response. So there may be reason to believe that that T-cell (CD8) response would remain intact, even if the neutralizing antibody response (which seems to target two specific regions/epitopes) does not. (Could explain lack of severe cases in vaccinated groups exposed to the variant?). Not sure how well this will extend to older groups, though, where immuno-senescence is a thing.

There’s no question the variants are bad news. But it may be possible that the vaccines can prevent the dying and hospitalizations, even if they do not completely prevent the spread (though they should help with that too - if it cuts R in half, that’s a big deal, and could allow us to crush the virus out of existence).

 

[uujjj2]

Mrs. Uujjj thinks this family of coronaviruses is here to stay, and we'll be getting annual booster shots for whichever new variants are popping up. No more pandemic/mass death events, but this virus won't be eradicated either.

 

[byeLT4]

Mrs. Uujjj thinks this family of coronaviruses is here to stay, and we'll be getting annual booster shots for whichever new variants are popping up. No more pandemic/mass death events, but this virus won't be eradicated either.

We missed our shot... By a long shot.....

 

[AlanSubie4Life]

Mrs. Uujjj thinks this family of coronaviruses is here to stay, and we'll be getting annual booster shots for whichever new variants are popping up. No more pandemic/mass death events, but this virus won't be eradicated either.

Entirely possible. The big question right now is whether the current vaccines will provide generally broad protection against all the variants - right now it is still kind of an unknown (they seem to all be extremely broadly effective against severe disease). For sure: A booster to update the new RBD and the NTD variants seems inevitable, probably by late summer (hopefully we’ll fix our production problems and be able to produce and administer 40 million a week).

Again; the RBD change is convergent evolution to obtain a particular functional improvement of the virus that gives it a reproductive advantage. There may be a limit to how much this region can change otherwise it won’t be better. For sure, there could be variants arising from immune escape to a new booster, but they may also not be very fit.

Also, these variants are only occurring because there is a lot of virus circulating. Once we suppress the virus this will nearly stop happening and then we can crush it. It’s not like influenza where it has a genome that can get shuffled (antigenic shift) and mutates all the time rapidly (antigenic drift). So suppressing the virus will allow a single vaccine to knock it out - potentially for good. The concern would be animal reservoirs, etc.

But we’d only be doing boosters routinely if this thing keeps circulating AND remains deadly. It may not - the variants that are escaping the current vaccines have not yet proven that they can create severe disease in a vaccinated population. We’ll see. If that’s not the case I could see there being little incentive to vaccinate against any new variants. Perhaps it will happen, if it is proven that immunity and severe disease risk increases with time since vaccination, and the virus is still circulating

Just a lot of unknowns still about how this will play out, exactly. I do tend to think that a single booster (possibly multi-valent or whatever they call it) is likely end of this year. After that, not so sure. Maybe one more round?

With the aid of a vaccine, it certainly could be eradicated, though animal populations would present difficulties. Just not sure whether the motivation will exist.

 

[heltok]

There’s no question the variants are bad news. But it may be possible that the vaccines can prevent the dying and hospitalizations, even if they do not completely prevent the spread (though they should help with that too - if it cuts R in half, that’s a big deal, and could allow us to crush the virus out of existence).

The problem I see with this analysis, which I have seen in many places, is that it assume that the current measurements against the spread will remain. Which seems pretty unfeasible. We have restriction fatigue already, it’s close to riots in many countries, economies are suffering and children are falling behind. And once we decide to loosen up and some superspreader-events are allowed, the superspreaders, who most have immunity to the old sars-cov-2, can start to get reinfected with the covid21-strains and start superspreading again.

If for example the Brazilian strain learns to spread as fast as the UK strain and goes around the world, it might reinfect superspreaders enough that we would see growth like we saw in spring 2020. Or if the UK-strain could learn to bypass antibodies like the brazilian strain has learned. And soon we will have 10-50% of people with antibodies to the 2020-strains from immunization it can start to learn how to bypass. Getting a mild case of covid might not kill you, but it’s Russian roulette that you will be the start of new strain that will kill millions.

So my fear is that we will have to keep current restrictions, masks until summer 2021. Which will have serious consequences for kids, poor people, tourist industry, live entertainment industry etc. Hopefully by then we will have enough of the new vaccines that target all current strain plus a few potential strains and that will be enough to elimate the virus completely.

 

[renim]

FWIW, it seems that die hard old bastards do exist. and are great plasma donors

59597603 (medrxiv.org)

page 11 High responders with strong and broad SARS-CoV-2 antibody responses are ideal plasma donors

it gets even better

there are Elite Responders veritable human factories of antibody vs SARS-CoV-2

 

[AlanSubie4Life]

Another way to look at it (have not personally confirmed but I think it is correct after 14 days from injection):

https://twitter.com/ashishkjha/status/1356079020878786561?s=21

 

[EVNow]

Another way to look at it (have not personally confirmed but I think it is correct after 14 days from injection):

View attachment 632833

https://twitter.com/ashishkjha/status/1356079020878786561?s=21

Still best to avoid getting infected. Even asymptomatic infection can scar the lungs worse than in a smoker. I’m going to be essentially in self quarantine before & after vaccine until the risk of infection reduces greatly. It’s already been 11 months - hopefully by this time next year the pandemic is under control.

Unfortunately Pfizer didn’t test whether the trial participants were getting asymptomatically infected.

 

[AlanSubie4Life]

Still best to avoid getting infected. Even asymptomatic infection can scar the lungs worse than in a smoker.

Certainly.

It is going to be interesting to see whether vaccination helps eliminate such damage. No hospitalizations in vaccinated folks suggests it might - but no guarantees. People have damaged lungs without hospitalization - but a primed immune system might ward off serious damage from an infection. Physically, the virus has to spread and multiply to cause damage. And asymptomatic and mild cases often mount ineffective antibody responses - which suggests that they might actually have significant viral spread in their body, causing such damage. This would presumably not happen with vaccination (but needs further study!). Anyway: let someone else find out before you do! We should know more about this aspect of vaccination in just a few months.

Summary: I am saying asymptomatic infection with vaccination (at the moment, regardless of variant) vs. asymptomatic infection without vaccination are probably fundamentally very different. But, TBD.

 

[madodel]

Certainly.

It is going to be interesting to see whether vaccination helps eliminate such damage. No hospitalizations in vaccinated folks suggests it might - but no guarantees. People have damaged lungs without hospitalization - but a primed immune system might ward off serious damage from an infection. Physically, the virus has to spread and multiply to cause damage. And asymptomatic and mild cases often mount ineffective antibody responses - which suggests that they might actually have significant viral spread in their body, causing such damage. This would presumably not happen with vaccination (but needs further study!). Anyway: let someone else find out before you do! We should know more about this aspect of vaccination in just a few months.

Summary: I am saying asymptomatic infection with vaccination (at the moment, regardless of variant) vs. asymptomatic infection without vaccination are probably fundamentally very different. But, TBD.

Lung damage, heart damage, and neurologic damage. If people stop taking any precautions because of being vaccinated we could see a big uptick in people with chronic organ damage.

 

[AlanSubie4Life]

Lung damage, heart damage, and neurologic damage. If people stop taking any precautions because of being vaccinated we could see a big uptick in people with chronic organ damage.

To be clear: No one should stop taking the easy precautions (masking, distancing, etc.) after being vaccinated! I actually think this is the main reason scientists are saying "we don't know" if the vaccine will prevent transmission...it seems quite likely that the vaccine will reduce transmission and in some cases prevent it...but if it leads to risk compensation (no masking, etc.) before cases go way way down, we will end up with bad consequences...and in the end we don't actually know how it behaves, either for transmission or for COVID complications, yet, and any result is unlikely to be a black and white answer, anyway. The last thing we need is another false dichotomy (think lockdown/no lockdown, 15 minutes, 6 feet, etc., etc.).

Again, there's ALSO reason to believe that these complications will occur at a much lower rate in vaccinated people (even if they are infected), but it's just not known yet. And no one should *assume* that the vaccine will eliminate such complications.

Still, I think scientists would be better served by just giving all the details and being open about reasons why they think the vaccine will help, rather than saying to people "we don't know." We do know some things! We just don't have hard evidence proving a particular result, at this point. But telling people it will likely reduce complications, reduce transmissibility, and nearly eliminate hospitalizations, is likely pretty well supported by known mechanisms of action of disease spread and morbidity, and by some analogous vaccines (and the hospitalization data is supported by the evidence - and indeed the ID experts are pointing this out now). It will provide incentive to vaccinate, and it makes logical sense. But it's possible to combine that message with one that says we don't know for sure, so we should apply the precautionary principle and wear masks for now, and try to prevent disease spread whenever possible even after vaccination. I'm not an infectious disease expert or anything, though.

It's just a tricky communications problem. Tell people only what we know for sure, and many people will want to wait to get the vaccine until there is an update (a completely wrong course of action). Tell people what you can reasonably conclude, but extrapolate too much and overstate effectiveness, and you'll have people taking risks that are not warranted (also bad). I just think being as open as possible about the data, and putting it in the context of what we know about other vaccines, and stating conclusions that might be reasonably drawn, but that we cannot be sure about (nuance!), is probably the best strategy. Nuance is tough though.

 

[madodel]

U.S. Cuts $231 Million Deal To Provide 15-Minute COVID-19 At-Home Tests

The Biden administration has made a $231.8 million deal with an Australian company to boost availability of the first at-home rapid test for the coronavirus, which causes COVID-19 that is available without a prescription. The test, made by Ellume, can send results to a smartphone within 15 minutes of receiving a sample.
​

Watched the CEO on CNBC just now. Currently $30 a test. They expect price to come down with increased production volume.

 

[EVNow]

To be clear: No one should stop taking the easy precautions (masking, distancing, etc.) after being vaccinated!

To me the question is - after vaccination should we end our self-isolation or not. For eg., should we start getting takeout food or get a haircut. Yes, with masks and distancing etc - though obviously distancing is not possible for getting a haircut or dental cleaning.

Unfortunately currently there is no way to understand the residual risk after vaccination. We can guess that it is lower than before vaccination - that doesn't help us make informed decisions.

U.S. Cuts $231 Million Deal To Provide 15-Minute COVID-19 At-Home Tests

The Biden administration has made a $231.8 million deal with an Australian company to boost availability of the first at-home rapid test for the coronavirus, which causes COVID-19 that is available without a prescription. The test, made by Ellume, can send results to a smartphone within 15 minutes of receiving a sample.
​

Watched the CEO on CNBC just now. Currently $30 a test. They expect price to come down with increased production volume.

This would really be very useful for us. Even though the caretaker we have has got vaccinated, she lives with people who are not.

ps : Ideally, employees would be asked to test this test daily and report to work only if they are clear. Can greatly reduce the spreading. The price has to come down for this to be practical.

 

[madodel]

This is from several days ago but I didn't find it mentioned yet. Apparently my wife is a trend setter. If you can't afford or find N95, Fauci and the Biden administration is suggesting people double mask.

Double Masking ‘Makes Common Sense,’ Fauci Says