This year we kill it: Corona Virus Thread Mark II

[Rogar Demonblud]

The South African variant is confirmed to exist in South Carolina and Maryland.

[sihnfahl]

And, in fun news, J&J released the efficacy of their one-shot COVID vaccination.

It's sitting at 72 percent for the current majority strain of COVID, but shrinks to 57 efficacy for the SA variant. That's about what the first dose of the Pfizer/BioN vaccine gives, but less than the first dose of Moderna.

There's a six-fold decrease in neutralizing titers for the Moderna vaccine towards the SA variant (so, yeah, definitely less effective), but still at a level that's believed to confer a relative immunity in a majority of individuals.
They're working on a booster shot that will improve the neutralizing titers. Means another shot, naturally, for those of us who've already received our second vaccination.

Local news - Our esteemed Governor has apparently decided the best method of distribution in a good part of our State is ... to give it to the pharmacies of our major grocery chain (Publix) ... and let them handle the logistics of vaccinating. Hasn't quite said his plan on getting the doses to Public pharmacies, though. Their website has crashed a few times, I believe, trying to keep up with the demand.

[warty goblin]

Speaking of fun with vaccine distribution, here's one.

My girlfriend is an elementary school teacher, which puts her right up on the list of essential workers to get vaccinated. For weeks, no word from the school board. Then about two weeks ago, they announce they have the vaccine!

...specifically they have 42 doses. For a district that employs thousands of people.

My girlfriend was so not amused she was actually amused.

[akma]

Local news - Our esteemed Governor has apparently decided the best method of distribution in a good part of our State is ... to give it to the pharmacies of our major grocery chain (Publix) ... and let them handle the logistics of vaccinating. Hasn't quite said his plan on getting the doses to Public pharmacies, though. Their website has crashed a few times, I believe, trying to keep up with the demand.

Sounds like the result of some backroom deal, and sounds like it would backfire.

On the Israeli front, which seems to be in stark contrast to the rest of the world, today the number of people who got the first vaccine passed 3 million. Anyone over 35+ can get the vaccine, and I know someone who got it while being younger a few weeks ago, since he told the nurses he lives with an elderly relative in bad health (which is true).

I'm not sure what percentage of the population will get vaccinated in the end, because there is some resistance to it. There was propaganda spread that the pharmacies use Israel as a testing ground for their vaccine and its side effects (possibly just a smear attempt against the prime minister), some people are anti-vaxxers, some populations are known for their lack of cooperation with the establishment... Anecdotical stories about people suffering from various things shortly after getting the vaccine seem to also have a lot of sway over some people.

Another issue is that there supposed to be a lockdown, but a ton of people simply ignore it. It is at least seem to be enforced on stores.

[sihnfahl]

I'm not sure what percentage of the population will get vaccinated in the end, because there is some resistance to it.

In the end, so long as the minimum percentage of the population is vaccinated, then it's just a matter of time and waiting. Eventually it'll come to a screeching halt, being unable to spread or infect enough people. Remember, Israel's r0 is already below one, and that means it's slowly fading out. The only thing that the unvaccinated will change is a r0 of, say, 0.6 versus a r0 of 0.2.

[Grey_Wolf_c]

In the end, so long as the minimum percentage of the population is vaccinated, then it's just a matter of time and waiting. Eventually it'll come to a screeching halt, being unable to spread or infect enough people. Remember, Israel's r0 is already below one, and that means it's slowly fading out. The only thing that the unvaccinated will change is a r0 of, say, 0.6 versus a r0 of 0.2.

Or, alternatively, until a mutation that gets around the vaccine arises, and the r0 goes back above 1. Which is made all the more likely the more people are not vaccinated, but in the presence of vaccinated people, because evolution really dislikes barriers.

(This cheery thought brought to you by the news that a new mutation seems to be arising in the UK)

GW

[sihnfahl]

Or, alternatively, until a mutation that gets around the vaccine arises, and the r0 goes back above 1. Which is made all the more likely the more people are not vaccinated, but in the presence of vaccinated people, because evolution really dislikes barriers.

Well, was referring specifically to Israel, which doesn't seem to have the issues with the new strains.

But, yes, in countries with low vaccination rate or slow vaccination programs, and with a higher r0, mutations will become likely.

In additional news, the Lancet reported the Sputnik V vaccine is about 92% effective after the second dose, per a peer-reviewed study published by Russia's Gamaleya National Research Centre for Epidemiology and Microbiology.

However, they only reported symptomatic cases, and didn't report asymptomatic cases or neutralizing titers.

[NichG]

From the analyses I've read, the mutations we're now seeing are more likely to have come from long-term persistent infections in immuno-compromised individuals than from population-level barriers to spread. The argument for that is that current level of population-level immunity isn't high enough to explain the level of selection pressure you'd need to see convergent evolution of the same mutations to the same loci in separate lineages, as is seen with the UK and SA variations. Basically, if you saw it just one place you could say that it's a lucky random mutation, but seeing it in multiple places suggests that its winning some much more competitive local race where the barriers its experiencing are far more severe before entering the global race where the barriers aren't yet that serious. So if it has hosts whose immune system is weakened, those hosts can put up a fight but also at the same time fail to totally wipe out the infection, thereby giving the local population much more rapid feedback and strong selection pressures to accelerate its evolution.

This does sort of make me think about ways to intentionally guide Covid's evolution, but they're all ethically fraught and also practically dangerous. In order to get Covid to globally take on some variant in place of other strains, you need that new variant to have a higher R in the population than the wild-type variant. Any kind of other change you want to make such as reduced lethality, you have to pay for by letting the transmissability go up. But increases in transmissability cause far more deaths than increases in lethality, so you'd really be playing with fire.

[sktarq]

This does sort of make me think about ways to intentionally guide Covid's evolution,....Any kind of other change you want to make such as reduced lethality, you have to pay for by letting the transmissability go up. But increases in transmissability cause far more deaths than increases in lethality, so you'd really be playing with fire.

Yup.

This can be done in the lab but also does show up in nature....one could easily describe this process as what we used for the first vaccine. Which was natural cowpox as a prophylactic for smallpox. People artificially boosted the prevalence of the desired infectious agent in order to block the feared one.

Basically most live virus vaccines are also closely linked to what you are describing as well so its a known technique. Attenuated polio is slightly transmissible even so vaccinating most of the population will actually cause more people to develop immunity than you actually vaccinated. But polio is also a good example of the dangers as well as the polio can mutate back to its dangerous form on occasion. We were (are? have not checked last years numbers) at the point where there reverse mutations from the vaccine are more common than the wild occurring polio cases now.

Now trying to do all this development in a non-laboratory situation seems....very high risk.

[farothel]

Or, alternatively, until a mutation that gets around the vaccine arises, and the r0 goes back above 1. Which is made all the more likely the more people are not vaccinated, but in the presence of vaccinated people, because evolution really dislikes barriers.

(This cheery thought brought to you by the news that a new mutation seems to be arising in the UK)

GW

That's why all vaccines already out there are now also tested against the new variants and new applications to health authorities have to include a variant analysis. It can also partially explain why the first ones have a lot higher efficacy rate then later ones, as they didn't have as many variants yet (the South African variant only starts to show up from November, the UK variant about that same time, at that time some vaccines had already filed for authorization).

[sihnfahl]

In the news, analysis shows that the AstraZeneca vaccine remains 76% effective in preventing symptomatic cases for up to 3 months after the first dose. It also appears that it may also help with preventing transmission in that timeframe, so supply-strapped nations may end up opting to defer the second dose, which confers a greater immunity, so as to get more people with the first dose.

[Rogar Demonblud]

And J&J is requesting the EUA from the FDA.

[sihnfahl]

And J&J is requesting the EUA from the FDA.

The meeting for that is in three weeks; the FDA is expediting the review process, yes, but ... still, three weeks.

And hopefully someone will get a distribution plan ready for the moment the EU is granted, just to get things out fast.

[Rogar Demonblud]

9% of the US has received the first dose of vaccine. 2% the second.

[farothel]

The meeting for that is in three weeks; the FDA is expediting the review process, yes, but ... still, three weeks.

And hopefully someone will get a distribution plan ready for the moment the EU is granted, just to get things out fast.

Normally it takes months. And they used 20 days for Pfizer's and 17 for Moderna's, so it's in the same ballpark.

Production has already started, although there seems to be some delays, but that's the case with all producers it seems. Normally vaccines aren't produced in these quantities on such short timelines, so it's normal there are some SNAFUs along the way.

[sihnfahl]

Normally vaccines aren't produced in these quantities on such short timelines, so it's normal there are some SNAFUs along the way.

These are abnormal times, yes.

Just a reminder that even with these abnormal times and expedited schedules, people still need patience.

Unfortunately, the number of significant mutations has increased the number of major strains of COVID to 4. The original strain most vaccines have been made for, the UK strain, the SA strain, and Brazil.

[NichG]

Fortunately at least from what I've read, the antibodies promoted from the mRNA vaccines seem to be fairly cross-reactive so far. Also sort of 'fortunately' in a deeply unfortunate way is that the emergent strains seem to really have two particular mutations that are effective - one that increases spread which is the one that shows up in the UK variant, and one that modifies the spike protein to escape natural immunity which is the one that shows up in the SA variant - and convergent evolution is driving for both mutations to show up on the same dominant strain. So we might only need two sequences rather than four in a few months...

Also I guess seeing the same mutation crop up in multiple independent lineages suggests that there aren't that many opportunities for immune escape available from where Covid is right now. I don't know if we'll see something running in circles in a red queen dynamic with the immune system, or the sort of convergent logarithmic returns dynamic (which you'd get if the spike proteins have a strong tie to viral functions), but here's hoping for the latter.

[sihnfahl]

Aaaand, to nobody's surprise, we're seeing pictures of large parties here in Florida. Maskless. For the Stupor Bowl.

Gods, this is going to be fun watching. Superspreader event.

[akma]

Aaaand, to nobody's surprise, we're seeing pictures of large parties here in Florida. Maskless. For the Stupor Bowl.

Gods, this is going to be fun watching. Superspreader event.

In Israel (and probably in the rest of the middle east) there are superspreader events that are much more ironic - funerals for people who died of covid, with hundreds or thousands of crowded participants.

[sihnfahl]

In Israel (and probably in the rest of the middle east) there are superspreader events that are much more ironic - funerals for people who died of covid, with hundreds or thousands of crowded participants.

That's happening in the US as well.

My main frustration is that it's such an avoidable situation.

Funerals are obligations. Take care to prevent spread, but still... funerals.

Sports are not obligations. Tailgate parties are not obligations.

[pendell]

That's happening in the US as well.

My main frustration is that it's such an avoidable situation.

Funerals are obligations. Take care to prevent spread, but still... funerals.

Sports are not obligations. Tailgate parties are not obligations.

As much as I hate the pandemic both for the deaths and for the largest economic contraction since 1946, I admit there is a part of me that appreciates we introverts are saving the world by staying at home and not doing anything .

Well, okay, I'm working sometimes as much as 12 hours a day via remote and zoom conference, and I don't appreciate that I don't have anywhere to go to get away from work. But even so, it's nice to not need an excuse to stay home in my rec hours and play video games.

Respectfully,

Brian P.

[Eldan]

Funerals are obligations. Take care to prevent spread, but still... funerals.

My great aunt died a few months ago. Six people max at the funeral service. We did keep that up. Only her three daughters and their husbands, none of the grandchildren or extended family.

[Rogar Demonblud]

I haven't been to a funeral in months. Save the limited seating space for the immediate family.

[farothel]

I have been, both my grandparents on my mother's side. But that was in September, when the restrictions were less strict around here. But yeah, seeing those pictures of hundreds or even thousands of people coming together, no matter the reason, always makes my skill crawl.

[Rogar Demonblud]

Heck, it made my skin crawl back in pre-COVID times.

[Keltest]

Heck, it made my skin crawl back in pre-COVID times.

Ditto. We didnt even have one for my father when he died.

[Rogar Demonblud]

And two tigers in the Ft Wayne zoo are COVID positive. Are we going to need to vaccinate every animal as well?

[Tvtyrant]

And two tigers in the Ft Wayne zoo are COVID positive. Are we going to need to vaccinate every animal as well?

It is possible: https://youtu.be/-M3L_Kykl6w

Imagine if covid just started mangling all mammal populations.

[farothel]

And two tigers in the Ft Wayne zoo are COVID positive. Are we going to need to vaccinate every animal as well?

There have been reports of cats getting infected, but as far as I know they can get it but they don't pass it on. Now minks are a different case. They seem to be able to pass it on, which is why at least in the Netherlands and Denmark they've been closing mink farms.

[Rogar Demonblud]

Unsurprisingly, gorillas get it too--the troop at the San Diego Zoo is in quarantine.