This year we kill it: Corona Virus Thread Mark II

[Strigon]

Update from The Washington Post . New data on the Delta variant shows that it seems likely that it is both more deadly than other variants and transmits more easily. It appears that , against delta, vaccination prevents serious illness but it doesn't prevent you from catching it or spreading it. Hence, the American CDC has issued guidance recommending mask-wearing indoors. This is being met by significant resistance.

We'll see. Other countries , as mentioned previously, have had Delta before the US has and they are trending downward. Understanding why this is will be critical to our ongoing struggle.

Respectfully,

Brian P.

"... Vaccinated individuals infected with delta may be able to transmit the virus as easily as those who are unvaccinated. Vaccinated people infected with delta have measurable viral loads similar to those who are unvaccinated and infected with the variant."

Note that this doesn't imply that being vaccinated doesn't provide protection against catching the disease, only that if you catch it while vaccinated, you can still spread it.
Everything I've read so far suggests that while Delta may be better at evading the vaccines, they still work against it more often than not.

[Samm]

Note that this doesn't imply that being vaccinated doesn't provide protection against catching the disease, only that if you catch it while vaccinated, you can still spread it.
Everything I've read so far suggests that while Delta may be better at evading the vaccines, they still work against it more often than not.

So according to this article in the New England Journal of Medicine, two doses of the Pfizer (BNT162b2) vaccine are about 88% effective for the delta variant and the AstraZeneca (ChAdOx1 nCoV-19) is 67% effective after two doses.

So just as you say, the vaccines are more effective against the alpha variant, but they still protect against the delta variant fairly well.

I think they also protect against severe illness very well, even if you do get the disease. From what I understand, the death rate in the UK is quite low compared to the number of cases because of the high rates of vaccination. Last year there were far more deaths with similar case numbers.

[comicshorse]

So according to this article in the New England Journal of Medicine, two doses of the Pfizer (BNT162b2) vaccine are about 88% effective for the delta variant and the AstraZeneca (ChAdOx1 nCoV-19) is 67% effective after two doses.

So just as you say, the vaccines are more effective against the alpha variant, but they still protect against the delta variant fairly well.

I think they also protect against severe illness very well, even if you do get the disease. From what I understand, the death rate in the UK is quite low compared to the number of cases because of the high rates of vaccination. Last year there were far more deaths with similar case numbers.

Today we had 26,144 new cases and 71 deaths
When we had that kind of number of new cases last year (December 19th 26,944) we had 241 deaths

[NichG]

Can you give the comparison with deaths two weeks after a day with the same case rates, since deaths are a lagging indicator?

[comicshorse]

Using the dates I first gave as the second point:

July 17th 2021 54,183 cases. The high water mark of the latest (and hopefully last) wave. And 41 deaths (bit of a lucky day I'd guess)

December 5th 2020 15,498 cases and 398 deaths

[Samm]

There are some nice plots on the BBC website:
https://www.bbc.com/news/uk-51768274

It might be easier to compare when you're looking at plots.

[NichG]

Using the dates I first gave as the second point:

July 17th 2021 54,183 cases. The high water mark of the latest (and hopefully last) wave. And 41 deaths (bit of a lucky day I'd guess)

December 5th 2020 15,498 cases and 398 deaths

Thanks!

So it's even stronger of an effect taking that into account: 71 deaths / 54183 cases -> 0.13% CFR vs 241 deaths / 15498 cases -> 1.5% CFR

Probably should be using 7 day averages or something of course because of lucky and unlucky days.

[Sean Mirrsen]

Probably should be using 7 day averages or something of course because of lucky and unlucky days.

I think more importantly, it should be noted that it's not like a certain percentage of newly infected just immediately drop dead.
The deaths on a given day are not in any way correlatable to the new cases on the same day, as the disease often takes upwards of a week, sometimes multiple weeks, to end in death.

[farothel]

I think more importantly, it should be noted that it's not like a certain percentage of newly infected just immediately drop dead.
The deaths on a given day are not in any way correlatable to the new cases on the same day, as the disease often takes upwards of a week, sometimes multiple weeks, to end in death.

Indeed. You see it clearly in the numbers. First the infections go up, a week or so later the hospital admissions and only then the death numbers. The same of course if numbers go down.

And it's also correct to use 7 day averages, as for instance in the week-end or official holidays there are less tests so less people get officially infected. The same with hospital admissions, you often see a spike on Monday. 7 day averages level out these ups and downs.

[NichG]

I think more importantly, it should be noted that it's not like a certain percentage of newly infected just immediately drop dead.
The deaths on a given day are not in any way correlatable to the new cases on the same day, as the disease often takes upwards of a week, sometimes multiple weeks, to end in death.

That's why I asked for a two week lag comparison. Deaths today divided by cases 14 days prior now vs in December.

The running average thing is to correct for the fact that they don't die exactly 14 days later either, and e.g. if you picked a Sunday for the cases you'd get a wild swing since testing is rare on weekends but deaths happen when they happen.

[Squire Doodad]

Hearing about a Delta Plus variant showing up in SK and the Bay area, desperately hoping this is some sort of convoluted April Fool's joke or misreading of data.
It seems at least the COVAXIN is good against it, but I really hope all the other vaccines are at least as effective as Delta at protecting against it.

It feels like we took too long, and now it's an obligatory phase 2 of pandemic hell.

If anyone has good news about this, please post it...

For the US there's a COVID vaccination tracker that appears to be showing the decline finally stopping and now a slow uptick in vaccination rates - the forecast just went from May 2022 for 70% to March 2022 over the last week, which is very nice.

[pendell]

There had better be. Florida is experiencing a surge in covid hospitalizations, with deaths to follow. ISTR one other state is as well.

Meanwhile, walking around a supermarket here in NC, there are only two customers wearing masks.

Looks to me as if Delta is going to sweep through the unvaccinated population like a flood. Hopefully, it will be fast and sharp but there could still be a lot of deaths and suffering before 'fast and sharp' is done.

And yes, it just might be the impetus some people need to go out and actually get the shot, rather than waiting longer.

Respectfully,

Brian P.

[farothel]

From what I've seen the different vaccines out there (I know only the ones that are approved in US and EU) do protect against the delta variant, or at least bringing the seriousness down to that of the common cold. Not fun to have, but you won't die from it. So yes, I would suggest people get vaccinated.

[warty goblin]

Looks to me as if Delta is going to sweep through the unvaccinated population like a flood. Hopefully, it will be fast and sharp but there could still be a lot of deaths and suffering before 'fast and sharp' is done.

And yes, it just might be the impetus some people need to go out and actually get the shot, rather than waiting longer.

Respectfully,

Brian P.

We'd better hope it isn't fast and sharp. Fast and sharp is what overwhelms hospitals. It also means any surge in vaccination is basically useless, since people are more likely to be infected before they have time to develop an effective immune response.

Unfortunately it probably will be fast, as Delta is infectious as hell, and the will for another round of restrictions is pretty unlikely to manifest at this point.

The thing that really, really worries me is if the next variant that gains primacy is even more able to bypass the vaccines and/or infection based immune response than Delta. Because we sure are creating the perfect petri dish to breed a monster like that, and if it does emerge, it will take over.

I have a feeling we could be in for another really bad time of it.

[NichG]

We'd better hope it isn't fast and sharp. Fast and sharp is what overwhelms hospitals. It also means any surge in vaccination is basically useless, since people are more likely to be infected before they have time to develop an effective immune response.

Unfortunately it probably will be fast, as Delta is infectious as hell, and the will for another round of restrictions is pretty unlikely to manifest at this point.

The thing that really, really worries me is if the next variant that gains primacy is even more able to bypass the vaccines and/or infection based immune response than Delta. Because we sure are creating the perfect petri dish to breed a monster like that, and if it does emerge, it will take over.

Well, immune escape is to be expected. The question is, if we use delta's sequence to make boosters, are they as effective as the original vaccine was for the original strain? As long as that remains true we could in principle keep up with boosters wherever new variants appear.

[Strigon]

Well, immune escape is to be expected. The question is, if we use delta's sequence to make boosters, are they as effective as the original vaccine was for the original strain? As long as that remains true we could in principle keep up with boosters wherever new variants appear.

Shoot, they don't even have to be as effective against the original strain. Delta being more infectious, if we have to trade some efficacy against the less infectious strain to gain some against the more infectious strain, we should do it.
With regards to Delta+, it has one more mutation, and it's a mutation that was previously around in other variants. It's probably worse than Delta, but I doubt the difference is half as large as the difference between the original virus and Delta. I'd also be very surprised if it beat the vaccines. Lowered their effectiveness by a percentage point or two? Maybe, and that would suck. But I wouldn't consider this to be much more than a footnote as of yet.

[NichG]

Shoot, they don't even have to be as effective against the original strain. Delta being more infectious, if we have to trade some efficacy against the less infectious strain to gain some against the more infectious strain, we should do it.
With regards to Delta+, it has one more mutation, and it's a mutation that was previously around in other variants. It's probably worse than Delta, but I doubt the difference is half as large as the difference between the original virus and Delta. I'd also be very surprised if it beat the vaccines. Lowered their effectiveness by a percentage point or two? Maybe, and that would suck. But I wouldn't consider this to be much more than a footnote as of yet.

Sorry, ambiguous phrasing.

If delta vaccine vs Delta >= original vaccine vs original strain, we're relatively okay

If delta vaccine vs Delta < original vs original strain, we're in trouble because it's finding mutations that generalize.

Cyclical rock scissors paper is ok, but if it figures out how to play dynamite...

[farothel]

Shoot, they don't even have to be as effective against the original strain. Delta being more infectious, if we have to trade some efficacy against the less infectious strain to gain some against the more infectious strain, we should do it.
With regards to Delta+, it has one more mutation, and it's a mutation that was previously around in other variants. It's probably worse than Delta, but I doubt the difference is half as large as the difference between the original virus and Delta. I'd also be very surprised if it beat the vaccines. Lowered their effectiveness by a percentage point or two? Maybe, and that would suck. But I wouldn't consider this to be much more than a footnote as of yet.

Do you have a website where you can see the difference between delta and delta AY.1 (the delta+ if I'm not mistaken)?

[comicshorse]

Is there a established figure (or even good guess) for the percentage of a country's population that need to be vaccinated to provide 'herd immunity' ?

In the UK first vaccinations seem to be slowing down alarmingly and we've vaccinated 89% of the population so far.

[NichG]

Is there a established figure (or even good guess) for the percentage of a country's population that need to be vaccinated to provide 'herd immunity' ?

In the UK first vaccinations seem to be slowing down alarmingly and we've vaccinated 89% of the population so far.

It depends on R0 and vaccine effectiveness. I've heard estimates of R0 up to ~8 for delta. We need R0 * (1-avg resistance) < 1 for herd immunity

For a vaccine effectiveness at V, that means R0 * ( (1-V) F + 1-F) = 1 is the threshold, or:

F = (1/V) (1-(1/R0))

So for R0=8 and effectiveness of V=0.84, the fraction needed would be 1.04 - that is, herd immunity would not be achieved with a vaccine alone. Combine with some other source of protection (changes to work habits, community structure, distancing, masking, boosters, etc) and that picture could change.

[Strigon]

Do you have a website where you can see the difference between delta and delta AY.1 (the delta+ if I'm not mistaken)?

No; I'm sorry if I seemed to be speaking authoritatively; this is all a very ameteurish opinion.
Everything I know comes from what I read about it originally, and the fact that I've heard little of importance to make me change my view.

The facts, as I see them, are this:
1) The Delta variant is significantly more infectious, and is better - though still not very good - at evading our current vaccines. In both these areas, it seems to be the strongest variant thus far.
2) The Delta-Plus variant is the Delta variant, with an additional mutation on the spike protein that has been seen elsewhere before. A brief Google search suggests the Beta and Gamma variants, specifically, had it.
3) The other variants with the mutation found in Delta-Plus are more transmissible than the original virus, but are still susceptible to the vaccine.
4) The Delta-Plus variant is certainly spreading, but it doesn't seem nearly as ubiquitous (yet) as the Delta variant.

My analysis - based on exactly 0 years of medical school - is that it's possible there may be some particular synergy between the standard Delta variant's mutations, and the additional one picked up by Delta-Plus. The far more likely scenario, though, is that the mutation only offers as much benefit to Delta as it did to Beta or Gamma, or may even have diminishing returns. Since Delta is far worse than either Beta or Gamma - at least one of which must have had other mutations as well, or else they wouldn't be two different variants - I find it reasonable to expect the added benefit from the mutation to be relatively small. I wouldn't be surprised if it eventually overtook Delta, but everything I've seen so far suggests a marginal improvement.

[Tyndmyr]

Variants aside(I keep getting Loki flashbacks with all this news), the death rate has remained fairly low even as the case rates have climbed. Here in MD, the death rate has stayed static at a seven day average of about 4 deaths. Infections have been curving upward for over a month now.

This indicates that lethality is fairly reduced. Not sure how to break that out by strain, because I don't have enough data as to what everyone has, but if it were more lethal, or even as lethal, we should have started seeing that with about a two week lag after the infectivity spike. Some silver lining, at least.

[NichG]

I wonder if delta's main difference from the other strains has nothing to do with immune escape, and is just taking a different point in the trade-off between duration of infectiousness and intensity of infectiousness.

If e.g. there's some threshold viral load at which the innate (as opposed to adaptive) immune system really starts to ramp up a response and starts killing infected cells, you could either have a virus which tries to stay high enough to be infectious but low enough to put off triggering that response; or you could have one which spikes its replication rate and tries to get as high of a peak viral load as possible, even if that shortens the period of time before the host's innate immune system starts damping it down. A higher peak viral load might mean being able to land some successful infections in hosts with existing immunity or reducing the effectiveness of interventions, at the cost of having to find a new host much more quickly.

[sktarq]

It depends on R0 and vaccine effectiveness. I've heard estimates of R0 up to ~8 for delta. We need R0 * (1-avg resistance) < 1 for herd immunity

For a vaccine effectiveness at V, that means R0 * ( (1-V) F + 1-F) = 1 is the threshold, or:

F = (1/V) (1-(1/R0))

So for R0=8 and effectiveness of V=0.84, the fraction needed would be 1.04 - that is, herd immunity would not be achieved with a vaccine alone. Combine with some other source of protection (changes to work habits, community structure, distancing, masking, boosters, etc) and that picture could change.

actually you could get herd immunity based on population size. Basically the virus could burn through the remaining unvaxed/ineffective vaxed so that people end up with antibodies that way. Because R0 is based on the idea that the population has no experience with virus. And after a time that is no longer the case. And since even the "ineffective" vaccinated tend to have pretty good health outcomes (in comparison) it may not even be all that costly in lives and health. Not ideal to be sure, but not some nightmare. Very much have to hide those who can't get the vaccine for health reasons until it blows over though. The Delta's high R0 if anything makes this more likely as the only way for it keep going is to have a new age cohort to infect by the time it comes around to a region again or mutate enough that previous exposure doesn't help...Delta soaks an area so fast those don't really have a chance to happen.




My current favorite line dealing with unvaxed. You know people were talking about this was only the flu 18 months ago? well if you get vaccinated that is basically true even if you get unlucky ... if you don't then it is nasty.

[NichG]

actually you could get herd immunity based on population size. Basically the virus could burn through the remaining unvaxed/ineffective vaxed so that people end up with antibodies that way. Because R0 is based on the idea that the population has no experience with virus. And after a time that is no longer the case.

You can add those previous infections to the vaccinated fraction of the same math. The issue is that immunity - from the vaccine or from prior infection - isn't 100% effective. It's not a fixed number at all really, but rather a function of time and intensity of exposure and other things...). So for something which is sufficiently contagious, propagating in an environment where hosts have lots of contact with each-other, herd immunity isn't necessarily achievable without changing some other variable - for example, how many people a carrier has contact with during their average infectious period, the profile of contact, etc. But the thing is, if R0 is actually that high, you can't just make those changes 'until things blow over' and then go back to how things were, because that returns to a situation where the virus can spread freely, which means you get to do it again, and again, and again...

[sktarq]

Except you don't.

If everyone gets immunized via either vaccine or just surviving it then there is nowhere for the vaccine to live and thus nowhere for it to come back from.

And this is how lots of pandemics actually died out back in the day. Hell the spanish flu seems to have gone that way.

With a reservoir to draw from (with many diseases the are animals that also carry the virus and thus can restart the whole mess) virus can go extinct from not having anyone new to infect.

And the higher the R0 the easier that is to happen.

[NichG]

Except you don't.

If everyone gets immunized via either vaccine or just surviving it then there is nowhere for the vaccine to live and thus nowhere for it to come back from.

Except that there's a world of difference between 95% immune and 100% immune. With 95% immunity, 1 in 20 exposures that would have been infectious to a naive host will still lead to infection. So if on average the infection would spread to >20 naive hosts per initial host (R0 of 20), then it could still continue to spread in a population which has 100% past exposure via repeat infections.

If delta has an R0 of 8 in naive hosts, and hosts with prior immunity have an maximum reduction in susceptibility of less than 87.5%, then delta could continue spread even if 100% of people in that population have been vaccinated or exposed to it.

It gets more complicated if the effectiveness of prior immunity varies within a population, and more-so if it varies with time since infection or vaccination. Probably a good chunk of that loss of effectiveness from ~95% down to ~83% is from waning immunity rather than loss of antibody affinity, so boosters should help that and may bring things back into the range of the possible even with R0 of 8, as long as they're synchronized and not staggered. Or one could combine the vaccine with a variety of NPIs to reduce R0 to the point where a 83% effective immunity is enough, though in that case one has to sustain those interventions until community transmission stops entirely - turning them off when the number of cases goes down to some 'comfortable' level is just going to tune R to 1, which is probably about the worst thing you can do in the sense of maximizing the survivable selection pressure experienced by covid.

[Tyndmyr]

Except you don't.

If everyone gets immunized via either vaccine or just surviving it then there is nowhere for the vaccine to live and thus nowhere for it to come back from.

Eh, it's worldwide, so even we we somehow jabbed erryone within 24 hours of birth, we'd still have an order of magnitude more unvaccinated people elsewhere.

The US is 51% fully vaccinated, with about 60% at least partially vaccinated. Even other first world countries like Australia are working on hitting 18%. Less developed countries are far further behind. There's no short term path to removing all reservoirs for the virus, even disregarding animal populations. Given how many variants we've seen so far, it seems highly probable they're gonna keep coming. It doesn't mutate as fast as the flu, but the pool of people who have it is large, so even a fairly modest mutation rate ends up predictably cranking out variants.

It seems highly probable that the 95% immunity does not apply to at least some variants. The flights from Texas to DC resulted in six vaxxed people getting sick out of what, 53? And those were divided into two aircraft, so the actual exposure may have been less. Several more vaxxed people were sickened in turn after landing. That's indicative of a significant breakthrough rate.

I don't have solid numbers as to precisely how it breaks down for each variant/vaccine combination, and there's probably some interesting number crunching to be done, but we are quite far from stamping it out altogether.

[pendell]

In other news, there is now a vaccine specifically targeting delta . It may be a good thing that this miserable pandemic is really jumpstarting our ability to produce vaccines quickly. If only we can get our testing regimen (hindered as it is by legal and political concerns) to move at the speed of our science, and if only we can convince people to actually get their shots.

Respectfully,

Brian P.

[halfeye]

Sometimes, people are just silly.

Authorities in north Germany have asked more than 8,000 people to get repeat Covid vaccinations because a nurse is suspected of having injected saline instead of vaccine in many cases.

https://www.bbc.co.uk/news/world-europe-58186032