This year we kill it: Corona Virus Thread Mark II

[halfeye]

Honest question:

For real? you are asking a lot of things that only make sense to ask if you already hate vaccines.

I don't know either way, but it seems at least plausible that preventing transmission isn't a guarantee with vaccines for illnesses where asymptomatic transmission is possible, and that our current vaccines only do that because we've had the time to perfect them.

If a vaccine prevents you getting the illness, it lessens the transmission, because it makes you more resistant to the virus which means less of your cells get taken over by the virus. The symptoms are not something independant of the production of new virus in your cells.

[Ibrinar]

This is akin to the current news saying that the vaccine is only valid for 90 days.

Realistically, the vaccine is almost certainly effective for far longer. It's just that the study was only 90 days long, because long studies slow deployment, and we needed to get this stuff rolling. There's no actual reason to suspect that immunity ends the day after the study did.

I am not aware of any vaccine in use that prevents the illness without impacting transmission. Given that these vaccines are not wholly novel in how they're made, we should expect them to work in the same fashion as existing vaccines, not in some entirely unusual way. All existing data is consistent with this, even if it's not wholly proven.

You won't find any that have no impact at all I assume but it is not like it was suggested as likely that there is absolutely no effect on transmission, so:
https://www.nature.com/articles/nm1213

Oral polio vaccine. The oral polio vaccine (OPV) is the classical oral-mucosal vaccine. In addition to its enormous impact for reducing polio in the world, this vaccine has also served as a useful tool for elucidating fundamental aspects of mucosal immunity in humans58. Like the injectable inactivated polio vaccine (IPV), OPV produces antibodies in the blood that will protect against myelitis by preventing the spread of poliovirus to the nervous system. But, superior to IPV, OPV also produces a local SIgA immune response in the intestinal mucosa—the primary site for poliovirus entry and multiplication. This intestinal immune response can rapidly stop person-to-person transmission of wild poliovirus, making mass campaigns with OPV a powerful strategy for the global eradication of polio.

Now I might be interpreting that wrong so I continued searching
https://polioeradication.org/polio-t...-vaccines/ipv/

However, as IPV does not stop transmission of the virus, OPV is used wherever a polio outbreak needs to be contained, even in countries which rely exclusively on IPV for their routine immunization programme.

Though this one attests https://pubmed.ncbi.nlm.nih.gov/11763328/ IPV good mucosal immunity in a monkey model.

In the current paradigm, inactivated poliovirus vaccine (IPV) induces serum immunity to protect the individual from poliomyelitis, but not mucosal immunity to prevent subsequent wild poliovirus infection. Therefore, it is believed not to be suitable to interrupt virus transmission in polio-endemic tropical and developing countries, where poliovirus transmission is thought to be predominantly faecal-oral, unlike in countries with excellent sanitation, where it is predominantly respiratory. Oral poliovirus vaccine (OPV), because it is believed to mimic natural (wild) poliovirus infection and to induce serum and mucosal immunity, is considered ideal to interrupt virus transmission in countries with poor sanitation and endemic polio. Moreover, the vaccine viruses are shed in the stools and it is presumed to spread faeco-orally to unvaccinated children in the vicinity, thus increasing its effectiveness in the community. These paradigms on both vaccines may be seen in standard textbooks of virology and paediatrics. In reality, IPV induces very high mucosal immunity in a monkey model, lasting at least 12 months and providing complete protection against oral challenge with wild virus.

Still scientist don't seem to think that that is a forgone conclusion.

I checked out mucosal immunity because it is suggested here as mechanism for how the covid vaccine could be less effective at preventing spread than protecting you https://theconversation.com/covid-19...res-why-156611 (That of course doesn't mean it actually is.)

I have checked it out because this forum has no eyeroll smiley I can direct at halfeye so I had to resort to lesser measures.

[Strigon]

For real? you are asking a lot of things that only make sense to ask if you already hate vaccines.

That's simply not true. I just have a vested interest in knowing if transmission will be reduced by a vaccine. The official word from every medical organization I've heard has been "we hope so" tinged with a bit of "probably".
It sure seems likely that they'd want to be very cautious about saying it definitely does, but only if there's a chance it doesn't. If they were certain it prevented transmission, I don't see any reason why they'd still want to err on the side of caution. That's why I asked whether you'd really know if there were vaccines that didn't stop transmission - if you're someone with education and experience with vaccines beyond that of the average person, your words carry more weight than if you're just saying what makes the most sense to you.

If a vaccine prevents you getting the illness, it lessens the transmission, because it makes you more resistant to the virus which means less of your cells get taken over by the virus. The symptoms are not something independant of the production of new virus in your cells.

Yes and no. Certainly any increase in resistance will reduce transmission somewhat, but it's not the case that preventing serious disease - or even any symptoms at all - will be guaranteed to eliminate, or even come close to eliminating, transmission. In particular with respiratory viruses, you tend to be most infectious during the earliest and least severe stages of the disease - when it's replicating in your nose and throat. At that point, your symptoms are minor - even potentially nonexistent. Nevertheless, you're shedding the virus at the greatest rate. If it moves into your lungs, and you get seriously ill, you're still contagious, but no more than earlier.
If the vaccine prevents the virus from taking hold of your system, great. If it just lets your immune system destroy the infection before symptoms appear, then you're not preventing transmission so much as reducing it. And if that's the case, it still makes sense for vaccinated people to wear masks for the same reason that people who feel healthy should wear masks - because you could be shedding the virus without knowing you're infected. The only difference would be that the vaccinated person would never know, while the unvaccinated person would find out when they start feeling sick.

Now, if your point is that it most likely prevents transmission entirely, or at least comes pretty darned close, then I agree. If I were to bet, that's where I'd put my money.
If your point is that any amount of immunity will, by a matter of course, reduce transmission, then I'd say "yes, but..." because transmission is a factor of both how contagious you are, and how social you are. If the vaccine reduces transmission without stopping it entirely, and you become more social after being vaccinated, society isn't necessarily any better off.
But if your point is that you can't prevent illness without also preventing transmission, then I'd have to disagree unless you've got substantial evidence.

[halfeye]

That's simply not true. I just have a vested interest in knowing if transmission will be reduced by a vaccine. The official word from every medical organization I've heard has been "we hope so" tinged with a bit of "probably".

That's the difference between science and politics, politics is about putting on a bold face and lying if you have to, and you usually have to, science is about estimating the truth as best you can and stating that as accurately as possible. If you want scientists to lie, you are mistaken.

Yes and no. Certainly any increase in resistance will reduce transmission somewhat, but it's not the case that preventing serious disease - or even any symptoms at all - will be guaranteed to eliminate, or even come close to eliminating, transmission.

What useful vaccines do is reduce the number of virus entities getting into the cells of the body.

If you are basically Mr TLDR, and you don't believe what you are told, then you must believe whatever you make up, because there is nothing else for you.

Resistance and transmission are not independent variables. Transmission depends on the number of virus entities being expelled from a person's body, if resistance is up transmission is down. There will be some virus entities emitted from anyone infected, there will be fewer if a person is more resistant. The severity of a virus may vary, rabies is very bad, the cold generally isn't, vaccines do not make a virus milder, they make the effect less severe by increasing resistance so fewer virus entities are in the body, the effect of each virus entity is the same as before, there are just fewer of them.

[NichG]

For real? you are asking a lot of things that only make sense to ask if you already hate vaccines.

If a vaccine prevents you getting the illness, it lessens the transmission, because it makes you more resistant to the virus which means less of your cells get taken over by the virus. The symptoms are not something independant of the production of new virus in your cells.

That's the difference between science and politics, politics is about putting on a bold face and lying if you have to, and you usually have to, science is about estimating the truth as best you can and stating that as accurately as possible. If you want scientists to lie, you are mistaken.

What useful vaccines do is reduce the number of virus entities getting into the cells of the body.

If you are basically Mr TLDR, and you don't believe what you are told, then you must believe whatever you make up, because there is nothing else for you.

Resistance and transmission are not independent variables. Transmission depends on the number of virus entities being expelled from a person's body, if resistance is up transmission is down. There will be some virus entities emitted from anyone infected, there will be fewer if a person is more resistant. The severity of a virus may vary, rabies is very bad, the cold generally isn't, vaccines do not make a virus milder, they make the effect less severe by increasing resistance so fewer virus entities are in the body, the effect of each virus entity is the same as before, there are just fewer of them.

The devil is in the details of the course of progression of the illness. In a normal Covid case, there's a progression from sinuses to the rest of the host's body. So the period of peak infectiousness is not necessarily the period of peak virus count in the body - it should the product of virus count and location-specific factors. It's easier to spread when there are peak concentrations in the sinuses or lungs. I'm trying to find stuff on the specific kinetics of this, and if I do I'll post it.

So the question isn't 'does the vaccine do nothing for transmission', but rather 'does the vaccine do enough for transmission that the overall replication factor of the disease in a partially vaccinated population will be below 1 without any other measures?'. If for example, the vaccine effectively lets the host's immune system kill the virus while its in the sinuses, then a vaccinated person isn't going to be a carrier and we get the full reduction in R by whatever the vaccine effectiveness is. If that's, say, the ~70% vaccines and we have ~70% of the population vaccinated, then its a reduction of R by about half; if those vaccinated people also masked with N95s, it'd be more like a reduction to a third; if only the unvaccinated people masked with N95s, it'd be a reduction to a quarter. If it's the 95% vaccines, then the relative effect of the vaccinated masking will be tiny and the effect of the remaining unvaccinated masking will be a lot more.

But now, what if the 95% vaccines stop Covid when it progresses to the rest of the body, but don't do much for the first few days its in the sinuses (which is also when its potentially most infectious)? Then that 95% self-protection vaccine could look like a 70% others-protection vaccine. 70% is still great, but the consequence of that result would be that people collectively wearing a mask while vaccinated could still have a significant effect on the progression of the overall pandemic.

So yes, vaccines generally have an impact on transmission, but also studying specifically what that impact is in this case is important. Because the specific magnitude of the effect is the difference between 'okay, most people are vaccinated now, so just do whatever and Covid will gradually die out in the area' versus 'okay, most people are vaccinated now, but if we don't continue to take precautions then we're going to have embers that periodically spin off escape variants and we'll all have to do this again and again'

Edit: Here's an example about the kinetics of where the virus is found in hosts (varying by severe or mild symptoms): https://www.jci.org/articles/view/138759/figure/1

[Strigon]

That's the difference between science and politics, politics is about putting on a bold face and lying if you have to, and you usually have to, science is about estimating the truth as best you can and stating that as accurately as possible. If you want scientists to lie, you are mistaken.


If you are basically Mr TLDR, and you don't believe what you are told, then you must believe whatever you make up, because there is nothing else for you.

I really don't know what to say to you anymore, man. The official word from every organization so far is that they don't know to what degree the vaccines block transmission. You're out here saying they absolutely do.
One of us is listening to what the scientists are saying, and it's not the one you seem to think it is.

[Keltest]

I really don't know what to say to you anymore, man. The official word from every organization so far is that they don't know to what degree the vaccines block transmission. You're out here saying they absolutely do.
One of us is listening to what the scientists are saying, and it's not the one you seem to think it is.

Of course theyre saying it. We can make some reasonable assumptions in this case, but when theyre speaking from exclusively hard data. Its not a question of disagreeing, we just have different standards we need to conform to.

[Forum Explorer]

The research has not yet shown if the Covid vaccines provide sterilizing immunity (preventing infection) or simply effective immunity (preventing disease). As such preventing possible transmission until the majority of people are vaccinated is still warranted hence continued mask use.

I mean, preventing disease should reduce transmission in the first place. The less sick you get, the less virus you end up shedding. Though that is very much reduce.

I heard that in Japan (and maybe other east Asian countries) it is the custom to walk around with a mask when you're sick. I'm guessing this custom will somewhat spread to other countries after the Coronavirus will finally die down.
The way people think of death of strangers is weird and doesn't make mathematical sense. Wars and massive riots can start because of a regrettable death of a few unimportant individuals (or even of one), but people are completely indifferent to things that kill many people every day.

That's true, and I hope so. I'm certainly going to start wearing a mask on the days when I'm feeling a little sniffly, but aren't sick enough to miss work.

That's simply not true. I just have a vested interest in knowing if transmission will be reduced by a vaccine. The official word from every medical organization I've heard has been "we hope so" tinged with a bit of "probably".
It sure seems likely that they'd want to be very cautious about saying it definitely does, but only if there's a chance it doesn't. If they were certain it prevented transmission, I don't see any reason why they'd still want to err on the side of caution. That's why I asked whether you'd really know if there were vaccines that didn't stop transmission - if you're someone with education and experience with vaccines beyond that of the average person, your words carry more weight than if you're just saying what makes the most sense to you.

Scientists almost never talk in absolutes. Look at evolution for example. Scientists will coach it in words like theory, even if they are basically 100% that it is a fact. That's just how they talk.

[asda fasda]

Scientists almost never talk in absolutes. Look at evolution for example. Scientists will coach it in words like theory, even if they are basically 100% that it is a fact. That's just how they talk.

Scientist are just normal people, and they do what all people do*. And yes, they are cautions, but that's because of:
a) Many of theories that well believed correct were latter proven wrong, see Newtonian Gravity which was believed true for hundreds of years until Einstein recognize that it was just the special case,
b) Reading data is hard, most of the science is not about observing the phenomenon but to understanding data gathered, which can have multiple issues, including that it's done with statistical analysis which always gives you only a probability that the answer is correct, and it's never 100%.
c) As they are signing their name below the claim they take personal responsibility for that and thus try to limit it. Find me any professional advisor that give you advise without 5 pages of disclaimers : ) - but even if that's and issue it's not the reason to ignore there reservations.

Oh and it's not really a fair to compere research over COVID-19, a disease that not existed 2 years ago, and evolution which was researched for 150 years.

*It always piss me off when media use term "Scientists" as they were some other species with mysterious traits and behaviors. Not to speak that as there are many different science fields the "Scientist" are pretty much as diverse as any other subgroup that exists, if not more as they exist in every culture and nation around the world.

[Forum Explorer]

Scientist are just normal people, and they do what all people do*. And yes, they are cautions, but that's because of:
a) Many of theories that well believed correct were latter proven wrong, see Newtonian Gravity which was believed true for hundreds of years until Einstein recognize that it was just the special case,
b) Reading data is hard, most of the science is not about observing the phenomenon but to understanding data gathered, which can have multiple issues, including that it's done with statistical analysis which always gives you only a probability that the answer is correct, and it's never 100%.
c) As they are signing their name below the claim they take personal responsibility for that and thus try to limit it. Find me any professional advisor that give you advise without 5 pages of disclaimers : ) - but even if that's and issue it's not the reason to ignore there reservations.

Oh and it's not really a fair to compere research over COVID-19, a disease that not existed 2 years ago, and evolution which was researched for 150 years.

*It always piss me off when media use term "Scientists" as they were some other species with mysterious traits and behaviors. Not to speak that as there are many different science fields the "Scientist" are pretty much as diverse as any other subgroup that exists, if not more as they exist in every culture and nation around the world.

Fair enough. However, it is also true that they are very much trained to not speak in absolutes. Like if you write the line 'this proves x' and it isn't actually absolutely true? You'll get marks taken off whatever assignment you handed in. And they pound that into your head, again and again. Do NOT speak in absolutes.

That was kinda my point though. Evolution has been researched for 150 years, and they still don't talk in absolutes about it. COVID-19 has only been around for a year and some, it is unreasonable to expect scientists to talk in absolutes about it.

[snowblizz]

Fair enough. However, it is also true that they are very much trained to not speak in absolutes. Like if you write the line 'this proves x' and it isn't actually absolutely true? You'll get marks taken off whatever assignment you handed in. And they pound that into your head, again and again. Do NOT speak in absolutes.

You'd never write "this proves X". Ok, there is one exception. Mathematics end a proof by writing, Q.E.D., quod erat demonstrandum. And mathematics is very specific in that it's the only or very few disciplines that actually deals in absolutes.

Only Sith deal in absolutes.*

That was kinda my point though. Evolution has been researched for 150 years, and they still don't talk in absolutes about it. COVID-19 has only been around for a year and some, it is unreasonable to expect scientists to talk in absolutes about it.

Yes. I suspect even gravity is only talked about in degrees of certainty. Not one physicist expects a ball to fall upwards though.



*yes I do think mathematicians are Sith

[Tyndmyr]

Honest question: do you expect you'd know of such a vaccine if it existed? Or, perhaps more relevant, what about vaccines that aren't in use? Because it's conceivable that vaccines were developed that had little or no effect on transmission, but were later replaced by vaccines that did reduce transmission once they became available.

I don't know either way, but it seems at least plausible that preventing transmission isn't a guarantee with vaccines for illnesses where asymptomatic transmission is possible, and that our current vaccines only do that because we've had the time to perfect them.

Poorly functioning vaccines happen, and are replaced, sure. That's generally covered as part of the testing protocol.

Asymptomatic transmission is possible for many diseases, that isn't a new thing. The length of time that covid has asymptomatic transmission is long, yes, but it's not the longest, and it's certainly not novel. We have no reason to suspect that this would make vaccination less efficient than the many other similar diseases we've vaccinated for.

Vaccines don't work by preventing symptoms, they work by preventing the disease. The immunity is not quite perfect, and efficacy rates vary...so we're always looking for better ones, but they're generally pretty good. Individual responses to a vaccine can vary somewhat based on individual factors, so not all people who take a vaccine may be equally protected...some people get lesser levels of immunities, and thus almost nothing is 100%, but we should expect vaccines to vastly lessen transmission.


Ibrinar, I read some of that, but I'm afraid I'm not following what point you're trying to make. These vaccines are effective at preventing transmission, yes. I'm agreeing with that. Did you intend this as a counterargument, or just expanding on that topic?

So the question isn't 'does the vaccine do nothing for transmission', but rather 'does the vaccine do enough for transmission that the overall replication factor of the disease in a partially vaccinated population will be below 1 without any other measures?'

Taking the most recent estimate as reported by the BBC, *current* levels of vaccination have already achieved this. https://www.bbc.com/news/health-52473523 Estimated to be between .7 and .9

Specific numbers in your area may vary. Some places have higher or lower vaccination rates. That said, as vaccination continues, we should expect R to drop everywhere, and getting sub 1 does not appear to be at all difficult with vaccinations. Widespread vaccination should end it as a pandemic.

If for example, the vaccine effectively lets the host's immune system kill the virus while its in the sinuses, then a vaccinated person isn't going to be a carrier and we get the full reduction in R by whatever the vaccine effectiveness is. If that's, say, the ~70% vaccines and we have ~70% of the population vaccinated, then its a reduction of R by about half; if those vaccinated people also masked with N95s, it'd be more like a reduction to a third; if only the unvaccinated people masked with N95s, it'd be a reduction to a quarter. If it's the 95% vaccines, then the relative effect of the vaccinated masking will be tiny and the effect of the remaining unvaccinated masking will be a lot more.

Per the CDC's study, masking mandates reduced the death rate by .9% after about 100 days. Transmission rate effect was slightly lower, and short term results were obviously lesser.

Vaccines are way, way better than .9% effective.

Wearing a mask until you can get a vaccine is entirely reasonable, but getting the vaccine is going to be way more important than any amount of masking, and masking once you have full resistance(about two weeks after your final shot) will provide an extremely low additional margin of safety.

It's really quite hard to overstate the efficacy of vaccines compared to other mitigation efforts. We may not know *exactly* how much they protect, but all data so far points to them being quite effective, with Pfizer claiming 95% effectiveness(Source: https://www.pfizer.com/news/press-re...sults-landmark )

Even if that is not true, and they are still, say, 70% effective, that's still amazing, and will still suffice to rapidly end the pandemic once mass vaccination is complete. Efforts post-vaccine largely won't matter, but getting vaccinations out there definitely matters a lot.

[sihnfahl]

Per the CDC's study, masking mandates reduced the death rate by .9% after about 100 days. Transmission rate effect was slightly lower, and short term results were obviously lesser.

You'll have to link that one.

Cause, here at the CDC, the results were as follows:

During March 1–December 31, 2020, state-issued mask mandates applied in 2,313 (73.6%) of the 3,142 U.S. counties. Mask mandates were associated with a 0.5 percentage point decrease (p = 0.02) in daily COVID-19 case growth rates 1–20 days after implementation and decreases of 1.1, 1.5, 1.7, and 1.8 percentage points 21–40, 41–60, 61–80, and 81–100 days, respectively, after implementation (p<0.01 for all) (Table 1) (Figure).

So growth rate decline stayed under 1% only to about 20 days. Once you hit 81-100 days, it was 1.8%.

Mask mandates were associated with a 0.7 percentage point decrease (p = 0.03) in daily COVID-19 death growth rates 1–20 days after implementation and decreases of 1.0, 1.4, 1.6, and 1.9 percentage points 21–40, 41–60, 61–80, and 81–100 days, respectively, after implementation (p<0.01 for all). Daily case and death growth rates before implementation of mask mandates were not statistically different from the reference period.

So death rate decrease was under 1% to 20 days after. But goes to 1.9% at 81-100 days....

[NichG]

Taking the most recent estimate as reported by the BBC, *current* levels of vaccination have already achieved this. https://www.bbc.com/news/health-52473523 Estimated to be between .7 and .9

Specific numbers in your area may vary. Some places have higher or lower vaccination rates. That said, as vaccination continues, we should expect R to drop everywhere, and getting sub 1 does not appear to be at all difficult with vaccinations. Widespread vaccination should end it as a pandemic.

Keep in mind that that's with all the current pandemic precautions in place, which without vaccination lowered R from ~4 to ~1-2.

The timing of Israel's downturn in cases per day suggests that around 40% of the population having their first shot plus NPIs remaining in place was the turning point.

A lot of people are eager for the vaccine so they can back off on things like masks, distancing, not eating in restaurants, working in person, etc.

Per the CDC's study, masking mandates reduced the death rate by .9% after about 100 days. Transmission rate effect was slightly lower, and short term results were obviously lesser.

Vaccines are way, way better than .9% effective.

Additive versus multiplicative makes this a misleading way of reporting it, especially without a link to the original source so we can check.

If the daily growth rate was 1.8%, a reduction of 0.9% per day is a factor of 2. Which is not at all small.

[Tyndmyr]

You'll have to link that one.

Cause, here at the CDC, the results were as follows:



So growth rate decline stayed under 1% only to about 20 days. Once you hit 81-100 days, it was 1.8%.



So death rate decrease was under 1% to 20 days after. But goes to 1.9% at 81-100 days....

I believe you're looking at the right study, but at the portion of it that is the effect of mask mandates and restaurant closures combined. Each measure on its own is of course less effective than both combined.

Additive versus multiplicative makes this a misleading way of reporting it, especially without a link to the original source so we can check.

If the daily growth rate was 1.8%, a reduction of 0.9% per day is a factor of 2. Which is not at all small.

It's been discussed previously, and as it looks like it was just linked again, should be good if you want to read it.

It's the same type of decrease, so we are comparing apples to apples here. The population being vaccinated will similarly decrease infectivity on every day, only to a much greater degree. R sinking far below zero due to vaccinations will absolutely have a multiplicative effect over a time period, greatly reducing the risk.

[NichG]

I believe you're looking at the right study, but at the portion of it that is the effect of mask mandates and restaurant closures combined. Each measure on its own is of course less effective than both combined.



It's been discussed previously, and as it looks like it was just linked again, should be good if you want to read it.

It's the same type of decrease, so we are comparing apples to apples here. The population being vaccinated will similarly decrease infectivity on every day, only to a much greater degree. R sinking far below zero due to vaccinations will absolutely have a multiplicative effect over a time period, greatly reducing the risk.

They're definitely reporting changes in percentage points of daily case growth (right column second paragraph first page of the PDF), not percentage relative decrease between mask and no mask. So that's additive.

Vaccine effectiveness is a multiplicative measure. So it's not apples to apples.

Unfortunately they do not actually report the baseline values in this report, only the changes. So it's impossible to say just from this paper how to convert their additive results into multiplicative.

They also do something a bit weird and define their daily percentage point growth as 100 * difference in natural log of daily cases from day to day. Rather than 100 * (ratio of cases - 1). The two measures will be approximately the same if the changes are small because ln(1+x) ~ x but if the day to day changes are large this will squash the values compared to a ratio.

Incidentally, this sort of thing is why scientists are obsessive about saying things precisely.

[sihnfahl]

at the portion of it that is the effect of mask mandates and restaurant closures combined.

They accounted for that.

During March 1–December 31, 2020, state-issued mask mandates applied in 2,313 (73.6%) of the 3,142 U.S. counties.

During the study period, states allowed restaurants to reopen for on-premises dining in 3,076 (97.9%) U.S. counties

Weighted least-squares regression with county and day fixed effects was used to compare COVID-19 case and death growth rates before and after 1) implementing mask mandates and 2) allowing on-premises dining at restaurants. Because state-issued policies often applied to specific counties, particularly when states began allowing on-premises dining, all analyses were conducted at the county level. Four regression models were used to assess the association between each policy and each COVID-19 outcome. The regression models controlled for several covariates: restaurant closures in the mask mandate models and mask mandates in the restaurant reopening models, as well as bar closures,** stay-at-home orders,†† bans on gatherings of ≥10 persons,§§ daily COVID-19 tests per 100,000 persons, county, and time (day). P-values <0.05 were considered statistically significant. All analyses were weighted by county population with standard errors robust to heteroscedasticity and clustered by state. Analyses were performed using Stata software (version 14.2; StataCorp). This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.¶¶

So they modeled depending on the situation in each reporting county, and collated like with like.

[Tyndmyr]

They also do something a bit weird and define their daily percentage point growth as 100 * difference in natural log of daily cases from day to day. Rather than 100 * (ratio of cases - 1). The two measures will be approximately the same if the changes are small because ln(1+x) ~ x but if the day to day changes are large this will squash the values compared to a ratio.

That I didn't catch. As you say, that is odd. That said, I would expect a relatively small, gradual change in daily rates due to the apparently gradually increasing effectiveness of implementation. So, probably not a large change there.

That said, rate of growth is largely what we're looking at either way. If half the population is vaccinated, that's going to vastly decrease the growth rate of a disease. Both measures are doing the same thing, preventing new cases. The lack of raw data does hinder some comparison, but in both cases, every new case prevented will prevent a bunch of new cases in turn as we iterate through generations of the disease. That's all R is, really. How many cases we get from each existing case. Masking, closures, and vaccinations are all attempts to lower that number.

They accounted for that.

I'd actually read a slightly different summary of the study(which is what this is) that implied the two were separate, and gave figures for each, summing to approximately the 1.8%. Unfortunately, the source study this is summarizing is just refusing to load for me. Not sure if an outage or what. Probably revist that later, since I would prefer to use whatever the actual numbers are.

In any case, the margin of error even in this presentation is...large*. So large that it does not rule out no effect whatsoever, or even a negative effect. I don't *think* it's a negative effect...it seems reasonable to suppose that masks and closures had at least some positive effect, however small. But, yknow, full disclosure and all that.

But whatever the effect is, it's definitely less than getting vaccinated. Yeah, we've got some uncertainty on both numbers, but they're not even the same order of magnitude. Even if all errors on the vaccine are overstating effectiveness, and understating the effectiveness of everything else, a vaccine is going to offer you far better protection than a mask.**

*Goin' off variation in results. Some variation in policy results is normal, but if you're seeing negative results, that's...odd. Perhaps some mandates are slightly different or something, but it doesn't seem like a mandate should make people catch the disease faster.

**To be exceedingly pedantic...than a policy of masking. Your personal mask could be far better or worse than the average, I suppose. Statistics being statistics, they're constrained to the average actually being used.

[warty goblin]

Got a vaccine appointment for next Thursday . Never have I been so excited at the prospect of getting stabbed by a complete stranger.

**To be exceedingly pedantic...than a policy of masking. Your personal mask could be far better or worse than the average, I suppose. Statistics being statistics, they're constrained to the average actually being used.

To be excessively pedantic, its not actually the effectiveness of the average mask, but the effect of masking averaged over the population. Since masking is likely to be nonlinear in effect, the distinction is actually important, E(f(x)) != f(E(x)) in general.

[Drakenkin]

I got my first dose of the Moderna vaccine two days ago! The whole day I was going on about how it was less painful than a flu shot, how I felt great, my arm wasn't even sore, and the like. Too cocky. Way too cocky. Yesterday was AWFUL, I got basically all of the symptoms I had when I actually got COVID last July.

I mean, I would still do it again. And I'm definitely going to get the second shot. I'm just going to go ahead and schedule the next day off work.

Also, is there a reason why even though I got the shot in my left arm, my right arm is sore?

[NichG]

That I didn't catch. As you say, that is odd. That said, I would expect a relatively small, gradual change in daily rates due to the apparently gradually increasing effectiveness of implementation. So, probably not a large change there.

That said, rate of growth is largely what we're looking at either way. If half the population is vaccinated, that's going to vastly decrease the growth rate of a disease. Both measures are doing the same thing, preventing new cases. The lack of raw data does hinder some comparison, but in both cases, every new case prevented will prevent a bunch of new cases in turn as we iterate through generations of the disease. That's all R is, really. How many cases we get from each existing case. Masking, closures, and vaccinations are all attempts to lower that number.

Basically what we need to relate all these things in a consistent system is the conversion constant between daily growth rate and R, which is essentially the duration of a case.

For example, in the initial Covid surges we saw doubling times ranging from 7 days in Italy (probably faster than normal due to imported cases dominating in the early phase at least) to something more like 14 days. So if we take, say, 12 days as the doubling time of Covid without any NPIs or previous immunity then that rate of 8% per day corresponds roughly to R0 which is in the 3-4 range or an 'R above 1' of, say, ~2.5. So a +3.2% additive change in the growth rate of cases per day corresponds roughly to +1 R, and -3.2% additive change in growth rate of cases per day corresponds roughly to -1 R. The CDC study reports that after 100 days, mask mandates had gotten about an (additive) reduction in case growth rate by 2%, so effectively masks on a non-immune population but one basically behaving according to the way people are behaving now (not the same as the start of Covid) is about -0.6 R. If current no-mask R values fluctuate between something like 0.9 and 1.5, then the study's 2% additive measure translates to a mask effectiveness of around a 30-50% multiplicative reduction in R.

70% vaccination rates with Moderna or Pfizer and assuming 95% effectiveness both for transmission and infection would basically be a reduction in baseline transmission of R0 by a multiplicative factor of 1-0.7*0.95. So from a base 'no NPIs' R0 of 3.5 we'd get to 1.2 and still be in trouble, or from an R including NPIs of 1.5 we'd get to 0.5 and be set. Does the additive logic of mask effect still work here? While the effects should stack (since one reduces exposure, and the other reduces the consequences of exposure), the specific additive way of considering the measure probably wouldn't keep the same number when the base R is reduced. So I'd say we should use the multiplicative equivalent for masks - lets say a 30% reduction in R (multiplying by 0.7) conservatively.

In that case, a baseline R0 of 3.5 becomes 1.2 with vaccine, and becomes 0.84 with general masking (both vax and unvax), and so we'd be set with vaccine and masks and no other NPIs such as restaurant closures needed. Or we can drop the masks and keep the restaurant closures, take your pick?

What if it's only masks for the unvax'd in the above scenario? Then you've got R = R0*( (fraction unvax'd) * (mask effect) + (fraction vax'd) * (vax effect) ), which is 3.5*( 0.3 * 0.7 + 0.7 * 0.05 ) = 0.86. So in the case of Moderna and Pfizer (and assuming that the 95% effectiveness applies also to transmission), you're exactly right - almost no direct effect of asking the vax'd to mask, only social side-effects.

How about if it's Astra-Zeneca with a 70% effectiveness? Then mask mandates for everyone + 70% vax rate gives R = 1.25 and even then we're still in trouble if we release other NPIs. Mask mandates for unvaxed + 70% vax rate gives R = 1.47. So asking the vax'd to mask is a difference in R of 0.2 That's not huge, but it's not so small either.

And if Pfizer and Moderna are 95% against serious/symptomatic Covid, but only 70% against transmission, then it puts us in the second scenario rather than the first.

I think at this point there's no justification in saying that there's no transmission reduction, but the precise amount of transmission reduction actually can matter quite a bit, because it only takes a bit to end up above or below R=1.

[Ibrinar]

Ibrinar, I read some of that, but I'm afraid I'm not following what point you're trying to make. These vaccines are effective at preventing transmission, yes. I'm agreeing with that. Did you intend this as a counterargument, or just expanding on that topic?

I don't know why you interpret " as IPV does not stop transmission of the virus" as "These vaccines are effective at preventing transmission" . But what I wrote/linked contains all info I wanted to add (namely that scientists do consider a vaccine being better at protecting people than preventing transmission an option and how that can be) and elaborating doesn't really seem worth the effort so do with it what you will.

[pendell]

I got my first dose of the Moderna vaccine two days ago! The whole day I was going on about how it was less painful than a flu shot, how I felt great, my arm wasn't even sore, and the like. Too cocky. Way too cocky. Yesterday was AWFUL, I got basically all of the symptoms I had when I actually got COVID last July.

I mean, I would still do it again. And I'm definitely going to get the second shot. I'm just going to go ahead and schedule the next day off work.

Also, is there a reason why even though I got the shot in my left arm, my right arm is sore?

Wait a minute ... if you've already had covid, surely a vaccine is redundant? What will the vaccine do for your immune system that actually fighting and beating the disease won't ?

In other news, I found out the 20 year old daughter of a friend just learned she had covid because she couldn't run any more. Testing revealed -- as I understand it -- significant lung scarring consistent with covid. She was an athlete. Was. :(.

Respectfully,

Brian P.

[Drakenkin]

Wait a minute ... if you've already had covid, surely a vaccine is redundant? What will the vaccine do for your immune system that actually fighting and beating the disease won't ?

In other news, I found out the 20 year old daughter of a friend just learned she had covid because she couldn't run any more. Testing revealed -- as I understand it -- both covid antibodies and significant lung scarring. She was an athlete. Was. :(.

Respectfully,

Brian P.

From what I understand the antibodies from actually contracting COVID don't last as long as the antibodies from the vaccine.

That's awful. Condolences to your friend's daughter. That has to be a tough blow.

[Sigako]

Antibodies from actual virus last only until you stop getting exposed and shortly after that. Vaccines are engineered to give a somewhat longer immunity.
If I understood things correctly, it's not about the quality of antibodies themselves, but that active virus interferes with immune system if there's no previous immunity for it, lowering the response. Although I may be getting it wrong - heard it on the news months ago and wasn't paying attention.

And now for something unrelated: in Russia there's already a 3rd independent vaccine developed and approved for distribution. So sad the 2nd one was a fraud.

[Sermil]

I just got vaccinated too (yay) and it got me to thinking...

You can't really socially distance while getting vaccinated; you've got to be within touch range. We all wore masks, but that's still closer than I've been to anyone outside my household in months. So, what would happen if you got infected at the same moment that you got vaccinated? Would the vaccine help? Hurt?

On the one hand, maybe the the vaccine gives you a headstart on producing antibodies. COVID-19 famously has a long asymptomatic period -- you often don't get symptoms for 4-5 days after infection, even if you eventually get very sick. In general, many of the symptoms of being sick are actually caused by your immune system ramping up -- the fever from your immune system trying to burn the intruder out, the fatigue as you divert all your energy resources into your anti-virus system, etc. The fact that you don't get symptoms for several days suggests to me that your immune system doesn't recognize that you are under attack for several days; there are several days where the virus is replicated and taking over more and more cells before the immune system finally says "Hold on, we have a crisis here, people" and really starts fighting. Presumably, antibody production only really starts at that point.

I can tell you that the side effects of the vaccine -- feverish feelings and fatigue -- happen within 12 hours of the J&J vaccine. So maybe the immune response, and particularly the antibody production, gets going faster, and maybe that helps.

On the other hand, maybe this just diverts resources from the actual infection; the body is so busy fighting off the fake vaccine "infection" that it ignores the real infection. Maybe it wears out the immune system so that when the real infection gets going 4 days later, the immune system is already tired -- or maybe the reverse, the immune system is already so oversimulated that it overreacts to the real COVID-19 and damages you. (I've heard a lot of the damage from COVID-19 is actually from the immune reaction to it.)


I doubt anyone knows the answer; it's not something that would be easy to design a study for. But it's fun to speculate! What do people think?

[NichG]

I just got vaccinated too (yay) and it got me to thinking...

You can't really socially distance while getting vaccinated; you've got to be within touch range. We all wore masks, but that's still closer than I've been to anyone outside my household in months. So, what would happen if you got infected at the same moment that you got vaccinated? Would the vaccine help? Hurt?

On the one hand, maybe the the vaccine gives you a headstart on producing antibodies. COVID-19 famously has a long asymptomatic period -- you often don't get symptoms for 4-5 days after infection, even if you eventually get very sick. In general, many of the symptoms of being sick are actually caused by your immune system ramping up -- the fever from your immune system trying to burn the intruder out, the fatigue as you divert all your energy resources into your anti-virus system, etc. The fact that you don't get symptoms for several days suggests to me that your immune system doesn't recognize that you are under attack for several days; there are several days where the virus is replicated and taking over more and more cells before the immune system finally says "Hold on, we have a crisis here, people" and really starts fighting. Presumably, antibody production only really starts at that point.

I can tell you that the side effects of the vaccine -- feverish feelings and fatigue -- happen within 12 hours of the J&J vaccine. So maybe the immune response, and particularly the antibody production, gets going faster, and maybe that helps.

On the other hand, maybe this just diverts resources from the actual infection; the body is so busy fighting off the fake vaccine "infection" that it ignores the real infection. Maybe it wears out the immune system so that when the real infection gets going 4 days later, the immune system is already tired -- or maybe the reverse, the immune system is already so oversimulated that it overreacts to the real COVID-19 and damages you. (I've heard a lot of the damage from COVID-19 is actually from the immune reaction to it.)


I doubt anyone knows the answer; it's not something that would be easy to design a study for. But it's fun to speculate! What do people think?

If we're talking the first dose of a two-dose vaccine, the first dose does provide some resistance, but during the first 7-8 days after the dose the number of Covid cases in the placebo and vaccine arms were basically the same, with a kink in the curve appearing around day 8, at which point suddenly the infection rate drops significantly. See Fig. 13 on p58 of Pfizer's report: https://www.fda.gov/media/144246/download.

[Sigako]

Our regulations require a negative test before you come to be vaccinated for the 1st time. Although noone really cares about them - tests are expensive, and don't you start about economical crisis in oh-so-poor America until you've seen us.
Second measure is scheduling - you must get an appointment first, and the times are usually set to limit crowding. Well, except for my second shot, when both doctor and assistant on paperwork duty were brain-dead idiots and there was a huge crowd, but everyone there was for a 2nd shot.

[Tyndmyr]

In that case, a baseline R0 of 3.5 becomes 1.2 with vaccine, and becomes 0.84 with general masking (both vax and unvax), and so we'd be set with vaccine and masks and no other NPIs such as restaurant closures needed. Or we can drop the masks and keep the restaurant closures, take your pick?

Restaurants are largely open everywhere, and overall rates of illness do not support a R0 of 3.5 or anywhere close to that, even so. This is true even in states without a masking mandate. I suspect your guess of 3.5 is substantially off, at least now.

Keep in mind that resistance gained from people having had the disease is somewhat of an additive effect to vaccines, and that this alone eventually kills pandemics. It is, after all, how Spanish Flu went away.

Vaccines is just speeding that process alone, without all the deaths and illness required to have everyone build herd immunity the hard way.

You can't use the initial R0 as valid for now. That's not how infectivity works. R is always dependent on current conditions.

Wait a minute ... if you've already had covid, surely a vaccine is redundant? What will the vaccine do for your immune system that actually fighting and beating the disease won't ?

Giving a vaccine to someone who has had the disease is generally less efficient than giving it to someone who has not. Having had the disease grants you some antibodies.

Levels of resistance vary, so getting vaccinated anyways is probably ideal, just to be sure. But from a large scale perspective, you'll want to hit the people with higher risk of getting the disease first, so people who have overcome it are probably not on top of the list in most cases.

Sorry about your friend, that sounds really awful.

I just got vaccinated too (yay) and it got me to thinking...

You can't really socially distance while getting vaccinated; you've got to be within touch range. We all wore masks, but that's still closer than I've been to anyone outside my household in months. So, what would happen if you got infected at the same moment that you got vaccinated? Would the vaccine help? Hurt?

Antibody production takes time. Usually, around two weeks to get roughly to long term levels. The vaccine *might* get your antibody production going faster and help a little, but you could certainly still be ill in that early period.

That said, probably not very likely. I'd imagine that everyone involved in vaccination is fairly aware of this and is being reasonably careful, and those giving the vaccine are almost certainly vaccinated themselves. That lowers risk quite a bit, regardless of social distancing.

[NichG]

Restaurants are largely open everywhere, and overall rates of illness do not support a R0 of 3.5 or anywhere close to that, even so. This is true even in states without a masking mandate. I suspect your guess of 3.5 is substantially off, at least now.

Checking back, it was a high estimate, but not outside of confidence intervals for the variants. 3.1 would be the conservative lower bound.

For classic Covid:

This estimates 2.6 but with a doubling time of 4 days: https://science.sciencemag.org/content/368/6489/395

This estimates 2.2 with a 7.4 day doubling: https://www.nejm.org/doi/full/10.1056/nejmoa2001316

For the B117 Covid variant that is now the majority of new cases, Re is about 0.4 - 0.7 higher, which they estimate to be a 40-80% increase in R (I'm unclear as to whether this should add or multiply R0 estimates): https://www.medrxiv.org/content/10.1...34v2.full-text

So the range of estimates would be 2.6 - 3.3 when treating the variant additively, or 3.1 - 4.7 if treated multiplicatively.

Keep in mind, this is for R0, not Re. R0 is the number with no interventions or behavioral changes or immunity from any source, so the actual Re we experience is different and generally lower. But it's hard to estimate and is entangled with the generation time of a Covid infection. Our R0 measurements all come from early in the pandemic, before there were large-scale measures taken.

Taking the initial Covid R numbers, the various behavioral changes associated with the pandemic are collectively responsible for over a factor of 2 reduction in spread. So that's what we have to exceed with collective sources of immunity to be able to completely relax those behavioral changes and still end the pandemic.