OT: COVID-19 thread #4

[molepharmer]

Thanks for the explanation for us lay folk. It blows my mind what they can do on the molecular or cellular level with genetics these days. How do they figure out what part of the virus RNA or DNA codes for making the spike protein in the first place? Do they start cutting out bits of it, and then see what goes missing? How do they go about cutting a genome? Do they do it chemically, or is it done under an electron microscope manually by a micro-surgery?

Not my area of expertise. You'd probably have better success thru google. DNA/RNA molecular biology and protein synthesis has come a long way in a short time. But basically the sequences are chopped up by enzymes called nucleases. There are a bunch of different nucleases and they each may chop at a specific point in the sequence. This gives fragments of various lengths, some overlapping, which can be pieced together to get the whole sequence (not trivial). They then have various tools and techniques to determine the most likely tertiary, 3-D structure. A somewhat key point is that these structures are not static but rather dynamic and can change slightly dependent upon the environment.

[Dresden]

I read that Bob Boone, a scouting exec with the Nationals, resigned rather than get vaccinated. I just don't get that, unless he was ready to retire anyway. He had been with them for 15 years. Two other scouts did as well.

[Dresden]

Thanks for the explanation for us lay folk. It blows my mind what they can do on the molecular or cellular level with genetics these days. How do they figure out what part of the virus RNA or DNA codes for making the spike protein in the first place? Do they start cutting out bits of it, and then see what goes missing? How do they go about cutting a genome? Do they do it chemically, or is it done under an electron microscope manually by a micro-surgery?

Not my area of expertise. You'd probably have better success thru google. DNA/RNA molecular biology and protein synthesis has come a long way in a short time. But basically the sequences are chopped up by enzymes called nucleases. There are a bunch of different nucleases and they each may chop at a specific point in the sequence. This gives fragments of various lengths, some overlapping, which can be pieced together to get the whole sequence (not trivial). They then have various tools and techniques to determine the most likely tertiary, 3-D structure. A somewhat key point is that these structures are not static but rather dynamic and can change slightly dependent upon the environment.

I suppose once they get one piece the way they want it, they have some way of replicating it so that they don't have to do that for every single vaccine.

[dice]

unethical study if you ask me, but apparently a 30% increase in mask wearing leads to about 10% less COVID transmission:

https://www.nbcnews.com/science/science-news/largest-study-masks-yet-details-importance-fighting-covid-19-rcna1858

[waffle]

yeah, I read that. Not unethical as I think it was observational.

Short answer is - Masks work

[Dresden]

Another interesting stat I heard today: if your are vaxed, your odds of dying from Covid are roughly the same as your odds of getting killed by a dog attack.

[dice]

yeah, I read that. Not unethical as I think it was observational.

the basis for the comparison was that masks were suggested for certain villages and not for others. it's not like we didn't already know that masks work. to not actively recommend them for an arbitrarily selected control group basically ensured higher COVID rates for those people

i don't know that this kind of study could be undertaken in a first world country because of the degree of pushback. but because it is done in bangladesh...

[Dresden]

It sounds like there is a new variant now- Mu - that may be resistant to the vaccine and prior infections. It's been detected pretty widely across the USA. What a disaster that would be.

[coldfish]

Mu is 1.621

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Percentage of sequenced cases by week:
8/28 0.2%
8/21 0.2%
8/14 0.2%
8/7 0.4%
7/31 0.6%
7/24 1.0%
7/17 1.7%
7/10 2.1%
7/3 2.4%
6/26 3.4%
6/19 3.6%

Delta makes up 99.4% of all cases as of last week.

[Chi town]

The vaccine outcomes are still better than totally unvaxxed + no previous COVID. The survivors benefit may be better but that initial risk is not worth taking IMO.

This only shows that natural acquired immunity is better than Pfizer and probably better than Moderna (although the magnitude is unknown) for Delta variant.

Israel also is almost exclusively Pfizer
Moderna seems to be better against the delta variant.

https://www.nbcchicago.com/news/coronavirus/moderna-vs-pfizer-is-one-vaccine-stronger-against-delta-variant/2603249/
The study reported that in July in Florida, where COVID cases are at an all-time high and the delta variant is prevalent, the risk of a breakthrough case was 60% lower for Moderna recipients as compared to Pfizer recipients.

Similarly, in Minnesota last month, the authors found that the Moderna vaccine (also known as mRNA-1273) was 76% effective at preventing infection, but the Pfizer vaccine (known as BNT162b2) was 42% effective.

The potential risk of either death or having long term pulmonary damage for most people isn't worth the risk to have better immune response. 23% of people report long term issues (1 mo +) after infection https://www.webmd.com/lung/news/20210624/23-percent-covid-patients-report-long-haul-symptoms

It likely is lower than 23% as obviously asymptomatic cases its likely they never knew.

The easier answer is better boosters, which will come. Mixing doses between vendors might also be beneficial https://www.nature.com/articles/d41586-021-01805-2

I know people who live abroad and those countries believe that mixing doses gives an overall immune response (out of need as well)--we will see in the data soon. Thailand is mixing Sino with AZ, Paraguay is mixing Sputnik with Pfizer. More is happening elsewhere-that is just what I heard anecdotally.

Long term is a month?

I’ve had lots of convos with people that have had COVID and many have said they still didn’t get taste or full lung function after a month. None have said after 6 months that they had any issue… all back to normal.

This continues to be a major risk for the obese. 80% of hospitalizations and deaths come from that population. Over 99% of people that get it recover and IMO that number is actually lower since so many people have had it and not been tested.

[dice]

Mu is 1.621

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Percentage of sequenced cases by week:
8/28 0.2%
8/21 0.2%
8/14 0.2%
8/7 0.4%
7/31 0.6%
7/24 1.0%
7/17 1.7%
7/10 2.1%
7/3 2.4%
6/26 3.4%
6/19 3.6%

Delta makes up 99.4% of all cases as of last week.

i'm assuming that the original (alpha) variant has not been effectively wiped out by the vaccine, but rather by the stronger variant (delta)?

[coldfish]

Mu is 1.621

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Percentage of sequenced cases by week:
8/28 0.2%
8/21 0.2%
8/14 0.2%
8/7 0.4%
7/31 0.6%
7/24 1.0%
7/17 1.7%
7/10 2.1%
7/3 2.4%
6/26 3.4%
6/19 3.6%

Delta makes up 99.4% of all cases as of last week.

i'm assuming that the original (alpha) variant has not been effectively wiped out by the vaccine, but rather by the stronger variant (delta)?

Yes. Its stunning how much more contagious delta is than all of the other variants. Its wiped almost all of them out globally.

At this point, its very likely that the next dangerous variant is a descendant of delta because delta has so many more advantageous mutations than anything else.

I sure hope they hurry up with the delta specific vaccine. IMO, it would really make a difference if we were using boosters aimed at delta.

[dice]

Mu is 1.621

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Percentage of sequenced cases by week:
8/28 0.2%
8/21 0.2%
8/14 0.2%
8/7 0.4%
7/31 0.6%
7/24 1.0%
7/17 1.7%
7/10 2.1%
7/3 2.4%
6/26 3.4%
6/19 3.6%

Delta makes up 99.4% of all cases as of last week.

i'm assuming that the original (alpha) variant has not been effectively wiped out by the vaccine, but rather by the stronger variant (delta)?

Yes. Its stunning how much more contagious delta is than all of the other variants. Its wiped almost all of them out globally.

At this point, its very likely that the next dangerous variant is a descendant of delta because delta has so many more advantageous mutations than anything else.

I sure hope they hurry up with the delta specific vaccine. IMO, it would really make a difference if we were using boosters aimed at delta.

have there been any announcements about the progress of delta-specific vaccine variation? i would assume that they can simply alter the previous one, making the development process the second time around much faster...but then maybe there still have to be trials, which would obviously take the same amount of time

[coldfish]

i'm assuming that the original (alpha) variant has not been effectively wiped out by the vaccine, but rather by the stronger variant (delta)?

Yes. Its stunning how much more contagious delta is than all of the other variants. Its wiped almost all of them out globally.

At this point, its very likely that the next dangerous variant is a descendant of delta because delta has so many more advantageous mutations than anything else.

I sure hope they hurry up with the delta specific vaccine. IMO, it would really make a difference if we were using boosters aimed at delta.

have there been any announcements about the progress of delta-specific vaccine variation? i would assume that they can simply alter the previous one, making the development process the second time around much faster...but then maybe there still have to be trials, which would obviously take the same amount of time

Yeah, they can modify the mRNA vaccines really quickly. The Pfizer CEO said they could change over the formulation of the entire manufacturing system in 100 days.

https://www.cnbc.com/2021/07/08/pfizer-says-it-is-developing-a-covid-booster-shot-to-target-the-highly-transmissible-delta-variant.html

Clinical trials likely already underway but organizations like the FDA are having a little trouble figuring out how to approve an mRNA change.

[dice]

even given all the vaccinations and the much improved scientific knowledge about how to both avoid getting infected and treat the infected, deaths approaching the peak level of the first wave:

[aguifs]

even given all the vaccinations and the much improved scientific knowledge about how to both avoid getting infected and treat the infected, deaths approaching the peak level of the first wave:

Holy ****. Here we go again

[coldfish]

Just to note, fatalities take some time to report and log. Sometimes weeks. Beyond that, you frequently are in the hospital for a while before you die.

https://covid.cdc.gov/covid-data-tracker/#hospitalizations

We hit peak hospitalized people around September 6th and are coming back down. Fatalities are probably near their peak at 1520 per day on a 7 day average. We hit 3600 in the winter.

https://covid.cdc.gov/covid-data-tracker/#trends_dailydeaths

Most people think this wave will begin to recede but not nearly as low as we got over the summer setting us up for another wave in the winter.

[dougthonus]

Yeah, they can modify the mRNA vaccines really quickly. The Pfizer CEO said they could change over the formulation of the entire manufacturing system in 100 days.

https://www.cnbc.com/2021/07/08/pfizer-says-it-is-developing-a-covid-booster-shot-to-target-the-highly-transmissible-delta-variant.html

Clinical trials likely already underway but organizations like the FDA are having a little trouble figuring out how to approve an mRNA change.

Not even remotely my field, but what do they do with flu shots? It would feel like the process is the same here. I wouldn't think an mRNA deliver system should change that.

[dougthonus]

One thing that annoys me about much of the COVID talk is that the vaccine was originally planned to stop transmission. You don't get a polio vaccine to get a lesser version of polio or a chicken pox vaccine to get a lesser version of chicken pox. You get these things to wipe it out.

Now many scientists are saying we're not sure we should make delta specific versions of the vaccine because it might start a never ending sequence of boosters and changing vaccines, and the vaccine protects against severe illness which is its purpose. Well no. The purpose, if possible, should be to end COVID. If the vaccines are allowing breakthrough cases to be common but the illness to be less severe, then that isn't going to help end COVID because the vaccinated can still spread it readily.

Obviously that goal may no longer be achievable and a vaccine that prevents severe illness creates a better outcome than not having it at all, but clearly if you could adapt the vaccine right now to be stronger against delta, even if you didn't give boosters but just gave better shots to the unvaccinated, then it would be much better than not doing that. It's a ridiculous assertion that we shouldn't be updating the vaccines for as long as we are creating them to best protect against whatever is currently available. It's so laughable on the surface that I can't believe it's even suggested.

We should be constantly modifying the vaccine like the flu shot to give it the best chance to protect against whatever is there. Who knows what the end game is here. Maybe it's that the world just develops enough antibodies that it's just another mild respiratory disease, maybe we can still wipe it out, maybe it requires yearly boosters and without them remains deadly. Who knows. What I can be pretty confident is that modifying the vaccine to be more effective can only help and not hurt.

[coldfish]

One thing that annoys me about much of the COVID talk is that the vaccine was originally planned to stop transmission. You don't get a polio vaccine to get a lesser version of polio or a chicken pox vaccine to get a lesser version of chicken pox. You get these things to wipe it out.

Now all the scientists are saying we're not sure we should make delta specific versions of the vaccine because it might start a neverending sequence of boosters and changing vaccines, and the vaccine protects against severe illness which is its purpose. Well no. The goal should be to end COVID. If the vaccines are allowing breakthrough cases to be common but the illness to be less severe, then that isn't going to help end COVID because the vaccinated can still spread it readily.

Obviously that goal may no longer be achievable and a vaccine that prevents severe illness creates a better outcome than not having it at all, but clearly if you could adapt the vaccine right now to be stronger against delta, even if you didn't give boosters but just gave better shots to the unvaccinated, then it would be much better than not doing that. It's a ridiculous assertion that we shouldn't be updating the vaccines for as long as we are creating them to best protect against whatever is currently available. It's so laughable on the surface that I can't believe it's even suggested.

We should be constantly modifying the vaccine like the flu shot to give it the best chance to protect against whatever is there, and the vaccine may end up needing to be a yearly booster like the flu and have to fit into the medical systems like other vaccines / flu shots do.

Random comments:
- Not my field of expertise like you but I'm a cleaner so I'm kind of used to it. I have read waaaay too much technical stuff in the last year just to understand.
- As far as your comment on how the flu shot is approved, I have not been able to determine the actual methodology. Its surprisingly hard to find out how the flu shot is approved annually. I think there is a lot of hand wringing as far as changing the covid vaccine because no one wants to make the call and be wrong despite the fact that delta is like 99.5% of cases in the US and the odds that the next variant is a delta mutation are extraordinarily high. I STRONGLY agree that the arguments against updating at this point are asinine.
- Speaking of asinine, I'm going to go off here. Asinine is kind of par for the course for this field (epidemiology). When you looked at the data early on, it was obvious that it was airborne. There are countless other things that they have completely crapped the bed on. Testing, testing accuracy, etc. This seems like it was a rather insular group and their methods are really behind the times. When you expose their thought processes to other hard sciences they frequently look like fools. I sure hope they can pull their heads out of their asses and learn something here. Doing things like updating building codes for ventilation could probably tamp down on everything from covid to the flu and common cold.
- If there was a chance of getting rid of covid, that window passed well before we even knew it existed. It was already spreading globally when we first started reading stories of it in December 2019. Once a virus gets to that point, its going endemic. We have only been able to get rid of smallpox. To a large degree, we were all lied to.