Coronavirus

[bkp_duke]

To add to the b117 and b1351 discussions. We will soon have a lot of b117 infections in people with some form of immunity, through vaccines and previous infections, that will lead to evolutionary pressure for B117 to evolve to be better at infecting people with some form of immunity. Soon some form of the B117 will emerge that will be as good or better than B1351 at evading antibodies. Imo that is what we should fear.

A lot of people still seem to simplify the pandemic into Covid-19, while in fact it is a lot of of sub pandemics that are constantly evolving. Covid-21 will likely be much worse than Covid-19. I wonder when China will be able to open up again, or if they will have to have do quarantines and lockdowns until we have vaccinated everyone with a newer vaccine that covers all possible future mutation. Because once they open up they not have to face an explosion of mild covid-19, but they will have an explosion of not as mild covid-21. Even if very few people die, having hundreds of million people with flu like symptoms at the same time will not be easy.

We are already WAY far afield from the original Wuhan variant, and the Pfizer and Moderna vaccines still cover all 8 current variants very well (even B.1.1.7, B.1.351, and P.1 - the Brazil variant).

If we can just get people to get vaccinated (big problem here in the US), and get enough vaccine produced (big problem globally), the odds of this being able to move through a mutational "escape" and maintain pandemic status are low.

 

[cwerdna]

It is almost eerie how case numbers are going down, hospitalized cases are down in our county while the CDC and Fauci keep saying this is going to get worse with these new variants just beginning to spread. It's weird how some states are just declaring victory and dropping what few restrictions they had. What is going to happen when this skyrockets again? Will these people wait again until they are out of body bags to start all over again?

On the bolded part, I noticed that most mainstream news outlets (both local and national) besides focusing on other news when they talk about COVID-19 seem to focus on vaccinations (and logistical probs including lack of supply and now complications due to severe storms in many places) and case counts + declines and that and hospitalizations. That was when the US was still having over 2K to 3.xK people dying a day of COVID-19.

From looking at the graphs near the bottom of United States Coronavirus: 28,317,703 Cases and 498,203 Deaths - Worldometer, if you turn on the 7-day moving average for daily new deaths in the US, it's still above 2000/day. I mean, it's peaked and hit a decline but I remember months back, it was a big deal that the US began hitting 1K deaths per day from COVID-19 and things were "bad" back then.

I guess the US is ok with 1K to 2K deaths per day from COVID-19 now?

 

[Walesi]

A company in Finland has developed a coronavirus breathalyzer: DSA Breathpass.

30 tests/hour capacity, result in 2 minutes.

 

[Bobfitz1]

To add to the b117 and b1351 discussions. We will soon have a lot of b117 infections in people with some form of immunity, through vaccines and previous infections, that will lead to evolutionary pressure for B117 to evolve to be better at infecting people with some form of immunity. Soon some form of the B117 will emerge that will be as good or better than B1351 at evading antibodies. Imo that is what we should fear.

A lot of people still seem to simplify the pandemic into Covid-19, while in fact it is a lot of of sub pandemics that are constantly evolving.

I would expect that the rate at which C-19 and its variants can mutate and evolve is a function of the ongoing volume of new cases. If that's correct then it would seem to follow that as vaccines and herd immunity continue to reduce daily new cases, the rate at which new more contagious variants appear is also likely to decline. I expect vaccine developers going forward will be adjusting their vaccine development efforts to improve effectiveness against a wider range of likely new variants.

 

[bkp_duke]

I would expect that the rate at which C-19 and its variants can mutate and evolve is a function of the ongoing volume of new cases. If that's correct then it would seem to follow that as vaccines and herd immunity continue to reduce daily new cases, the rate at which new more contagious variants appear is also likely to decline. I expect vaccine developers going forward will be adjusting their vaccine development efforts to improve effectiveness against a wider range of likely new variants.

Only partially. It's a factor of:
1) the proof-reading error rate of the viral replication machinery (which is about 2.5X lower than influenza, for reference)
2) the number of cases

You are correct that if we can get vaccines quickly, we have a very good chance of squashing this thing, even with current variants.

 

[AlanSubie4Life]

https://twitter.com/shamezladhani/status/1361636096585654273?s=21


Seems about right; at these levels we would see a LOT of stories about reinfections, even though they are not really an issue (wrt herd immunity) if there is no underlying immune escape by the virus (note of course that this study likely does not have B.1.351 playing any significant role - B.1.1.7 does not show evidence of immune escape).

Not sure if it’s a coincidence that the efficacy of prior infection is similar to the efficacy of the first vaccine dose (within the wide confidence intervals). Probably not. This is probably on average an older cohort than the vaccine trial so making these comparisons is probably not that meaningful in any case.

 

[AlanSubie4Life]

Interesting blurb on B.1.1.7. (Tweet has nice GIFs.) One interesting implication is that some of the increase in transmissibility may be from a reduction in serial interval (time between transmissions) rather than a change in R0, which make it not quite as fearsome (in terms of changing the herd immunity threshold). These two factors both impact the final exponential growth rate, but fast transmission doesn’t affect the herd immunity threshold. It also implies that the NPIs we are all used to using may continue to be nearly as effective. In reality, B.1.1.7 is probably also more transmissible, but the exact degree matters for pandemic trajectory.

https://twitter.com/viruswhisperer/status/1360991304134631427?s=21

 

[chronoreverse]

Slightly not on topic but XKCD is great as usual:

 

[renim]

2 studies from Australia

Innate cell profiles during the acute and convalescent phase of SARS-CoV-2 infection in children | Nature Communications
compares the response of Children infected VS Children exposed (but negative on PCR testing) ie how children fight of COVID19 without being infected.

Immune responses to SARS-CoV-2 in three children of parents with symptomatic COVID-19 | Nature Communications
further detail within a single family unit.
"Our combined salivary and serological findings show that, despite having no virological evidence of infection, all three children developed antibody responses against various SARS-CoV-2 epitopes. Of the three children, C3, who remained asymptomatic throughout, demonstrated the most robust antibody response. We also observed that symptom resolution in A2, C1, and C2 coincided with a spike in salivary anti-S1 IgA, but not IgG. SARS-CoV-2 likely infects the salivary glands and is detectable in saliva22. Our data, therefore, provide evidence that control of SARS-CoV-2 at the site of infection may be mediated by a mucosal IgA antibody response."

 

[Jeff N]

Another study showing concern about the potential for vaccine escape with the B.1.351 variant from South Africa, this time from Pfizer regarding their mRNA vaccine.

“A laboratory study suggests that the South African variant of the coronavirus may reduce antibody protection from the Pfizer Inc/BioNTech SE vaccine by two-thirds, and it is not clear if the shot will be effective against the mutation, the companies said on Wednesday.

The study found the vaccine was still able to neutralize the virus and there is not yet evidence from trials in people that the variant reduces vaccine protection, the companies said.”

Pfizer says South African variant could significantly reduce vaccine protection

 

[TEG]

Hopefully they are working on a new vaccine variation to better protect against that mutation.

 

[Jeff N]

Hopefully they are working on a new vaccine variation to better protect against that mutation.

Yep, both Pfizer/BioNTech and Moderna have said they are working on updated vaccines that will also include mRNA for spike protein based on the B.1.351 variant.

 

[TEG]

Yep, both Pfizer/BioNTech and Moderna have said they are working on updated vaccines that will also include mRNA for spike protein based on the B.1.351 variant.

Any thoughts on timeframe to availability?

 

[alloverx]

2 studies from Australia
Immune responses to SARS-CoV-2 in three children of parents with symptomatic COVID-19 | Nature Communications
further detail within a single family unit.

I recall a video about this family and I think I posted a link to it last year. Very interesting.

 

[wycolo]

Just got Pfizer#2 today, LOL. [returns to hibernation]
--

 

[AlanSubie4Life]

Another study showing concern about the potential for vaccine escape with the B.1.351 variant from South Africa, this time from Pfizer regarding their mRNA vaccine.

“A laboratory study suggests that the South African variant of the coronavirus may reduce antibody protection from the Pfizer Inc/BioNTech SE vaccine by two-thirds, and it is not clear if the shot will be effective against the mutation, the companies said on Wednesday.

The study found the vaccine was still able to neutralize the virus and there is not yet evidence from trials in people that the variant reduces vaccine protection, the companies said.”

Pfizer says South African variant could significantly reduce vaccine protection

Weirdly inconsistent numbers and I am too lazy to look up the paper:

“The study by Pfizer and scientists from the University of Texas Medical Branch (UTMB), which has not yet been peer-reviewed, showed a less than two-fold reduction in antibody titer levels,”

In any case it’s a way better result than we have had before. It is either just 50% less (2x less) or 33% (3x less) than the prior result of about 6x (average) as I recall.

But it doesn’t really mean anything concrete, because this virus didn’t have all the mutations, and it also wasn’t the real virus (lentivirus). It may well be correlated with actual in vivo results but it’s hard to say.

So hopefully we’ll have clinical data soon.

All of these numbers, including the 6x less effective number, should be plenty to keep this vaccine effective, with efficacy nearly unchanged - if the neutralizing activity in these tests translates into actual clinical efficacy. (Because it starts with such sky-high antibody levels.)

 

[bkp_duke]

Any thoughts on timeframe to availability?

Completely depends upon the FDA. "Swapping out" the mRNA for a new strand is relatively simple. That's the beauty of this technology.

What I don't know, is how well incorporating multiple mRNA strands into a single vaccine dose works with this technology. Most certainly there is a minimum threshold of mRNA that you need per variant to induce an adequate immune response, but it's not clear to me what that is (probably 25% or so of the regular dose, giving the ability to incorporate possibly 3 variant strands into one dose - assuming some excess for losses, etc. - but that's a complete guess on my part). Might also be better to go with a booster shot, composed entirely of just the new strand.

This is what clinical trials are designed to tease out.

 

[TEG]

From the time they come up with a new tested/approved strand, I don't know how long it takes to put that into the production pipeline and get it through all the logistics into people's arms. Is it just a matter of dropping a new "template" into the production machinery and within days(?) or weeks(?) the vaccinations centers would have the updated batches? For instance, I have no idea how much "lag" exists in the mass scale replication equipment. I also have no idea how many different production factories would need to get updated.

 

[bkp_duke]

From the time they come up with a new tested/approved strand, I don't know how long it takes to put that into the production pipeline and get it through all the logistics into people's arms. Is it just a matter of dropping a new "template" into the production machinery and within days(?) or weeks(?) the vaccinations centers would have the updated batches? For instance, I have no idea how much "lag" exists in the mass scale replication equipment. I also have no idea how many different production factories would need to get updated.

The government approval would be a far longer process than the logistics.

 

[madodel]

NEPA health networks reschedule COVID-19 vaccines due to shortages

So remember when everyone was saying just give all the first vaccine doses to as many people as possible and worry about the second dose later. Well in Pennsylvania some of the providers screwed up and gave doses that were supposed to be allotted for the second dose as a first dose. Now the state is scrambling to get people rescheduled.