Continuation The One Covid-19 Science and Medicine Thread Part 4

[zooterkin]

Originally Posted by Cosmic Yak

https://www.worldometers.info/coronavirus/country/uk/

I mean a graph of the ZOE Covid study daily figures. The official daily ones are completely inaccurate now.

[Chris_Halkides]

At substack Eric Topol wrote, "To recap, we have a highly unfavorable picture of: (1) accelerated evolution of the virus; (2) increased immune escape of new variants; (2) progressively higher transmissibility and infectiousness; (4) substantially less protection from transmission by vaccines and boosters; (5) some reduction on vaccine/booster protection against hospitalization and death; (6) high vulnerability from infection-acquired immunity only; and (7) likelihood of more noxious new variants in the months ahead...Congress should immediately allocate for an Operation Warp Speed (OWS)-like initiative to bring nasal vaccines over the goal line. Three of these are in late stage clinical trials and success of any would markedly ameliorate our problems of transmission, no less the alluring aspect of achieving mucosal immunity and being variant-proof."

He also drew attention to a mutation in BA.2.12.1, namely L452Q. This is leucine (a very non polar side chain) to glutamine (a polar, uncharged side chain). He did not elaborate on this point.

[Puppycow]

An interesting topic in the New York Times:

How Often Can You Be Infected With the Coronavirus?

Quote:

The spread of the Omicron variant has given scientists an unsettling answer: repeatedly, sometimes within months.

Quote:

An infection with Omicron produces a weaker immune response, which seems to wane quickly, compared with infections with previous variants. Although the newer versions of the variant are closely related, they vary enough from an immune perspective that infection with one doesn’t leave much protection against the others — and certainly not after three or four months.

Still, the good news is that most people who are reinfected with new versions of Omicron will not become seriously ill.

So, it's actually going to be not unlike the "common cold" coronaviruses from now on. Maybe deadlier than those in the short term, but over time, assuming the same evolutionary pressures, why wouldn't it become very similar to those other human coronaviruses in the long term? It has already shown a tendency to evolve into more infectious, but less deadly variants. I don't know if that's inherently less deadly, or that humans are rapidly becoming resistant or resilient to it through vaccination and prior exposure.

[Puppycow]

Actually I don’t think I know about this individual. But those claims appear to be ludicrous on their face. I don’t think I want to know.

I do think that there is room for rational debate over whether all of the interventions were ultimately worth it or not. But the debate should be based on reality, not fantasy. The vaccines at least have been a net benefit. That much seems to be quite obvious. Measures that bent the curve in the first year and a half of the pandemic and prevented the hospitals from being overwhelmed were also a net benefit. But at a certain point, the marginal benefits to vaccinated people began to diminish and I think we’ve reached a point where the most heavy-handed approaches like those being taken in China are not yielding a net benefit anymore.

[Puppycow]

Originally Posted by Chris_Halkides

At substack Eric Topol wrote, "To recap,.

Either he’s too pessimistic or everyone else is too optimistic. I mean, he’s even accusing the CDC of being too complacent.

Time will tell. Either time will prove him right and he will be a genius and a prophet or these dire predictions will appear to be increasingly hysterical as time goes on.

He does have a good point though about how long it seems to be taking to get a new version of the vaccines ready.

Consider this: more time has passed since the first Pfizer vaccine was approved than it took to develop the vaccine. Is it taking longer the second through than it did the first time? Seems counterintuitive.

[Dr.Sid]

It's not taking longer. There is just no demand at the moment. We are simply waiting, till **** hits the fan again.

[RecoveringYuppy]

Originally Posted by Puppycow

Seems counterintuitive.

Would you expect molecular biology to be intuitive?

If you want an answer that would appeal to intuition consider that maybe the first vaccine took advantage of the obvious biological markets to target and the second has to target the less obvious and possibly more evolutionarily advanced markers.

[marting]

So far IHME's projections are holding up

80k/day (7 day average) as of now. Estimates that only 12% of infections are caught so actuals are around 500k/day. Deaths fairly flat and declining to about 200/day by the end of June.

https://www.healthdata.org/sites/def..._America_4.pdf

A most curious set of projections is shown in figure 24.1 which shows 4 different models. Three of the four show virtually identical declines but the fourth (SIKJalpha, a UCSD model) is wildly different with deaths/day increasing rapidly to 15,000/day by Aug.

So much for models.

[marting]

Originally Posted by Puppycow

Either he’s too pessimistic or everyone else is too optimistic. I mean, he’s even accusing the CDC of being too complacent.

Very pessimistic I think. For instance he says that vaccines are now only 80% effective against hospitalization so is a 4 fold increase over the 95% effectiveness seen in the Delta wave. But that misses the impact of the much higher immunity levels from vaccines and everything though Omicron. It also doesn't factor in the lower severity of Omicron and it's progeny. Also, it's not surprising vaccine effectiveness against hospitalization is down with a large percentage of unvaccinated being previously infected and so having some degree of immunity.

My take is that Eric is concerned that complacency will result in not doing the rapid research and deployment of advanced vaccines such as pan coronavirus vaccines. Especially because the more rapid evolution of SARS-CoV-2 has the potential to produce a much more pathogenic virus. Evolution won't select for that but it could be an accident of evolution just as the more pathogenic Delta was.

Hospitalizations have been going up but ICU rates are stable. We will probably see some further increase but nowhere near the Omicron Jan. wave. So many have been vaccinated and/or infected at this point that existing immunity seems to be keeping people from getting serious disease/dying even while not stopping infection.

I don't expect a return to widespread masking/closing schools and such absent a new, virulent variant. Certainly possible and it needs to be planned for and detected as early as possible if it happens. But I don't expect a materially more virulent strain to appear since Omicron infected huge numbers and spawned a lot of variants with no indication of any with increased virulence.

[Chris_Halkides]

Originally Posted by Puppycow

Actually I don’t think I know about this individual. But those claims appear to be ludicrous on their face. I don’t think I want to know.

Which individual do you mean? If you mean Professor Topol, I first became acquainted with him via his twitter feed. He was debunking the story because of an amino acid sequence similarity between the spike protein and another protein, that the vaccines could cause infertility. IIRC there was a pentapeptide for which four of the five amino acids (1, 2, 4, and 5) were the same between two proteins, but there was a large difference at position 3. Professor Topol thought that five amino acids was too short to be of immunological significance in this regard. I don't have a link to this particular tweet right now, but I will keep looking. Since then he has helped to debunk other myths.
EDT
I found a discussion of the infertility myth, although I am still coming up empty handed regarding Dr. Topol's twitter discussion. Written using the one-letter code for the amino acids, the two sequences were VVLQN in syncytin-1 and VVNQN in the spike protein. The side chain of L (leucine) is hydrocarbon and therefore non polar. The side chain of N (asparagine) is moderately polar, because both H-bond donors and H-bond acceptors are present. Regarding the twitter discussion, IIRC Dr. Topol asked one or more immunochemists, and a five-amino acid stretch was not long enough for it to be likely that antibodies directed against the spike protein would cross react with syncytin-1.

[marting]

I consider Topol one of the most consistent, credentialed, observers of this pandemic. He was an early advocate of vaccination, but he was also critical of the really poor data collection/analysis of "breakthrough" infections which were clearly climbing well beyond the 95% efficacy of the original Modena/Pfizer studies. As time went on and studies out of Israel and UAE showing declining efficacy in the face of both Delta and time after vaccination, he strongly pushed for recognition and response to this. To the point he was even accused of being an anti-vaxxer. That was ridiculous. He has consistently pointed out the high degree of effectiveness against severe disease.

While Topol is emphasizing the risk side of things based on the rapid evolution of more infectious variants he has not, unlike some that should know better, jumped on the atrocious "study" claiming that Omicron, Delta, Alpha, and the original strain have near identical virulence. Rather he's using legit stats to press for accelerated vaccine research and deployment.

Topol's twitter feed is my goto for the most up-to-date info.

[marting]

Eric Topol says, in a tweet earlier today:

https://twitter.com/EricTopol/status...CgueORtLIqAAAA

Quote:

Hospitalization and ICU admissions in the United States

The absolute number is still low compared with the Omicron (BA.1) wave. But the rate of rise (log-plots) is similar to the Delta wave

However, the actual numbers for the last 12 days and a similar period in Delta shows the Delta growth was 75% while the current Omicron growth is 33%. I wouldn't call that similar.

[Puppycow]

Originally Posted by Chris_Halkides

Which individual do you mean?

Actually I was responding to a post that appears to have been moved to the conspiracy theory thread by a moderator. So my post is no longer in its original context. The person referred to is Steve Kirsch. Here is the post I was responding to.

[Puppycow]

I would like to point out that Worldometer has been tracking Covid deaths since the beginning of the pandemic and for about a two year period worldwide deaths as a moving average had been around 5,000/per day or higher, since April 2020 until this year. At times over 10,000/day. They are now down to less than 1,700/per day and appear to be continuing a downward trend.

https://www.worldometers.info/coronavirus/

(Scroll down to daily deaths and check the 7-day moving average box)

Maybe there's a better source for the same data, but I don't know. I don't yet see any sign of deaths being on the rise again (worldwide). Cases are another story perhaps, but deaths at least are now considerably lower than they have been at any time for a period of almost 2 years.

[marting]

Real world evidence that Paxlovid and Molnupiravir are effective with Omicron. While not as effective as with Delta which is where they were tested, they still show considerable effectiveness with Omicron. Especially considering the drugs were started on hospitalized patients. Trials were with symptomatic patients earlier in the infection.

Retro study in Hong Kong.
https://www.medrxiv.org/content/10.1....19.22275291v1

[The Atheist]

Originally Posted by marting

Real world evidence that Paxlovid and Molnupiravir are effective with Omicron.

Now, if we can just get the cost reduced to a point where we stop young people dying, it might be worth knowing.

[marting]

Well, this is interesting. Over the last couple months there has been a shift in likelihood of hospitalization v whether "fully vaccinated" (2 doses) or "fully vaccinated with booster(s)"

A few months ago the risk of hospitalization was lower for boosted v fully vaccinated. Now it's actually higher for boosted. Strange.

Further, the difference between vaccinated and un-vaccinated has been dropping. Unvaccinated is still much more likely to be hospitalized but the benefit of vaccination against hospitalization has been decreasing. Eric Topol has been commenting on this saying hospitalization effectiveness has dropped to 80% or so from 95% with Omicron. Looks to be even more with the latest variant.

https://www.sandiegocounty.gov/conte...19%20Watch.pdf

From Dates: 4/10-4/23/2022
Per 100k in each group

Not "fully vaccinated" 0.52
"Fully vaccinated" 0.21
"Vaccinated and boosted" 0.28

That said, overall deaths/hospitalizations are quite a lot lower than back in Jan. So even if vaccinations aren't providing the benefit they did back in Delta days or even in the initial Omicron days, the overall impact of the new variants is less in all groups.

[The Atheist]

Originally Posted by marting

A few months ago the risk of hospitalization was lower for boosted v fully vaccinated. Now it's actually higher for boosted. Strange.

Wouldn't that be an expected result of boosters being heavily skewed towards older people?

I notice in NZ that the booster rate for 65+ is very high, tapering down to next to nothing for 18-30s. I imagine other countries are similar.

It's also why we need the bloody Paxlovid supply to be sorted asap!

[marting]

Originally Posted by The Atheist

Wouldn't that be an expected result of boosters being heavily skewed towards older people?

I notice in NZ that the booster rate for 65+ is very high, tapering down to next to nothing for 18-30s. I imagine other countries are similar.

It's also why we need the bloody Paxlovid supply to be sorted asap!

Yeah. Could be. But here in San Diego booster rates have been pretty high for older people since the first of the year. However, recently more younger people have been getting covid at higher rates. Since the overall numbers hospitalized are still quite small, that may be the cause. But the drop in ratio of boosted/not vaccinated to under 50% from >90% 6 months ago surprised me. Bigger change than what I would expect. But if the drop from 95% to 80%, which Topol has noted is accurate, then the age shift could easily explain the rest.

Of course what's needed are age adjusted numbers. Have to wait for a study.

Edited to add:
CDC has just changed its recommendations to urge people over 50 to get a second booster if over 4mo from the last:

https://www.nytimes.com/2022/05/20/u...d-booster.html

Quote:

The C.D.C. said it was changing its advice because of a steady rise in infections over the past month, coupled with “a steep and substantial increase in hospitalizations for older Americans.”

[The Atheist]

Originally Posted by marting

Yeah. Could be. But here in San Diego booster rates have been pretty high for older people since the first of the year. However, recently more younger people have been getting covid at higher rates. Since the overall numbers hospitalized are still quite small, that may be the cause.

There's also the fact that oldies were boosted first, so have the most-waned efficacy.

Hence this:

Originally Posted by marting

Edited to add:
CDC has just changed its recommendations to urge people over 50 to get a second booster if over 4mo from the last:

I'm expecting the same to happen here within days, and since I was boosted in January and we're just hitting winter, I'm keen to get that 4th shot.

[marting]

Originally Posted by The Atheist

There's also the fact that oldies were boosted first, so have the most-waned efficacy.
...CDC change....
I'm expecting the same to happen here within days, and since I was boosted in January and we're just hitting winter, I'm keen to get that 4th shot.

I've been waiting so when I get second boost it will provide peak effectiveness with max overlap of the wave. That's pretty close to now since I think the wave will peak here in about 1.5-2 months. Growth rate (33%/12 days) is slower than omicron (75%/12 days). Also will probably get a flu shot at the same time. It has a similar decay and I've been watching flu stats to optimize jab timing. Haven't had a flu shot in almost 3 years as it was pretty much non-existent but the optimum time looks like now. Flu, while still well below the normal winter peaks is well above the norms this time of year.

[Puppycow]

Originally Posted by marting

Well, this is interesting. Over the last couple months there has been a shift in likelihood of hospitalization v whether "fully vaccinated" (2 doses) or "fully vaccinated with booster(s)"

A few months ago the risk of hospitalization was lower for boosted v fully vaccinated. Now it's actually higher for boosted. Strange.

It could be a timing issue. As far as I can tell, that data lumps people of all ages together, and I'll bet that if you were to only look at people over 75 and compare them with people of similar age, you'd get a different result. And another thing is that probably there's a self-selection bias going on, where the people who are most vulnerable either because of age or pre-existing conditions are more likely to get boosted.

Quote:

https://www.sandiegocounty.gov/conte...19%20Watch.pdf

I noticed something strange about the graph for Confirmed Cases on page 7. On the right side, it suddenly becomes all orange. Maybe that's just because data for that period is incomplete. But in that case I think they should use a different color, like grey, and label it as unknown.