To Vaccinate or Not---The Rat Flu Odyssey Continues

[skaredshtles]

Is there a difference between asking people to ignore and asking for a ban?

Different strokes and all, just curious since ban talk usually gets full hand wringing treatment.

Fuck if I know. But check it:

[Summit]

Several times today I've been asked by colleagues some variation of, "how much longer this will go? on I can't do it!" Or simply been told, PAPR in hand, "a few more months of this and I'm quitting healthcare." So many already have.

I reassured with facts, but I couldn't feel it in my heart.

I mentally wrote COVID a letter this weekend after dealing with yet another COVID emergency on Saturday night:

Dear Asshole Virus,

You suck. I know I've threatened to quit like 50 times in the last 2 years, but I really thought we'd be done singing the Delta blues and entering the controlled phase of the pandemic, also revered as "endemic." But no. You had to Omicron all over this shit show. I am embracing the suck and looking at the epi curve burning brightly, but quickly. No mas, por favor. No next wave. No Megatron variant. If this isn't done by the spring, then I'm done with this field.

Peace, Summit

[skaredshtles]

Putting people on ignore just because you're tired of hearing things you don't agree with is not all that different than hiding in echo chambers of like minded people.

But putting purposeful morans/trolls on Ignore is just good business.

[NakedShorts]

https://www.yahoo.com/news/israeli-v...103152468.html


Also, after catching the Rona you will notice you will be much less fearful of it and others.

[Summit]

To boost against Omicron, we are best off using an Omicron targeted booster, which despite the speed and agility of mRNA, will be deployed at the tail end of the Omicron wave.

[NakedShorts]

Is it so no el that injecting your body with poison over and over again could be bad. Sure you will fight off Covid but everything else will get you...

[SumJongGuy]

Is it so no el that injecting your body with poison over and over again could be bad. Sure you will fight off Covid but everything else will get you...

Lemme guess.. 75% of ventilator patients are vaccinated for........................ MEASLES?

[altasnob]

To boost against Omicron, we are best off using an Omicron targeted booster, which despite the speed and agility of mRNA, will be deployed at the tail end of the Omicron wave.

Moderna's "Omicron coronavirus variant will enter clinical development in the next few weeks and the company expects to be able to share data with regulators around March"

https://www.reuters.com/business/hea...ch-2022-01-17/

They can't just skip the clinical trials though, correct? So there is no way to speed that up?

[LongShortLong]

The current CDC estimate is that Delta is now .5% of all cases.

Imma disagree with the CDC. IIRC, they are guessing, projecting from month old data. Eyeballing local sewer data (from yesterday) says 10-20% delta. https://soe-wbe-pilot.wl.r.appspot.com/charts. Also delta prevalence has increased in the last month. Omicron has increased faster.

CDC needs to do a better job of collecting data, sponsoring studies, convening colloquia, and integrating new tech. They are half blind and consistently several steps behind. The leader, but not a leader.

[wooley12]

Are you that ignorant at this point?

[NakedShorts]

[liv2ski]

Guys, this is not Rocket Science, just apply a little common sense for fucks sake

[LongShortLong]

Lemme guess.. 75% of ventilator patients are vaccinated for........................ MEASLES?

Could be #fakenews
Could also be Simpson's paradox, a type of faulty analysis. Aggregate your data by age, then then vax status. Also compare ventilator rates instead of counts. You'll find the unvaxxed are 10x more likely to be ventilated.

Thought exercise: Consider a 100% vaxxed population, where the vax provides less than full protection against ventilation. This population will have ventilator patients, and they will ALL be vaxxed. Add in some unvaxxed, and they will be mostly vaxxed.

[altasnob]

Imma disagree with the CDC. IIRC, they are guessing, projecting from month old data. Eyeballing local sewer data (from yesterday) says 10-20% delta. https://soe-wbe-pilot.wl.r.appspot.com/charts. Also delta prevalence has increased in the last month. Omicron has increased faster.

CDC needs to do a better job of collecting data, sponsoring studies, convening colloquia, and integrating new tech. They are half blind and consistently several steps behind. The leader, but not a leader.

Is the CDC in charge of sequencing? Large difference in sequencing rates between states. And states that you wouldn't think would be leaders in sequencing (like Wyoming) are:



https://www.nature.com/articles/d41586-021-03698-7

When I play around with nextstrain it sure doesn't look like there is still 10 to 20% Delta anywhere. Omicron dominates everywhere. And as far as I can tell, this is based on the latest sequencing data. I see 3% of Delta (includes both Delta variants) as of 1/8/22 in the US.

https://nextstrain.org/groups/neherlab/ncov/21K.Omicron

[bennymac]

2000 vaccinated people and 20 go into hospital

100 unvaccinated people and 10 go into hospital

NakedSharts screams "There are twice as many vaccinated people in the hospital as there are unvaccinated!"

[Mofro261]

Imma disagree with the CDC. IIRC, they are guessing, projecting from month old data. Eyeballing local sewer data (from yesterday) says 10-20% delta. https://soe-wbe-pilot.wl.r.appspot.com/charts. Also delta prevalence has increased in the last month. Omicron has increased faster.

CDC needs to do a better job of collecting data, sponsoring studies, convening colloquia, and integrating new tech. They are half blind and consistently several steps behind. The leader, but not a leader.

Er hem... your link specifically says between 1.5-7% at those locations for Delta during the last 2 weeks, none of them increasing. https://soe-wbe-pilot.wl.r.appspot.c...ncompare-delta

Note S gene and del143-5 are the same gene marker but 2 different regions. To get the Delta data, look at the del156-7 marker (also in the S gene). These deletions are found in ~90%, but not all, of the respective Omicron and Delta strains.

[LongShortLong]

Is the CDC in charge of sequencing? Large difference in sequencing rates between states. And states that you wouldn't think would be leaders in sequencing (like Wyoming) are:



https://www.nature.com/articles/d41586-021-03698-7

When I play around with nextstrain it sure doesn't look like there is still 10 to 20% Delta anywhere. Omicron dominates everywhere. And as far as I can tell, this is based on the latest sequencing data. I see 3% of Delta (includes both Delta variants) as of 1/8/22 in the US.

https://nextstrain.org/groups/neherlab/ncov/21K.Omicron

I agree the data sources disagree. What data is entered in nextstrain? Is there any effort to get a representative sample? Perhaps it's biased toward researchers choosing to sequence the hot new thing?

The sewer data I linked is only representative of the local area. I looked for the Boston data to compare, but they don't discriminate variants.

It's unclear to me why delta would go away, unless NPIs increased, or until omicron infects enough of us to raise resistance.

[skiJ]

part of my concern is looking at this as a small percentage of a Very large number is not insignificant -

700,000 new cases Daily ;
Pick your percentage -
.5% is still 3500 cases weekly ;
7% would be almost 50,000 cases of delta - and

please remember variants develop in those infected, when there is also a susceptible population.
from my perspective given our omicron - and delta - experience, everyone could be at risk for a new variant, And there are certainly sufficient covid cases for variants to develop.

Summit's letter of Resignation is amusingly sobering.

Please ,,, try to find your long view --

tj

[SumJongGuy]

But putting purposeful morans/trolls on Ignore is just good business.

Agreed
That's approaching harassment (to everyone) if they're nefarious instead of honestly believing what they're debating..

[jono]

Aggregate your data by age, then then vax status.

This^^. All the "whole population" data that's not stratified by age has been suspect (or demonstrably misleading) for a year now. You can't ignore the fact that vax rates in the general population are pulled up by the old while bad outcomes among the unvaccinated are pulled down by the young. Because the old are far more vaccinated.

Maybe Liv2ski can show that better with a Venn diagram.

[LongShortLong]

Er hem... your link specifically says between 1.5-7% at those locations for Delta during the last 2 weeks, none of them increasing. https://soe-wbe-pilot.wl.r.appspot.c...ncompare-delta

Note S gene and del143-5 are the same gene marker but 2 different regions. To get the Delta data, look at the del156-7 marker (also in the S gene). These deletions are found in ~90%, but not all, of the respective Omicron and Delta strains.

Thanks, that;s interesting. I was making a similar comparison, but using omicron's Del 143-145 vs S (or N). In the link I posted, S and N were already high when omicron appeared, and the gap between S/N and Del 143-145 remained and grew. I assume this gap is non-omicron variants, but you say some omicron variants do not have Del 143-145, so the omicron fraction would be greater than I claimed.

[SumJongGuy]

Could be #fakenews
Could also be Simpson's paradox, a type of faulty analysis. Aggregate your data by age, then then vax status. Also compare ventilator rates instead of counts. You'll find the unvaxxed are 10x more likely to be ventilated.

Thought exercise: Consider a 100% vaxxed population, where the vax provides less than full protection against ventilation. This population will have ventilator patients, and they will ALL be vaxxed. Add in some unvaxxed, and they will be mostly vaxxed.

It also doesn't state they are all on the ventilators for COVID. I mean weren't a bunch of people already on ventilators before COVID was a thing? People are intubated for all kinds of things every day. I don't see them saying they're only counting COVID patients on ventilators there..

[bodywhomper]

https://twitter.com/EricTopol/status...26194623086596

Thanks!! And thanks, jono for the journal article link.

Topol is SO prolific on Twitter, it’s very comprehensive but hard to keep up. There’s a good interview and conversation between Bob Wachter and Topol last week. https://youtu.be/lCAvFHd3B38

[Mofro261]

It's unclear to me why delta would go away, unless NPIs increased, or until omicron infects enough of us to raise resistance.

Delta went away because it does not have a fitness advantage over Omicron. It simply cannot compete with Omicron as well for hosts due to it's increased transmissibility, despite not being quite as replication competent( average CT's 1 log higher for Omicron, 23 vs 20 for Delta). Just like Wu-1 was obliterated by Alpha, and then Alpha completely was wiped off the map by Delta, now Delta bows out to Omicron.

Good thing too as much of the data suggests infection with Omicron will not cross protect against any other strains in unvaccinated people, but breakthrough in vaxxed individuals do look to have cross-protection against all strains but Beta (also a goner).

Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination. https://www.medrxiv.org/content/10.1....13.22269243v1
(UCSF, Jen Doudna)

Collectively, our study shows that while the Omicron virus is immunogenic, infection with this variant in unvaccinated individuals may not elicit effective cross-neutralizing antibodies against other variants. In vaccinated individuals, however, Omicron infection effectively induces immunity against itself and enhances protection against other variants.

Also- Nextstrain is a compiler of covid data from the network of worldwide GISAID affiliates. https://www.gisaid.org/

[teledad]

That MedRxiv link is missing a character, here's one that works:

https://www.medrxiv.org/content/10.1....13.22269243v1