Dontshootrude

JCS Criminal Psychology YouTube channel needs to be on the first page. It is one of my favorite channels.

At this time last year GT was down 52-7. So this is a nice change.

COVID vaccine immunity is waning — how much does that matter?

I've only read the letter. Do you have a link to the full report?

Oh, I agree. I just like to go with the flow. See where it leads me.

Interesting MMWR published today. https://www.cdc.gov/mmwr/volumes/70/wr/mm7038e1.htm?s_cid=mm7038e1_w Key table: Moderna dominance continues. This is in 21 hospitals. It is good news, but Jesus, the UK and Israel are making the US public health system look horrible. Our data sets are small, inconsistent, and fragmented. It is really difficult to get good large scale data sets in the US in a timely fashion. The pandemic has really exposed how vulnerable and unorganized we are.

Funny/CSB story. CDC has protesters come and go, but there is one dude that is always right outside CDC rain or shine, hot or cold, with about 10 signs walking up and down the sidewalk that say things like "Infertility," "Genocide," "Obey," etc. As crazy as he is I tip my cap to him for being so incredibly dedicated and so confident in himself that he can do that just about every day by himself. It is a shame he has latched onto something this crazy, because if he would have picked something productive no doubt he would have been highly successful. Something tells me the Nicki Minaj protesters won't be so driven.

That nature review on lipid delivery of mRNA was interesting It lead me to this paper in which people got eight shots and they were continuing to develop good immune responses. That is encouraging news and helps alleviate my concerns regarding decreasing efficacy due to the immune system recognizing the capsule! As to the other papers, those were published right as we were mass deploying the vaccines. I was more concerned then, but thankfully recent data has held up well, especially against severe disease. I'm optimistic that will continue. ETA: I also found the references that highlight the diverse array of vaccine induced epitopes and how well they are holding up for the vaccines. https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1 https://www.sciencedirect.com/science/article/pii/S2666379121002044

I disagree. Truth is there are fundamental biological reasons why I think it unlikely that COVID will be able to find a mutation that will significantly escape our vaccines. When replicating, coronaviruses, including COVID, have a proofreading mechanism (PDF warning) that will verify the genetic sequence that is being replicated. It is not as robust as that in eukaryotic cells (human, mammals for example) whence the mutations we do see, but it does exist. Compare COVID to a true rapidly mutating virus like flu. Flu has two mechanisms that allow it to radically mutate in short periods of time. 1. Genetic drift - random point mutations in the genome from the highly error prone replication enzymes that lack proof reading that it uses to replicate its RNA genome 2. Genetic shift - completely swapping out entire gene segments for new ones creating a whole new unique flu virus. Only Influenza A viruses can do this which is why they are responsible for the pandemic strains. To highlight this, check out the two files attached to this post. The COVID_Variant_Alignment file are the top five variants of concern aligned against the original COVID sequence provided to CDC back in January 2020 that the vaccine was designed against. An * under the specific base means the nucleotide is the same among all six strains. Notice how much of the sequence is the same among all six, and you really must hunt to find changes. I've also attached an alignment from a surface protein of flu, a true rapidly mutating virus for comparison. Notice how inconsistent the flu is and you'll see why it is so challenging to design effective vaccines and therapeutics. Shifting back to the vaccines, the spike protein is a big protein. I've seen studies that report CD8+ (T killer cells, the ones that seek out and kill infected cells) recognizes 52 epitopes (spots on the protein). CD4+ cells (T helper cells, which help drive antibody responses) recognize 23 epitopes across the entire spike protein. I'll try to find my references for this later, but offhand I can't recall exactly which study addressed this. It is hard to imagine, given how stable COVID is, that it will find a way to alter all of these regions and still remain infectious. Comparing the Beta variant vs Delta is encouraging too. Beta is actually more genetically distant than delta and the vaccine was less effective against it compared to delta. But Delta has outcompeted it nonetheless. This is a good article that partially addresses what I'm saying above. And one finally thing I should mention regarding the immune response to the lipid capsule delivery vehicle. I wouldn't say I'm extremely worried about this. I'd just like to see it addressed before I take a shot that decreases my risk of hospitalization from 1 in 300,000 to 1 in a couple of million. COVID_Variant_Alignment.txt Influenza_H1gene_alignment.txt

Continuing our Surly literature review, I ran across a couple interesing things today. The first is more booster data relating to younger age groups than what was published in the NEJM paper I posted yesterday. This reinforces the data we have seen that in younger healthy populations the breakthrough cases are increasing but remain mild in nature. Also, this encouraging preprint out of the UK was posted today. This is of course very preliminary, but I liked the concluding statement: Given the slow mutating nature of coronaviruses I'm optimistic in the long term efficacy of our vaccines.

Not yet, but today was a pretty big day for publications. Two studies were released in the New England Journal of Medicine relating to the Pfizer vaccine. 1. A follow up study on the original 44,000+ clinical trial participants. Those that got the vaccine are continuing to do very well. Efficacy had wained from 95% to 83%. https://www.nejm.org/doi/full/10.1056/NEJMoa2110345?query=featured_home 2. This is the big one. The Israelis just published their 3rd shot trial involving over 1 million people. It's very well designed and controlled. In people 60 and older the third shot reduced severe disease by 19.5x, essentially bringing the vaccine efficacy back to what it was when they first received it. They don't specifically discuss side effects, but the absence of that data is probably a good sign. Based on this study I'm going to tell my parents to sign up for a booster. https://www.nejm.org/doi/full/10.1056/NEJMoa2114255

https://www.npr.org/2021/09/14/1036835868/elizabeth-holmes-trial-hotelier-bill-evans-goes-incognito?utm_campaign=storyshare&utm_source=twitter.com&utm_medium=social Bizarre.

One last great article for tonight. This one on the history and development of mRNA vaccines. https://www.nature.com/articles/d41586-021-02483-w

Great article on why vaccines won't cause worse variants. https://www.science.org/content/blog-post/vaccines-will-not-produce-worse-variants

Oh I don't know about that. I agree it has been clear that there are people that would benefit from a third shot, but at which age that benefit starts to be measurable will really be tied down with this study. It is the first well designed and controlled study on a large number of people regarding boosters that I will have seen. Maybe I missed a few? Please link if so.

I'll be eagerly awaiting this publication later this week. It has been ambiguous at which age at which the third shot will make sense at this point. From this sneak peak out of Israel it looks like the answer will be 60 years of age and those who are immunocompromised.

Yep. Those naïve to infection, and those that think pork makes better BBQ than beef and anyone who has liquid smoke in their house should have their ass mandated into oblivion.

Nothing. Bill Gates on the other hand has given my lab tens of millions of dollars, so maybe I should STFU and start moving product.

The data supports your position. Truthfully, I think we are making a big mistake by drawing a line in the sand with regards to vaccination and disregarding people in your situation. If I were in charge, that official antibody test that proves that you had it and mounted an immune response against the virus should be good enough to count as "vaccinated" and you shouldn't be subject to any punitive measures. At the very least they should only require you to get a single mRNA shot. But it is what it is. You'll probably need to get it, particularly if you want to travel and if the mandates end up sticking. Here is a little blurb with links to the studies that I wrote to someone who asked the same thing a little while ago: Studies are showing no real world benefit from getting the vaccine after recovering from infection, and there is plenty of protection to reduce the chances of reinfection and severe disease. And we also have studies demonstrating immunity from natural infection will be long lasting, possibly even providing lifetime protection, and might be more robust than vaccination alone. With regards to vaccine breakthrough, reinfections among those who recovered from natural infection tentatively don't show as high of viral loads as those that were only vaccinated. There are a couple studies that demonstrated the neutralizing antibodies get significantly better months after infection and are able to better neutralize the variants, likely because the remnants of the virus has been shown to stay in your small bowel for months after the infection is over. This allows your immune system ample time to learn and develop a better response. The data on those that are getting vaccinated after recovering from COVID does show that you do get a better immune response than those that only had the vaccine or recovered from infection and there are no significant side effects from making that choice. It is actually paradoxically good, almost like 1+1=4. In pregnant women, getting vaccinated will provide a benefit to the child, as that boost will provide better protection during the pregnancy and while nursing after birth. There has been no benefit to getting the second mRNA shot in COVID recovered individuals, so if you are young and healthy and need to be vaccinated for work or travel the Johnson and Johnson shot would be a good option so you don’t have to deal with the hassle of getting the second shot. The one exception to this is young females should probably stick with the mRNA vaccines as the risk of the rare clotting condition CVST is not observed in the Moderna or Pfizer vaccines. And don’t misconstrue what I’m saying. If you haven’t had COVID the choice is still clear. Vaccination is by far your best option for gaining immunity. The relative risks of the vaccine vs getting COVID greatly favor vaccination. The mRNA vaccines are holding up very well and appear to be generating long term immune cells, and when measuring spike specific immune responses the vaccine appears to have a slight edge on natural infection. The difference between vaccine vs natural immunity is likely not going to be meaningful. Say we are executing someone by firing squad, and you decide to put 11 people on the line instead of 12. Does that really matter?

This is a great article. It is nice seeing top level scientists push back against the politicians. Some of my favorite excerpts: We need to be shifting focus to get more vaccine to resource poor parts of the world where the virus is currently raging out of control. If we are going to see a variant that can escape the vaccines to a high degree it will likely be the result of the uncontrolled spread in these areas. This ends faster, we save more lives, and we can get the economy back to normal faster when all of humanity has access to the vaccine and not just us.

I think it is safe to say that if those 600,000+ had been vaccinated a significant portion of them would have lived. That statement shouldn't tickle any mathletic autism bones.

The UK public health system has been a wealth of information throughout the pandemic. I've been extremely impressed with them. Today they published an in depth breakdown of the breakthrough cases that resulted in death among their population. Main points: Table 1 is really interesting, and shows how important the second shot is. Other interesting things to note: The fully vaccinated COVID deaths have a median age two years older than the unvaccinated (84 vs 82) and looking at the numbers compared to the unvaccinated, we are talking about very few people relative to the overall population. 98.8% of their COVID deaths are either unvaccinated or not fully vaccinated. It is remarkable how well the vaccines are working.

I have had the Koda 16 for a year now and just converted mine to natural gas this weekend. I love it.

Yep. Their decision to separate the shots by an extra week and tripling the amount of mRNA seems to be really paying off. That said, I got Pfizer in January and I'm still not seeking out a booster. In my age group it is still working fine.