COVID-19 and SARS-CoV-2 info

[Like Ra]

The estimated R₀ of Delta is somewhere between 5 and 8.

I've never seen this, any sources?

Sinovac's efficacy rate of roughly 50%

Janssen is just a bit better, than Sinovac, Astra is better, than Janssen, Sputnik (in theory) is a bit better, than Astra (yet the quality is very unstable, so should also be avoided), but fortunately US and EU have access to Moderna/Pfizer - the future of the vaccination (as monoclonal therapy is way beyond the reach of 99% of population).

Speaking of Delta - for some strange reason (vaccination?) the level of Delta in NL is quite stable - 0.3-0.5% for weeks. NL had 4 waves, though. While IN only 2.

[Like Ra]

Did you guys have any weird post-vaccination effects? I could not even touch my shoulder for a couple of days after Pfizer. My wife had headache, shoulder and joint pain for ~3 days after Moderna.

[boundsolo]

Did you guys have any weird post-vaccination effects? I could not even touch my shoulder for a couple of days after Pfizer. My wife had headache, shoulder and joint pain for ~3 days after Moderna.

I had the Pfizer shot. The following day every joint, especially my hips, hurt and I was exhausted. Just the one day and everything was back to normal. My wife had no effects at all.

[Vixien]

My wife and I received AZ. 24 hours later we got a fever. I had 37.5 C, she up to 38.5 C We felt very exhausted, the wife's arm hurt a lot. Everything passed in the next 24 hours. We are scheduled for a second dose at the begining of the July.

[Zooy]

i did not have any effects with either pfizer, but my wife was a bit sick for a day after her second moderna shot.

[Penguin]

Did you guys have any weird post-vaccination effects? I could not even touch my shoulder for a couple of days after Pfizer. My wife had headache, shoulder and joint pain for ~3 days after Moderna.

One guy I know had some serious pain and swelling in his shoulder for a day or so post injection.  He was more or less out of it.

I got vaccinated with Moderna, two shot four weeks apart.  I had an achy shoulder for a day or two, but nothing worse than what I'd had when I got the pneumovax shot a decade ago, and as pain went, it was meh.  On a 1-10 scale, maybe a two.  Maybe.  I expected much worse.

I suspect it's a total crapshoot.

[Penguin]

The estimated R₀ of Delta is somewhere between 5 and 8.

I've never seen this, any sources?

Yes, here are a couple.

First, here's a piece that's up on PubMed, The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant.  Look at Figure 1.  Here's a higher resolution copy, from the preprint copy at imgur:

here

What this shows is that an R₀ value of about 4.5 for Alpha, is the one practicing epidemiologists are actually using.

And Delta is being reported as about half again as infectious as Alpha!

There's also a recent piece on the BBC news that cites an estimated Alpha R₀ of between 4 and 5, and an estimated Delta R₀ of between 5 and 8.

So I based my back-of-the-envelope calculation on the minimum value in that Delta R₀ range estimate.

[Like Ra]

Ah, it's "potential", not "real".

A good comparison! I love graphs!

[Penguin]

Ah, it's "potential", not "real".
A good comparison! I love graphs!

No, what it is, is "estimated".


Delta hasn't been around nearly as long as Alpha, and it isn't as well understood.  Note that in the BBC piece, the older strains have smaller uncertainties.
But R₀ is always estimated, even for bugs that have been around for a while, since it represents

• the reproduction number in the absence of immune individuals, and
  
• it can be calculated from differing models that inevitably will give differing results.
  

See the wikipedia page for R₀.

[Penguin]

The article to which most conspiracy theorists refer:

"A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence"
Published in "Nature Medicine" on 09 November 2015

https://www.nature.com/articles/nm.3985
https://doi.org/10.1038/nm.3985

Abstract

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV underscores the threat of cross-species transmission events leading to outbreaks in humans. Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations1. Using the SARS-CoV reverse genetics system2, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis. Evaluation of available SARS-based immune-therapeutic and prophylactic modalities revealed poor efficacy; both monoclonal antibody and vaccine approaches failed to neutralize and protect from infection with CoVs using the novel spike protein. On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations.

Sometimes you can mine gold by going up-thread.  This gem went completely under my radar last year.  Belated thanks for posting it.  I wish I'd seen it earlier.

I'm very surprised to read that the conspiracy theory crowd seems to like this piece.  I'd have thought they'd hate it.  Since it helps undermine their conspiracy theory de jour, namely, that Covid got started in a virology lab.  Don't even get me started about what I think of the "Wuhan Virology Lab" story.

The way I'm reading it, it presents a solid bit of circumstantial evidence in favor of the contention that Covid is simply the latest in a whole series of zoonoses.

In other words, it's a "spillover", to use a term David Quammen helped make popular a few years ago.  Just like the 2003 iteration of SARS, and Ebola, and HIV-1, and Nipah, and Lyme disease, and the 2004-2005 H5N1 flu strain that gods-thankfully guttered out, and a whole host of other nasties that have shown up over the course of the last 40 or 50 years.