March Coronavirus Open Thread

Elizabeth

This thread was created on 3/8/2020, or approximately one million years ago in virus time. It’s getting pretty bloated now, and a lot of things that were high value at the time have been eclipsed by events, making karma not a very useful sorting tool. So I’m declaring this thread finished, and asking everyone to move over to the April Coronavirus Open Thread.

Interested in what happened in this thread? Here’s the timeless or not-yet-eclipsed highlights:

Scott Alexander comes up with Hammer and Dance 6 days before Tomas Pueyo
Spiracular on why SARS-Cov-2 is unlikely to be lab-created.
Two documents collating estimates of basic epidemiological parameters, in response to this thread
Discussion on whether the tuberculosis vaccine provides protection against COVID-19.
Suggestive evidence that COVID-19 removes sense of taste and smell.
Could copper tape be net harmful?

Interested in what happened in this thread? Here’s the timeless or not-yet-eclipsed highlights:

Scott Alexander comes up with Hammer and Dance 6 days before Tomas Pueyo
Spiracular on why SARS-Cov-2 is unlikely to be lab-created.
Two documents collating estimates of basic epidemiological parameters, in response to this thread
Discussion on whether the tuberculosis vaccine provides protection against COVID-19.
Suggestive evidence that COVID-19 removes sense of taste and smell.
Could copper tape be net harmful?

Paper on some of nCOV's mutations

Incidentally, also strong evidence against it being a lab-strain. It's a wild strain.

Closest related viruses: bats and Malayan pangolins

Mutation Descriptions

Polybasic Cleavage Sites (PCS): They seem to have something to do with increased rates of cell-cell fusion (increased rate of virus-induced XL multi-nucleated cells). Mutations generating PCS have been seen in Influenza strains to increase their pathogenicity, and they had similar effects in a few other viruses. So it's not exactly increasing virus-cell fusion, it's actually... increasing the rate at which infected cells glom into nearby cells. Fused cells are called syncytia.

O-linked glycans : Are theorized (with uncertainty) to help the virions masquerade as mucin, so hiding from the immune system. (Mutation unlikely to evolve in a lab on a petri dish)

Arguments strongly in favor of it being a wild strain

It's not that similar to one of the known lab-strains, so it probably was wild
The "polybasic cleavage site" and "O-linked glycans" mutations would have required a very human-like ACE-protein binding site, so basically only human or ferret cells
O-linked glycans are usually evolved as an immune defense, which isn't something cell cultures do.

(Just following the recommendation to move this out of shortform so it can be tagged later.)

Chinese virology researcher released something claiming it SARS-2 might even be genetically-manipulated after all? ZC45 and/or ZXC21 backbone. Claims that the RaTG13 genome was a concocted cover-up. After assessing, I'm not really convinced of the GMO claims, but the RaTG13 story seems to have something weird going on.

https://zenodo.org/record/4028830#.X2EJo5NKj0v

See here for my further thoughts on this.

EDIT: After assessing, I'm not finding the GMO claims convincing. The RaTG13 story does seem to have something weird going on, and there's several people ... (read more)

1Spiracular7y

Despite the virus being characterized in pangolins, after looking into this, I now think it is basically incorrect to think of this as primarily a "pangolin virus." The pangolins were a dying canary in a coal mine, and probably caught it from something else that serves as the real reservoir species for this nCOV precursor*. See: further explanation here

10Spiracular7y

More specifically: * It was not genetically modified for use as a bioweapon * The mutations don't resemble other well-known and well-characterized pathogenicity mutations too closely, in sequence or location * It probably wasn't cultured as cell-culture in a lab-setting for an extended period * The virus was not notable to science prior to this event Or in other words, it doesn't look planned. Its most recent mutations look much more like a "natural variation let it jump species" sort of situation. This doesn't address situations like, for example, "dead bats with a wild-type virus being left near a bunch of ferrets or pangolins," or something to that effect. (ETA: Or... accidental release like this is still possible.)

57

March Coronavirus Open Thread

57

57

57

March Coronavirus Open Thread

57

57

Paper on some of nCOV's mutations

Mutation Descriptions

Arguments strongly in favor of it being a wild strain