[ProtectOurFreedom]

...continued...

We know that Wuhan went from an index case in ~Nov-Dec 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~9-10 weeks. We now believe that the Seattle area seeding event was ~Jan 15 and we're now ~7 weeks later. I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia.

We are currently estimating ~600 infections in Seattle, this matches my phylodynamic estimate of the number of infections in Wuhan on Jan 1. Three weeks later, Wuhan had thousands of infections and was put on large-scale lock-down. However, these large-scale non-pharmaceutical interventions to create social distancing had a huge impact on the resulting epidemic. China averted many millions of infections through these intervention measures and cases there have declined substantially.

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The author concludes "This suggests that this is controllable. We're at a critical junction right now, but we can still mitigate this substantially." and provides the same list of steps that we can take to mitigate exponential growth (as everybody else has).

This is where his article gets odd and seems to go off the rails. He says the severe and harsh steps the Chinese took got their spread under control (which I personally doubt). But then he ignores their seeming success using draconian public health methods (possible in a communist country) and goes on to say we can control this with the easy steps of frequent hand washing, avoiding crowds, cough into your sleeve, don't touch your face, disinfect surfaces, etc.

It seems like the author is assuming facts not in evidence.

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Thanks for FReepers LilFarmer and 21twelve for posting links to this article in the last couple days. I thought it is important enough to have its own post.

[ProtectOurFreedom]

Pinging the original FReepers who posted links to this. Thanks for making this available via links in other threads!

[ifinnegan]

This us stilled inferred.

If true (certainly possible, it’s a logical inference) it shows how benign the virus is.

There’s nothing cryptic about epidemics.

[ifinnegan]

“I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia.”

This may be the stupidest statement here since back in January when the one guy said there’d be 100 million cases by March 1st.

[WildHighlander57]

Many thanks for posting this info!!

Ping!

[sauropod]

Interesting article.

Thanks for posting.

[Savage Rider]

I have one question: I was in the Seattle Pike Place Market over the weekend. Should I self quarantine for 9 to 10 weeks?

[CharleysPride]

Fascinating information, thanks for posting.

[GOPJ]

https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus-wuhan-china/

from link:

Unlike other related coronaviruses, the 2019-nCoV virus has a unique sequence about 1,378 bp (nucleotide base pairs) long that is not found in related coronaviruses.

Looking at the phylogenetic tree recently published derived using all the full genome sequence, we see the 2019-nCoV virus does not have clear monophyletic support given the bootstrap value of 75 (Fig 1).
Close-up on Bootstrap value of 75 for available 2019-nCoV from Lu et al., 2020 The Lancet article [Full Text]

There is no doubt that there is a novel sequence in 2019-nCoV; we confirmed this via sequence alignment. Here’s the DOT plot:

The gap in the line shows a lack of sequence homology beween the most similar bat coronavirus and 2019-nCoV. The inserted sequence, which should not be there is here:
inserted-portionDownload

A database search by the first team to study and publish the whole genome sequence for the origins of the inserted sequence turned up no hits (Ji et al., 2020). They conducted a codon-bias analysis which led them to speculate that perhaps there had been a recombination event between a coronavirus in snakes with a coronavirus from bats (Ji et al., 2020). [Full Text]

This led to criticism on Wired(3) with quote dismissing the snake origin hypothesis as lacking evidence. There is, however, clear evidence that the novel sequence, which I will refer to henceforth as INS1378, is from a laboratory-induced recombination event. Specifically,

(1) The sequence similarity to other coronavirus sequences is lower to its most similar sequences in any coronavirus than the rest of the genome (IPAK finding)

(2) The high sequence similarity of INS1378 to a SARS spike protein (2; IPAK Confirmed).

(3) We also found significant sequence similarity of INS1378 to a pShuttle-SN vector that was in use in the 1980’s in China to create a more immunogenic coronavirus (IPAK finding, details below, Option 4).

[BenLurkin]

What exactly do these mutation do?

Make it deadlier, less deadly, easier to transmit, harder?

And what causes the mutation? What had the germ run into that caused it to have to change?