{"id":6737,"date":"2020-02-08T19:21:34","date_gmt":"2020-02-08T23:21:34","guid":{"rendered":"http:\/\/stateofthenation.co\/?p=6737"},"modified":"2020-02-08T19:24:16","modified_gmt":"2020-02-08T23:24:16","slug":"research-scientist-presents-critical-insights-into-wuhan-coronavirus","status":"publish","type":"post","link":"http:\/\/stateofthenation.co\/?p=6737","title":{"rendered":"Research Scientist Presents Critical Insights Into Wuhan Coronavirus"},"content":{"rendered":"

On the Origins of the 2019-nCoV Virus, Wuhan, China<\/h1>\n

\"\"<\/p>\n

James Lyons-Weiler, PhD \u2013 1\/30\/2020<\/p>\n

RECOMBINATION technology has been in use in molecular virology since the 1980\u2019s. The structure of the 2019-NCoV virus genome provides a very strong clue on the likely origin of the virus.<\/em><\/p>\n

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.<\/p>\n

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).<\/p>\n

\"\"<\/a>
Close-up on Bootstrap value of 75 for available 2019-nCoV from Lu et al., 2020 The Lancet article [Full Text<\/a>]<\/figcaption><\/figure>\n

There is no doubt that there is a novel sequence in 2019-nCoV; we confirmed this via sequence alignment. Here\u2019s the DOT plot:<\/p>\n

\"\"<\/figure>\n

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:<\/p>\n

inserted-portion<\/a>Download<\/a><\/div>\n

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<\/a>]<\/p>\n

This led to criticism on\u00a0Wired(3)<\/a>\u00a0with 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,<\/p>\n

(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)<\/p>\n

(2) The high sequence similarity of INS1378 to a SARS spike protein (2; IPAK Confirmed).<\/em><\/p>\n

(3) We also found significant sequence similarity of INS1378 to a pShuttle-SN vector that was in use in the 1980\u2019s in China to create a more immunogenic coronavirus (IPAK finding, details below, Option 4).<\/p>\n

Here, I review four Option on the origins of the 2019-nCoV Coronavirus isolated from human patients from Wuhan, China.<\/p>\n

Option 1. Natural coronavirus related to bat coronaviruses, Not a Recombined Virus<\/strong>.<\/p>\n

Evidence for: Phylogenetic clustering with Bat coronaviruses.<\/p>\n

Evidence against: Low bootstrap support (N=75) and presence of a INS1378.<\/p>\n

Status:\u00a0Falsified hypothesis.<\/em><\/p>\n

Test: Survey coronviruses in animals in the wild.<\/p>\n

Option 2. A recombined virus that naturally picked up a SARS-like spike protein in it N-terminus (3\u2032 end) of the viral genome.<\/strong><\/p>\n

Evidence for: The INS1378 codon bias similar to snakes ($)<\/p>\n

Evidence against: Insufficient match in database search to other known CoV spike proteins (Ji et al., 2020)<\/p>\n

Status: Speculative hypothesis. Unlikely.<\/p>\n

Test: Find an isolate that matches 2019-nCoV in the wild and reproducibly independently isolate the virus from a wild animal (a match will confirm).<\/p>\n

Option 3. A recombined virus made in a laboratory for the purpose of creating a bioweapon.<\/strong><\/p>\n

Both China and the US hinted at the other side\u2019s potential liability in playing a role in bringing about a novel coronavirus in the lab specifically for the purpose of being used as a bioweapon. To add to the intrigue, a Chinese Scientist was released from BSL-4 laboratory in Manitoba, Canada for violating protocols, allegedly sending samples of deadly viruses to mainland China.<\/p>\n

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