based on the virus genome there is no indication it was engineered.
No surprise that the mainstream media would be working overtime to "debunk" these "crackpot stories and dangerous advice".
Our job here is to look deeper, and try to distinguish fact from fiction. Not that it's ever easy.
I found this interesting article series this morning, by
James Lyons Weiler. Up until 2015, Weiler was a high-powered academic with Hillman Cancer Center, and founded the Genomics Research Core at University of Pittsburgh. His project was closed in 2014, and in 2015 he decided to open an independent research institute, IPAK
(Institute for Pure and Applied Knowledge). Lately his research seems to be focused on vaccine safety.
In the series, Weiler explains what he considers "Moderately Strong Confirmation" that the new virus is a bioengineered recombinant product. His explanation of why he thinks his confirmation is only "moderately strong" makes no sense at all to me.
He doesn't think we're looking at a bioweapon. His guess is that it's a result of some sort of project to develop a vaccine against SARS coronavirus. Some scientist named Marc Wathelet in the comment section strongly disagrees, apparently arguing for natural recombination. The debate prompted Weiler to go back through his results again, and he's sticking to his story. The technical level is above my ability to follow.
https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus-wuhan-china/
The disease progression in of 2019-nCoV is consistent with those seen in animals and humans vaccinated against SARS and then challenged with re-infection. Thus, the hypothesis that 2019-nCoV is an experimental vaccine type must be seriously considered.
Evidence for: Sequence homology between INS1378 to pShuttle Coronavirus vaccine; presence of a SARS-like Spike protein in bat coronavirus, otherwise most similar to bat coronaviruses; low bootstrap value.
Evidence against: Low sequence homology (but highly signifiant). NB these viruses are RNA viruses and they can evolve quickly, even under laboratory conditions.
Status: Most likely.
https://jameslyonsweiler.com/2020/0...e-2019-ncov-virus-genomes-and-their-analyses/
There are two ways on this planet for viruses to recombine: in nature, via co-infection with a common host, and in the laboratory. I evaluated the likelihood of those two outcomes two days ago, and the article went viral, helped by the coverage by the Highwire team. Some have misinterpreted the article as saying that I have ruled out a bioweapons origin; however, I have not. The level of evidence supporting an accidental laboratory release of vaccine type, or of a bioweapon, or of a vaccine experiment gone wrong, sensitizing people to serious illnesss and death upon subsequent exposure, are all about the same. What gives a vaccine program the edge is the match between the outcomes in SARS vaccine research in animals and the symptoms and mortality profile of nCoV in humans.
... scientists are speculating exclusively about natural recombination events, when the sequence they are analyzing has major genomic differences partly inconsistent with the most recent common ancestory of the 2019-nCoV being HKU9-1, in a world in which laboratory recombination research into viruses to make vaccines is 100% known to be ongoing.
We can say with certainty that 2019-nCoV has at least two ancestors: the ancestry of the entire genome, and the ancestry of the SARS spike protein.
I discount the wild recombination idea because natural selection would likely remove individual animals if the recombination occurred in nature due to high mortality. So recombination in the wild is purely speculative.
This looks like an attempt to develop a vaccine to me.
“HIV Sequences” Unsurprising – Maybe
A report of four additional sequences put into the Spike protein, which at the amino acid level are short sequences, but that the nucleotide level are, combined, improbably there by chance, point more toward a bioweapon. The E-values of the match to the HIV sequences are not significant, and there are many more matches to other non-HIV sequences. The presence of all four sequences, the pathogenetic capacity of those additonal novel sequences of are unknown, are of interest to some, but most who understand sequence analysis will attribute their matching to chance.
So who, or what, put SARS spike glycoprotein sequence into 2019-nCoV remains a mystery.
https://jameslyonsweiler.com/2020/0...irmation-of-a-laboratory-origin-of-2019-ncov/
... I procured the spike protein coding sequence (CDS) of these from NCBI’s nucleotide database and aligned them using Blast, with the sequence from the first 2019-nCoV protein as the anchor. (Oddly, that Genbank entry does not label the S protein CDS as a spike glycoprotein, instead annotating it only as a “structural protein”).
The resulting massive alignment confirms a major unique inserted element in 2019-nCoV not found in other bat coronaviruses, nor in SARS in the homologous genomic position...
Blasting the novel sequence region against all non-viral sequences (to pick up vector technology) again results in pShuttle-SN (no surprise) but now this time is also picked up a recombinant coronavirus clone Bat-SRBD spike glycoprotein gene from UNC, USA. (Genbank entry) and other synthetic constructs.
As I published earlier, before anyone points fingers at the Chinese, note that recombinant viruses have been in play in laboratories all across the world in many nations. ...
It is worth pointing out that due to the length of overlap, the sequence strength is considered moderately strong: highly significant E-value, high %identity, but short sequence length. These findings cannot be considered strong validation for obvious reasons: produced by the same analyst, using (part) of the same data.