This guy may be on to something (re: virus origin)

[intrepidity]

It's all very technical, but a great discussion about the genetics involved.

A recent (unpublished, just a post on a website) hypothesis of where the furin cleavage site came from, from this discussion here:

http://virological.org/t/tackling-rumors-of-a-suspicious-origin-of-ncov2019/384/3

SOURCE OF FURIN SITE IN SARS-CoV-2 IS COPY CHOICE ERROR FROM MIXED INFECTION OF BATS

I have found a probable source of the putative insert that adds the RRAR furin site to SARS-CoV-2.

Ten of the 12 nucleotides in the RRAR insert are identical to a sequence in the spike protein gene of Bat Coronavirus HKU9 isolated from a Rousettus fruit bat in Guangdong province in 2011.

In HKU9 they code for TSAG in the loop region known in the Gao terminology as SD3. The first CT of the putative insert is still orphan, but there is a relevant possible source for the rest, albeit out of frame.

The “Insert” is CT CCTCGGCGGG, the last ten identical to the sequence in HKU9.

The sequence context has other similarities, i.e the “cagac” upstream and a “c” downstream of the “insert” as aligned here:

HKU9 gcatttgta caga------cctcggcgggc ctctgt

CoV-2 tatcagact cagac ttgct cctcggcgggc acgtagt

Total of 14 of 19 identical nucleotides in two runs with one gap. That’s a lock.

Copy choice errors in mixed infections do not have to be in an exact context, since it is not a recombination, but RNA polymerase hopping from one template strand to another. In this case the two templates code for the same gene, between regions about a thousand nucleotides from one another, out of a genome of 30,000 nucleotides. There could easily have been evolution of the site since the mixed infection, over a period of years.

This cannot be a coincidence.

The natural range of the host for Bat RaTG13, closely related to SARS-CoV-2, the microbat Rhinolopus affinis, overlaps that of the Rousettus fruit Macrobat in Yunnan province. The latter is used for bush meat. Also, Microbats and Macrobats are known to co-habit the same caves. An alternate source of virus for a human infection could be mixed bat guano from such a cave with a mixed population.

So the definitive source of the pandemic is a mixed infection of viruses similar to SARS-CoV-2 and Bat HKU9 – copy choice error resulting in an insert in SARS-CoV-2. Could occur in bats, intermediate animal or human.

Human in incubation with SARS-CoV-2 could hop a max speed train, direct line from Kunming in Yunnan Province and disembark in Wuhan train station 6.5-8 hours later, sometime last fall. The line began service in 2017.

Infected in Yunnan, does not spread it there, but goes to Wuhan, where he/she either falls ill or spreads it asymptomatically to another person, initiating the pandemic there. The initial outbreak occurs a short distance from the Wuhan train station for good reason – that is where it arrived.

This accidental mixed infection in the wild, and infection of a human by some form of bush meat or bat guano, who carries it by high speed train to Wuhan – this is the most likely series of events leading to the pandemic.

The only laboratory required is the natural laboratory of the bat cave with multiple species of bats and bat coronaviruses.

Found it.

William R. Gallaher. Ph.D.
Professor of Microbiology, Immunology and Parasitology, Emeritus
Louisiana State University School of Medicine
New Orleans, LA 70112
[e-mail]

The whole thread, plus links therein, are interesting reading for those following this story.

[brewens]

1. I wondered quite awhile ago if it really started out in the boonies and just first showed up

in Wuhan. I thought it might have gone around a little in some small towns and not raised any alarms, especially if no one died from it. No matter how remote the place is, someone goes in and out of there. They could have ended up anywhere and spread it, maybe starting sooner than they think.