[2] 2019-nCoV genome, origins and mutations discussed
Date: Fri 24 Jan 2020
Source: STAT News [abridged, edited]
https://www.statnews.com/2020/01/24...navirus-genome-tracing-origins-and-mutations/
Since the sequencing of the 1st 2019-nCoV sample, from an early patient, scientists have completed nearly 2 dozen more, said Andrew Rambaut of the University of Edinburgh, an expert on viral evolution. That pace is "unprecedented and completely unbelievable," said Andersen [molecular biologist Kristian Andersen of Scripps Research, an expert on viral genomes], who worked on sequencing the Ebola genome during the 2014 outbreak. "It's just insane."
The genome of the Wuhan virus is 29 903 bases long, one of many clues that have led scientists to believe it is very similar to SARS.
By comparing the 2 dozen genomes, scientists can address the "when did this start" question. The 24 available samples, including from Thailand and Shenzhen as well as Wuhan, show "very limited genetic variation," Rambaut concluded on an online discussion forum where virologists have been sharing data and analyses. "This is indicative of a relatively recent common ancestor for all these viruses."
Given what's known about the pace at which viral genomes mutate, if nCoV had been circulating in humans since significantly before the 1st case was reported on 8 Dec 2019, the 24 genomes would differ more. Applying ballpark rates of viral evolution, Rambaut estimates that the Adam (or Eve) virus from which all others are descended 1st appeared no earlier than 30 Oct 2019, and no later than 29 Nov 2019.
The progenitor virus itself was almost certainly one that circulates harmlessly in bats (as SARS does) but has an "intermediate reservoir" in one or more animals that come into contact with people, Andersen said. Presumably, that reservoir is one of the species of animals at the Wuhan market thought to be ground zero for the outbreak. The ancestor of 2019-nCoV existed in that species for some unknown time, never infecting people, until by chance a single virus acquired a mutation that made it capable of jumping into and infecting humans.
The genome sequences suggest that was a one-time-only jump. "The genomes [from the 24 samples] are very uniform," Andersen said. "If there had been multiple introductions," including from many different animals, "there would be more genomic diversity. This was a single introduction."
That means that what's sustaining the spread is human-to-human transmission (suggesting that closing Wuhan's animal market is very much an after-the-horse-has-fled-the-barn reaction).
Unfortunately, genetic analysis can't identify what animal species the coronavirus jumped from into humans. But an analysis by a team from the Wuhan Institute of Virology, posted to the preprint server bioRxiv [see item 1], determined that the genome of this coronavirus (the 7th known to infect humans) is 96% identical to that of a bat coronavirus, suggesting that species is the original source. (Writing in the New England Journal of Medicine on Friday [24 Jan 2020], another team of scientists in China reported that the new coronavirus is 86.9% identical to the bat SARS-like coronavirus.) [reference below]....
[NEJM citation: Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med [Epub 24 Jan 2020]
https://www.nejm.org/doi/full/10.1056/NEJMoa2001017]
