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Comment by remarkEon | Hacker News Reader

to someone who doesn’t know anything about the relevant science (me) the use of the word “insertions” seems to imply this was engineered. Can someone who actually understands this explain what this document is saying?

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Well, the conclusion of this paper is that the odds of this virus coming to be naturally are very small. Which is a very scientific way of saying "we think this was man-made".

But, that is what the paper is saying. Extraordinary claims, extraordinary evidence is what I think. I feel the evidence here is quite small, but I'm not a bio-data-scientist.

Is it an extraordinary claim? The sequence matching should be easy to verify as the genome has been published. If the sequences are short or common enough maybe it would be a more likely coincidence.

That said: What are the priors on a "natural" virus erupting in the only city in China with a level 4 biohazard facility?

Source: http://english.www.gov.cn/state_council/ministries/2018/01/0...

So if it's not extraordinary it's still going to require evidence, which without peer review we still pretty much have none.

This is evidence, but it requires corroboration from other evidence. Peer review doesn't provide additional evidence - it's just a sober second opinion that lends credence (or not) to the proposed evidence and interpretation.

Just wanted to clarify the language here.

Totally right - and thank you for the clarification in language.

Indeed, the paper seems to suggest that the natural occurrence of this virus is the extraordinary claim.

> This indicates that these insertions have been preferably acquired by the 2019-nCoV, providing it with additional survival and infectivity advantage. Delving deeper we found that these insertions were similar to HIV-1. Our results highlight an astonishing relation between the gp120 and Gag protein of HIV, with 2019-nCoV spike glycoprotein. These proteins are critical for the viruses to identify and latch on to their host cells and for viral assembly (Beniac et al., 2006). Since surface proteins are responsible for host tropism, changes in these proteins imply a change in host specificity of the virus. According to reports from China, there has been a gain of host specificity in case 2019-nCoV as the virus was originally known to infect animals and not humans but after the mutations, it has gained tropism to humans as well.

> Our analysis of the spike glycoprotein of 2019-nCoV revealed several interesting findings: First, we identified 4 unique inserts in the 2019-nCoV spike glycoprotein that are not present in any other coronavirus reported till date. To our surprise, all the 4 inserts in the 2019-nCoV mapped to short segments of amino acids in the HIV-1 gp120 and Gag among all annotated virus proteins in the NCBI database. This uncanny similarity of novel inserts in the 2019- nCoV spike protein to HIV-1 gp120 and Gag is unlikely to be fortuitous. Further, 3D modelling suggests that atleast 3 of the unique inserts which are non-contiguous in the primary protein sequence of the 2019-nCoV spike glycoprotein converge to constitute the key components of the receptor binding site. Of note, all the 4 inserts have pI values of around 10 that may facilitate virus-host interactions. Taken together, our findings suggest unconventional evolution of 2019-nCoV that warrants further investigation. Our work highlights novel evolutionary aspects of the 2019-nCoV and has implications on the pathogenesis and diagnosis of this virus.

So, maybe, maybe not. What's the likelihood of natural occurences resulting in these inserts ? Are these novel evolutionary aspects natural or engineered ?

Can't outright say "It was made in a lab" but can say "Something's new here".

Insertions can occur naturally.

https://en.wikipedia.org/wiki/Insertional_mutagenesis

> Because many viruses integrate their own genomes into the genomes of their host cells in order to replicate, mutagenesis caused by viral infections is a fairly common occurrence. Not all integrating viruses cause insertional mutagenesis, however.

This paper does seem to allege that these particular sets of insertions aren't via natural causes, though.

There could be naturally occurring insertions, but they would generally look similar to an associated coronavirus, or something else local, not 4 discrete changes that are all nearly identical to a (very well studied) virus that should be completely unrelated..

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