Table 1 shows four alignments. The first two are only six contiguous residues, so can easily happen by chance. Three has multiple mistmatches as well as the gap (red). Four has an even larger gap to get the alignment.
Take any two viruses and there's a decent likelihood of finding similar alignments.
- Some layman.
The PDF itself is MS Word, has numerous typos/little care (words like 'alingment'), random font changes back and forth between Times New Roman and the default MS Word font (Calibri?))
For HIV related fearmongering about "well, why would they know to treat it with HIV meds??", people are looking at this already because previous SARS-CoV has previous investigation with HIV medication, it is not unique to nCOV: https://www.ncbi.nlm.nih.gov/pubmed/14985565, https://www.ncbi.nlm.nih.gov/pubmed/15144898, https://www.ncbi.nlm.nih.gov/pubmed/14519691 - these are from 2003-2006.
=====
This study is crap.
My comment from another thread. This paper isn't peer reviewed or published. It's just an online journal.
I've worked pretty closely with gag in my PhD thesis. Gag is the conglomerate protein that gets cut by the protease to generate the hiv capsid, matrix, and carrier proteins. Gp120 is the receptor protein.
This is a really fucking dumb study and these scientists should be ashamed. Those amino acids are so short. They just went and looked for a virus to match. You can go and blast the amino acids yourself. Just copy and paste from the journal entry into NCBIs BLASTp. I did it and there's hundreds of matches to those sequences. HIV didn't even come up in the first 100. The 4th residue is missing like 6 amino acids. There are conserved regions in viruses. Their "gp120" match compares 6 amino acids out of 850 in the whole protein for example.
They found 4 sections that were in the new virus but not SARS. They then took these differences and ran them against all known viral proteins. They only looked at proteins with 100% matches, but if you look at the table they didn't match 100% for alignment. So like one is ABCEFG and they match it to an HIV protein that is ABCXYZEFG and they are calling those total matches. There's also tons of viruses that match these tiny sequences, they just noticed all 4 have HIV matches so they ignore the other matches and only looked at HIV.
Go blast it yourself if you want.
[HIV] - https://en.wikipedia.org/wiki/Structure_and_genome_of_HIV
[gp120] - https://en.wikipedia.org/wiki/Gp120
damn they're lucky!
https://biorxiv-cache.s3-us-west-2.amazonaws.com/2020.01.30....
> [ABSTRACT] We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.