How to investigate the origin of SARS-CoV-2 yourself

The real pleasure of doing science is finding new things yourself. I show you in this blog how you can make discoveries yourself. A few days ago I blogged about the video of Dr. Wilson. The good thing about his approach is that he helps us to find out basic facts about the origin of SARS-CoV-2 ourselves. In his video he gives a few hints how to do it, but does not give the full details. Here he shows how you can enter bat viral sequences in the NCBI software:

NC_045512, MG772933, MG772934

and the fourth: RaTG13. These are the identifiers of human SARS-CoV-2 RNA viral sequence and of the evolutionarily closely related bat viral sequences. Everybody can compare them. You don't need to be a professional virologist. You don't need any training. It is free access. You don't need an account.  Just a few mouse clicks as shown in this video:

video 1 min 36 sec

What the video shows: start with this NCBI virus screen. The Virus field should be empty because we are using only Accessions. Accessions are identifiers of specific sequences.

enter them in the Accession field and Submit.

For a start, I want to focus in the Spike protein. So, click on the  [Protein (70)] tab. Sort the Protein column. Select the surface glycoprotein, spike protein, spike glycoprotein by hitting 4 check boxes:

4 Spike protein accessions are selected

After hitting the Align button the real magic happens. The result is an alignment of the 4 protein sequences of the Spike protein. Optionally, hit the Sequence ID button to get the standard SARS-COV-2 sequence on top. In the video I show how to find the famous PRRA sequence. The PRRA sequence is very important and it is said to have caused the pandemic outbreak of SARS-COV-2 in humans [1]. The PRRA sequence sits in the middle of the Spike protein. The Spike protein gets the virus into human cells. It's an evolutionary innovation.

I guessed that PRRA must be somewhere in the middle of the 1273 AA Spike sequence, between position 600 en 700.

and there it is: the famous PRRA insertion!

 

A little bit sliding to the left and right, and there it is: on position 682! PRRA ! Sensation! That is the pleasure of discovering things yourself: PRRA is present in the SARS-COV-2 Spike protein and not in the 3 most closely related bat Spike protein sequences. It is an insertion relative to the other sequences. The alignment tool made it perfectly clear. If scientists told you it is there, it would not impress you very much. But seeing is believing. The gap in the other 3 sequences is not a real gap. It is a virtual gap necessary to align the rest of the sequence. There can be no real gap in a RNA or DNA string.

We are talking here about an insertion of only 4 amino acids: P R R A or 3 x 4 = 12 bases. Is that really a big evolutionary problem? Is all the fuss about 4 amino acids?

Please don't overlook the fact that the SARS-COV-2 Spike protein can be aligned with bat sequences! That means they are evolutionary similar enough that the Alignment tool succeeds in aligning them. Yes, there are many differences, but they are all single amino acids substitutions. So, they do not cause a complete failure of the alignment. Dr. Wilson points out that we don't expect these single amino acid substitutions if those bat viruses were used to create the SARS-CoV-2 virus in the lab. In fact, the engineered virus should be nearly 100% identical to an existing bat virus, except for the PRRA site. But that is not what we see. It would be pointless to create hundreds of pointless mutations. Conclusion: SARS-CoV-2 virus is not engineered.

Possible reply: but the putative engineers didn't use those bat sequences, but others! My reply: but where are they? Nobody have found them. The fact that nobody has found bat viral sequences 99,9% identical to SARS-CoV-2 is a problem for both hypothesis, the natural and the unnatural. Evolutionary biologists did not find the missing link, and 'Intelligent Design theorists' did not come up with the sequences that were used to create SARS-CoV-2.

Finally, we are comparing sequences with the first-ever sequenced SARS-CoV-2 in Dec 2019 in Wuhan in a human. Not with the highly mutated sequences of today. The bat sequences are older. The hunt is for bat viral sequences more recent or more similar to SARS-CoV-2. This blog will certainly not be the final blog about the origin of SARS-CoV-2!

I recommend readers of this blog to view the video of Dr. Wilson again (8 min) to have a better understanding of his arguments for the hypothesis that the SARS-CoV-2 virus has a natural origin. It doesn't make sense to repeat all his arguments here.

Notes

1. The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV, Nature, 9 Oct 2020.

 

Previous blog

•  No, the coronavirus still was NOT made in a lab, 20 February 2021