Submitted:
02 October 2021
Posted:
05 October 2021
Read the latest preprint version here
Preprints on COVID-19 and SARS-CoV-2
Abstract
At present, the polybasic furin cleavage site on the spike glycoprotein of the SARS-CoV-2 is still a missing link. Remarkably, the two arginine residues this of site are encoded by the CGG arginine codon, which is rare in Betacoronavirus proteins. Arginine dimers are common at viral furin sites, but are not CGG-CGG encoded. The question is: Is that genetic footprint, encoding arginine pairs, unique to the SARS-CoV-2? To address the issue, using Perl scripts, here I dissect in detail the NCBI Virus database in order to report the arginine dimers that exist in Betacoronavirus proteins. As main result, a set of Middle East respiratory syndrome-related coronavirus (MERS-CoV) (isolates: camel/Nigeria/NVx/2016, host: Camelus dromedarius) have the CGG-CGG encoded arginine pair in the spike protein polybasic furin cleavage site. In addition, CGG-CGG encoded arginine pairs were also found in the orf1ab polyprotein from HKU9 and HKU14 Betacoronavirus, as well as, in the nucleocapsid phosphoprotein from few SARS-CoV-2 isolates. To quantify the presence probability of CGG-CGG arginine-arginine in Betacoronavirus, a First-Order Markov Chain was defined. It is highly unlikely to find it in betacoronaviruses wildlife, but it is there. Collectively, results shed light on recombination as origin of the virus CGG-CGG arginine dimer in the S1/S2 cleavage site.
Keywords:
SARS-CoV-2
; MERS-CoV
; arginine dimer
; polybasic furin cleavage site
; aginine codon usage
; Markov model
; bioinformatics
Copyright: This open access article is published under a Creative Commons CC BY 4.0 license, which permit the free download, distribution, and reuse, provided that the author and preprint are cited in any reuse.
