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Infect Genet Evol
. 2021 Jan 23;104729.
doi: 10.1016/j.meegid.2021.104729. Online ahead of print.
SARS-CoV-2 and other human coronavirus: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics
Chiranjib Chakraborty 1 , Ashish Ranjan Sharma 2 , Manojit Bhattacharya 3 , Rudra P Saha 4 , Sanmitra Ghosh 4 , Soham Biswas 4 , Saikat Samanta 4 , Garima Sharma 5 , Govindasamy Agoramoorthy 6 , Sang-Soo Lee 7
Affiliations
- PMID: 33497837
- PMCID: PMC7826164
- DOI: 10.1016/j.meegid.2021.104729
Abstract
In recent years, a total of seven human pathogenic coronaviruses (HCoVs) strains were identified, i.e., SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Here, we performed an analysis of the protease recognition sites and antigenic variation of the S-protein of these HCoVs. We showed tissue-specific expression pattern, functions, and a number of recognition sites of proteases in S-proteins from seven strains of HCoVs. In the case of SARS-CoV-2, we found two new protease recognition sites, each of calpain-2, pepsin-A, and caspase-8, and one new protease recognition site each of caspase-6, caspase-3, and furin. Our antigenic mapping study of the S-protein of these HCoVs showed that the SARS-CoV-2 virus strain has the most potent antigenic epitopes (highest antigenicity score with maximum numbers of epitope regions). Additionally, the other six strains of HCoVs show common antigenic epitopes (both B-cell and T-cell), with low antigenicity scores compared to SARS-CoV-2. We suggest that the molecular evolution of structural proteins of human CoV can be classified, such as (i) HCoV-NL63 and HCoV-229E, (ii) SARS-CoV-2, and SARS-CoV and (iii) HCoV-OC43 and HCoV-HKU1. In conclusion, we can presume that our study might help to prepare the interventions for the possible HCoVs outbreaks in the future.
Keywords: Antigenic variation; Human coronavirus; Molecular phylogenetics; Protease recognition sites; S-protein.