SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study.

Ehsan Ahmadi,Ramin Hosseinzadeh,Leila Mohamed Khosroshahi,Farshid Noorbakhsh,Mohammad Reza Zabihi,Etsuro Ito

doi:10.1371/journal.pone.0260360

Ehsan Ahmadi, Ramin Hosseinzadeh + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0260360

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Abstract

Recent emergence of SARS-CoV-2 and associated COVID-19 pandemic have posed a great challenge for the scientific community. In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance.

Highlights

Current COVID-19 pandemic which is caused by a newly emerged betacoronavirus has led to immense health and socio-economic problems around the world
SARS-CoV-2 is a member of betacoronaviruses, which belong to Nidovirales order of positive sense ssRNA viruses [13]
As described in the Methods section, Delta-BLAST followed by thee PSI-BLAST iterations were used to perform the comparisons and best E value/alignment scores were determined for each SARS-CoV-2 protein

Summary

Introduction

Current COVID-19 pandemic which is caused by a newly emerged betacoronavirus has led to immense health and socio-economic problems around the world. Emergence of three deadly coronavirus epidemics over the last 20 years has challenged this view and is likely indicative of the dynamic evolution of these pathogens [5, 6]. This necessitates investigations that can provide a better insight regarding coronavirus genes, proteins and biological behavior. One approach towards better understanding of a new pathogen is comparative analysis of its nucleic acids, proteins and molecular structures. The results of these types of analyses can go beyond ordinary phylogenetics and might have applied clinicopathological implications. Viral vaccines including polio and MMR have been suggested as candidates that might give rise to this potential ‘cross-protective’ phenomenon, raising the possibility for the existence of similar molecular structures [7,8,9,10]

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Conclusion