Genetic comparison among various coronavirus strains for the identification of potential vaccine targets of SARS-CoV2

Abstract

On-going pandemic pneumonia outbreak COVID-19 has raised an urgent public health issue worldwide impacting millions of people with a continuous increase in both morbidity and mortality. The causative agent of this disease is identified and named as SARS-CoV2 because of its genetic relatedness to SARS-CoV species that was responsible for the 2003 coronavirus outbreak. The immense spread of the disease in a very small period demands urgent development of therapeutic and prophylactic interventions for the treatment of SARS-CoV2 infected patients. A plethora of research is being conducted globally on this novel coronavirus strain to gain knowledge about its origin, evolutionary history, and phylogeny. This review is an effort to compare genetic similarities and diversifications among coronavirus strains, which can hint towards the susceptible antigen targets of SARS-CoV2 to come up with the potential therapeutic and prophylactic interventions for the prevention of this public threat.

Keywords: COVID-19; ER stress; Genomic comparison; SARS-CoV2; Target antigenic sites; Vaccine development.

Fig. 1

Coronavirus virion structure depicting structural proteins: S (spike), M (membrane), E(envelope) and N(Nucleocapsid).

Fig. 2

Genomic organization of coronaviruses.

Fig. 3

Genomes of different CoV strains.

Fig. 4

An Evolutionary tree of various coronavirus strains.

Fig. 5

Flowchart displaying CoV induced generation of ER stress and activation of the UPR signaling cascade.

Fig. 6

(a) Structure of coronavirus particle displaying different proteins. (b)The S protein is the major target for vaccine development. This picture depicts Electron microscopy obtained image of the Structure of SARS-CoV-2 spike glycoprotein (PDB ID: 6VXX) (c)Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 obtained by X-ray diffraction (PDB ID:6M0J).

Fig. 7

(1). (A) MSA of KRSFIEDLLFNKV motif, (B) MSA of Receptor (ACE-2) binding domain of S1 subunit of spike protein, (C) MSA of Nucleocapsid (N) protein of various beta coronavirus strains representing sequences for SARS-CoV2, SARS, MERS, HCoV HKU1 and HCoV OC43. (2). Phylogenetic trees of (A) S protein and, (B) N protein of different beta CoVs. Both the trees demonstrate close homology of novel SARS CoV-2 with SARS-CoV.