CoronaVR

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COVID-19 is a pandemic disease caused by SARS-CoV-2 which has become a health emergency througout the World.
Till date, there is no FDA-approved drug or vaccine available to combat this deadly pathogen.
To help the researchers fight against SAR-CoV-2, we have developed CoronaVR, an integrative multi-omics platform dedicated to the Corona virus genomic and proteomic analysis along with comparative genomics, vaccine epitopes and therapeutic knowledge.

It is classified into different sections representing individual components i.e. "Epitopes", "Genomes", "Therapeutics", "Primers" and analysis tools.
It delivers sophisticated analysis such as genome search, codon usage bias, phylogenetic inferences at whole genome; gene and protein level with user-friendly visual environment.
It also includes graphical Corona genome browser, CoronaBrowse for the collective representation of SARS-CoV-2 annotation and regulatory information.
It has a dedicated section for vaccine epitope candidates under the heading " Epitopes" that harbors information about predicted B-cell (linear and discontinous) and T-cell (MHC-I & II binders, CTL epitopes, CD8 & CD4 immunogenic )epitopes of SARS-CoV-2 alongwith the conservancy.
Furthermore, CoronaVR also deals with therapeutically imperative constituents i.e. molecular diagnostics primers, siRNAs, miRNAs, sgRNAs.

We have used various online prediction tools such as IEDB, NetCTLpan, Vaxijen, ToxinPred, AllerTop to predict probable vaccine candidates against the SARS-CoV-2.
We predicted linear and discontious B-cell epitopes using IEDB tools Bepipred and Ellipro respectively. For MHC-I and II binders, CD8 and CD4 immunonogenic epitopes, we used respective tools available at IEDB and CTL epitopes by CTLpan.
For antigenicity, toxicity and allergenicity prediction, we used Vaxijen v 2.0, ToxinPred and AllerTop 2.0 respectively. We used IFNepitope specifically for MHC-II binders to predict IFN gamma inducing epitopes.
We also performed cross-conservancy analysis of our predicted epitopes with other coronaviruses, specifically SARS-CoV and population coverage only for T-cell epitopes to predict protection that can be provided to a population by our shortlisted epitopes.
Since no experimental epitopes are available from SARS-CoV-2 till now, we extracted experimentally verified epitopes of SARS-CoV and mapped them on SARS-CoV-2 proteins to find cross-protective epitopes.

In this section, we have summarized the details of predicted B-cell, immunogenic (CD8 and CD4) epitopes and MHC-I & II binders.

T-cell epitopes
The below image shows the screenshots for predicted MHC-I, MHC-II and CTL epitopes, their source protein, start and stop positions, length and conservancy with other coronaviruses.

The below image shows the experiemntally proven T and B-cell epitopes of coronaviruses and their respective details available at IEDB..

To navigate through the genomes and proteomes, we set up an "Corona genome browser" which facilitates graphical dynamic visualization of annotations.

The upper panel shows the positional scale (ruler) to navigate through genomes/proteome along with reference sequence. Distinct annotation features were shown in separate color blocks.

Cblast:: To find similarity and align query sequence to the Corona genomes and genes.

This tool provide graphical view of some important physico-chemical properties of input sequence like Percentage of amino acid composition, hydrophobicity, Preference for beta strands etc.