Stephen Moss

Teams: Not specified

Organizations: Not specified

https://orcid.org/0000-0002-1399-293X
EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

Abstract (Expand)

The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent … need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.

Authors: Cristina S. Ferreira, Yasmmin C. Martins, Rangel Celso Souza, Ana Tereza R. Vasconcelos

Date Published: 2021

Publication Type: Journal

ONTViSc (ONT-based Viral Screening for Biosecurity)
Work-in-progress

ONTViSc (ONT-based Viral Screening for Biosecurity)

Introduction

eresearchqut/ontvisc is a Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity. It takes fastq files generated from either amplicon or whole-genome sequencing using Oxford Nanopore Technologies as input.

The pipeline can either: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly ...

Type: Nextflow

Creators: Marie-Emilie Gauthier, Craig Windell, Magdalena Antczak, Roberto Barrero

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.683.1

pox-virus-amplicon/main

A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

Type: Galaxy

Creators: Viktoria Isabel Schwarz, Wolfgang Maier

Submitter: WorkflowHub Bot

1: Plant virus detection with kraken2 (SE)
Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

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3: Plant virus exploration
Work-in-progress

Just the cleaning then assembly of all reads. TO explore further follow one of the paths described in "Global view" (WF 0)

Type: Galaxy

Creators: None

Submitter: johan Rollin

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2: Plant virus confirmation
Work-in-progress

Mapping against all plant virus then make contig out of the mapped reads then blast them.

Type: Galaxy

Creators: None

Submitter: johan Rollin

Download
1: Plant virus detection with kraken2 (PE)
Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

Download
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