Using COVID‐19 as a teaching tool in a time of remote learning: A workflow for bioinformatic approaches to identifying candidates for therapeutic and vaccine development

Abstract

The COVID-19 pandemic has led to an urgent need for engaging computational alternatives to traditional laboratory exercises. Here we introduce a customizable and flexible workflow, designed with the SARS CoV-2 virus that causes COVID-19 in mind, as a means of reinforcing fundamental biology concepts using bioinformatics approaches. This workflow is accessible to a wide range of students in life science majors regardless of their prior bioinformatics knowledge, and all software is freely available, thus eliminating potential cost barriers. Using the workflow can thus provide a diverse group of students the opportunity to conduct inquiry-driven research. Here we demonstrate the utility of this workflow and outline the logical steps involved in the identification of therapeutic or vaccine targets against SARS CoV-2. We also provide an example of how the workflow may be adapted to other infectious microbes. Overall, our workflow anchors student understanding of viral biology and genomics and allows students to develop valuable bioinformatics expertise as well as to hone critical thinking and problem-solving skills, while also creating an opportunity to better understand emerging information surrounding the COVID-19 pandemic.

An online Google Colab project for exploring the SARS CoV‐2 genome and mRNA vaccines

“…Biochemistry and molecular biology students increasingly need programming and data science skills to be fully functional scientists (Barone, Williams, and Micklos 1 ; Sayres et al 2 ). The COVID‐19 pandemic has forced much teaching online, leading to the need for assignments and projects that can be carried out remotely 3 . The project described here is an online assignment that illustrates the use of Python in the analysis of the SARS CoV‐2 genome.…”

“…The COVID-19 pandemic has forced much teaching online, leading to the need for assignments and projects that can be carried out remotely. 3 The project described here is an online assignment that illustrates the use of Python in the analysis of the SARS CoV-2 genome.…”

Bioinformatics approach used in undergraduate research to predict siRNA as ZIKV therapeutics

“…This workflow can be effectively used as a standalone projectbased approach for biology students to learn bioinformatic skills. 4 Currently, few undergraduate programs provide training in the design and implementation of NGS applications. Authors have introduced NGS to undergraduates interested in pursuing careers in the biomedical sciences.…”

Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

“…Students create a sequence alignment and use Foldit to model the 3D structure of the protein (17). Bryce and colleagues guide students through analysis of genetically related viral genomes to identify small well-conserved regions of the viral replicase polyproteins PP1a and PP1ab for drug or vaccine targets (18). Lorusso and Shumskaya developed online laboratory exercises for multiple sequence alignment, phylogeny construction, and protein modeling using SARS-CoV-2 data and the PyMOL molecular visualization system (19).…”