Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

Abstract

This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome, its proteins, its origins and its evolution are explored. Specifically, this Guide introduces a range of bioinformatics tools for comparing and analysing nucleotide and protein sequences. On reading the Guide and completing the exercises, you will be able to: discover SARS-CoV-2 genome(s) available in a public nucleotide repository; compare SARS-CoV-2 genome sequences, look for their differences (mutations) and identify the variants; translate the spike gene into its encoded protein sequence; discover the 3D structure of the spike protein; understand the impact of mutations on infectivity and immune responses; and infer the origin of SARS-CoV-2 by comparing coronavirus spike protein sequences from different animal origins.