Use of Bioinformatics Technologies and Databases to Teach Analysis of Genetic Sequences to Undergraduate Students in Physics, Biotechnology, and Biology: The Specific Case of the SARS-CoV-2 Spike Protein

Michelle Abigail Fuentes-Acosta,Daniel Osorio-González,Jorge Mulia-Rodríguez

doi:10.4236/ce.2021.121014

Abstract

Worldwide, the implementation of computational tools has allowed the advancement of our understanding, specifically, biotechnological information tools have made possible to tackle global challenges such as the COVID-19 pandemic; therefore, such tools are essential for science students. We propose an activity to teach the use of information and database biotechnologies and their utility for the alignment and comparison of sequences. We use as query sequence the corresponding to SARS-CoV-2 Spike protein in its closed state, and we compare it with 200 sequences obtained from the NCBI databases to identify the mutations and their domain. In the results, we show the frequency of the mutations, domain, and country of the isolated SARS-CoV-2 genome. The activity we propose is aimed at first-year undergraduate students in physics, biology, and biotechnology.

Highlights

SARS-CoV-2, the virus responsible for the COVID19 pandemic, has been the subject of several investigations
We use as query sequence the corresponding to SARS-CoV-2 Spike protein in its closed state, and we compare it with 200 sequences obtained from the National Center for Biotechnology Information (NCBI) databases to identify the mutations and their domain
The best educational practices require that the contents of the courses are contextualized within an immediate social reality, and in this paper, we present a proposal for teaching the use of NCBI databases for the alignment and comparison of sequences of the Spike protein from SARS-CoV-2

Summary

Introduction

SARS-CoV-2, the virus responsible for the COVID19 pandemic, has been the subject of several investigations. The structural proteins that make up the virus are Spike (Spike or S), nucleocapsid (N), matrix (M), and envelope (E) (Cascella, Rajnik, Cuomo, Dulebohn, & Di Napoli, 2020; Guo et al, 2020) In this activity, we will approach the Spike glycoprotein which consists of a class I fusion trimer in a metastable prefusion conformation and undergoes substantial structural rearrangement and numerous conformational changes to fuse the viral membrane with the host cell membrane. It should be noted that SARS-CoV-1 and SARS-CoV-2 have an unusually high proportion of evolutionary convergent amino acid sites in the RBD of Spike and its associated protein, ORF3a, which could explain that both viruses are adapted for the same receptor (ACE2) in addition to both having general structural homology (Wrapp et al, 2020; Wu, 2020; Zhou et al, 2020)

Methods

Results

Conclusion