Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic

Abstract

Novel coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which can be transmitted from person to person. As of September 21, 2021, over 228 million cases were diagnosed as COVID-19 infection in more than 200 countries and regions worldwide. The death toll is more than 4.69 million and the mortality rate has reached about 2.05% as it has gradually become a global plague, and the numbers are growing. Therefore, it is important to gain a deeper understanding of the genome and protein characteristics, clinical diagnostics, pathogenic mechanisms, and the development of antiviral drugs and vaccines against the novel coronavirus to deal with the COVID-19 pandemic. The traditional biology technologies are limited for COVID-19-related studies to understand the pandemic happening. Bioinformatics is the application of computational methods and analytical tools in the field of biological research which has obvious advantages in predicting the structure, product, function, and evolution of unknown genes and proteins, and in screening drugs and vaccines from a large amount of sequence information. Here, we comprehensively summarized several of the most important methods and applications relating to COVID-19 based on currently available reports of bioinformatics technologies, focusing on future research for overcoming the virus pandemic. Based on the next-generation sequencing (NGS) and third-generation sequencing (TGS) technology, not only virus can be detected, but also high quality SARS-CoV-2 genome could be obtained quickly. The emergence of data of genome sequences, variants, haplotypes of SARS-CoV-2 help us to understand genome and protein structure, variant calling, mutation, and other biological characteristics. After sequencing alignment and phylogenetic analysis, the bat may be the natural host of the novel coronavirus. Single-cell RNA sequencing provide abundant resource for discovering the mechanism of immune response induced by COVID-19. As an entry receptor, angiotensin-converting enzyme 2 (ACE2) can be used as a potential drug target to treat COVID-19. Molecular dynamics simulation, molecular docking and artificial intelligence (AI) technology of bioinformatics methods based on drug databases for SARS-CoV-2 can accelerate the development of drugs. Meanwhile, computational approaches are helpful to identify suitable vaccines to prevent COVID-19 infection through reverse vaccinology, Immunoinformatics and structural vaccinology.

Keywords: Application; Bioinformatics technology; COVID-19; SARS-CoV-2.

Graphical abstract

Fig. 1

The descriptive workflow of the most important methods and applications of bioinformatics technologies on COVID-19.

Fig. 2

Structure of SARS-CoV-2. (A) Schematic representation of the structure of SARS-CoV-2. It has four structural proteins, S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins; the N protein holds the single-strand, positive-sense RNA genome, and the S, E, and M proteins together create the viral envelope. (B) SARS-CoV-2 genome comprises a 5′ untranslated region (5′ UTR) including 5′ leader sequence, open reading frame (ORF) 1a/b, envelope, membrane and nucleoprotein, accessory proteins such as orf 3, 6,7a, 7b, 8, and 9b, and 3′ untranslated region (3′ UTR) in sequence. (C) SARS-CoV-2 structure is based upon amplification targets of the NTS method. NTS detected 12 fragments including ORF1ab and virulence factor-encoding regions (M. Wang et al., 2020).

Fig. 3

Phylogenetic analysis of full-length genomes of SARS-CoV-2 and representative viruses of the genus Betacoronavirus. 2019-nCoV=SARS-CoV-2 = severe acute respiratory syndrome coronavirus type 2. MERS-CoV = Middle East respiratory syndrome coronavirus. SARS-CoV = severe acute respiratory syndrome coronavirus (Roujian Lu et al., 2020).