Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.

Citing Articles

VITALdb: to select the best viroinformatics tools for a desired virus or application.

Koul M, Kaushik S, Singh K, Sharma D Brief Bioinform. 2025; 26(2).

PMID: 40063348 PMC: 11892104. DOI: 10.1093/bib/bbaf084.

Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering.

Liao Y, Ma H, Wang Z, Wang S, He Y, Chang Y Proc Natl Acad Sci U S A. 2025; 122(6):e2406659122.

PMID: 39908098 PMC: 11831182. DOI: 10.1073/pnas.2406659122.

SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.

Rice A, Troendle E, Bridgett S, Firoozi Nejad B, McKinley J, Bradley D Genome Med. 2024; 16(1):150.

PMID: 39702217 PMC: 11658175. DOI: 10.1186/s13073-024-01409-1.

The CABANA model 2017-2022: research and training synergy to facilitate bioinformatics applications in Latin America.

Campos-Sanchez R, Willis I, Gopalasingam P, Lopez-Juarez D, Cristancho M, Brooksbank C Front Educ (Lausanne). 2024; 9.

PMID: 39686965 PMC: 7617245. DOI: 10.3389/feduc.2024.1358620.

Phylogenetic Insights into H7Nx Influenza Viruses: Uncovering Reassortment Patterns and Geographic Variability.

Feoktistova S, Ivanova A, Degtyarev E, Smirnova D, Volchkov P, Deviatkin A Viruses. 2024; 16(11).

PMID: 39599771 PMC: 11598867. DOI: 10.3390/v16111656.

References

Schneider G, Fechner U . Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov. 2005; 4(8):649-63. DOI: 10.1038/nrd1799. View

Martin R, Lochel H, Welzel M, Hattab G, Hauschild A, Heider D . CORDITE: The Curated CORona Drug InTERactions Database for SARS-CoV-2. iScience. 2020; 23(7):101297. PMC: 7305714. DOI: 10.1016/j.isci.2020.101297. View

Sheppard S, Dikicioglu D . Dynamic modelling of the killing mechanism of action by virus-infected yeasts. J R Soc Interface. 2019; 16(152):20190064. PMC: 6451399. DOI: 10.1098/rsif.2019.0064. View

Zimmer C, Yaesoubi R, Cohen T . A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLoS Comput Biol. 2017; 13(1):e1005257. PMC: 5240920. DOI: 10.1371/journal.pcbi.1005257. View

El-Gebali S, Mistry J, Bateman A, Eddy S, Luciani A, Potter S . The Pfam protein families database in 2019. Nucleic Acids Res. 2018; 47(D1):D427-D432. PMC: 6324024. DOI: 10.1093/nar/gky995. View

Aguilera L, Rodriguez-Gonzalez J . Modeling the effect of tat inhibitors on HIV latency. J Theor Biol. 2019; 473:20-27. DOI: 10.1016/j.jtbi.2019.04.018. View

Ngcapu S, Theys K, Libin P, Marconi V, Sunpath H, Ndungu T . Characterization of Nucleoside Reverse Transcriptase Inhibitor-Associated Mutations in the RNase H Region of HIV-1 Subtype C Infected Individuals. Viruses. 2017; 9(11). PMC: 5707537. DOI: 10.3390/v9110330. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Brockmann D, Helbing D . The hidden geometry of complex, network-driven contagion phenomena. Science. 2013; 342(6164):1337-42. DOI: 10.1126/science.1245200. View

10.

Sola I, Mateos-Gomez P, Almazan F, Zuniga S, Enjuanes L . RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biol. 2011; 8(2):237-48. PMC: 3230552. DOI: 10.4161/rna.8.2.14991. View

11.

Corman V, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D . Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020; 25(3). PMC: 6988269. DOI: 10.2807/1560-7917.ES.2020.25.3.2000045. View

12.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

13.

Garzon J, Deng L, Murray D, Shapira S, Petrey D, Honig B . A computational interactome and functional annotation for the human proteome. Elife. 2016; 5. PMC: 5115866. DOI: 10.7554/eLife.18715. View

14.

Li D, Liu C, Luo R, Sadakane K, Lam T . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10):1674-6. DOI: 10.1093/bioinformatics/btv033. View

15.

Holzer M, Marz M . PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. Bioinformatics. 2020; 37(7):1018-1020. DOI: 10.1093/bioinformatics/btaa695. View

16.

Upton C, Hogg D, Perrin D, Boone M, Harris N . Viral genome organizer: a system for analyzing complete viral genomes. Virus Res. 2000; 70(1-2):55-64. DOI: 10.1016/s0168-1702(00)00210-0. View

17.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N . COPASI--a COmplex PAthway SImulator. Bioinformatics. 2006; 22(24):3067-74. DOI: 10.1093/bioinformatics/btl485. View

18.

Westerhoff H, N Kolodkin A . Advice from a systems-biology model of the corona epidemics. NPJ Syst Biol Appl. 2020; 6(1):18. PMC: 7293297. DOI: 10.1038/s41540-020-0138-8. View

19.

Mitchell A, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G . MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 2019; 48(D1):D570-D578. PMC: 7145632. DOI: 10.1093/nar/gkz1035. View

20.

Bouckaert R, Vaughan T, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A . BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019; 15(4):e1006650. PMC: 6472827. DOI: 10.1371/journal.pcbi.1006650. View