Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Author:

Hufsky Franziska1,Lamkiewicz Kevin1,Almeida Alexandre2,Aouacheria Abdel3,Arighi Cecilia4,Bateman Alex5,Baumbach Jan6,Beerenwinkel Niko7,Brandt Christian8,Cacciabue Marco9,Chuguransky Sara10,Drechsel Oliver11,Finn Robert D12,Fritz Adrian13,Fuchs Stephan11,Hattab Georges14,Hauschild Anne-Christin15,Heider Dominik16,Hoffmann Marie17,Hölzer Martin18,Hoops Stefan19,Kaderali Lars20,Kalvari Ioanna21,von Kleist Max11,Kmiecinski Renó11,Kühnert Denise22,Lasso Gorka23,Libin Pieter24,List Markus6,Löchel Hannah F15,Martin Maria J25,Martin Roman15,Matschinske Julian26,McHardy Alice C27,Mendes Pedro28,Mistry Jaina25,Navratil Vincent29,Nawrocki Eric P30,O’Toole Áine Niamh31,Ontiveros-Palacios Nancy25,Petrov Anton I25,Rangel-Pineros Guillermo32,Redaschi Nicole33,Reimering Susanne34,Reinert Knut17,Reyes Alejandro35,Richardson Lorna36,Robertson David L37,Sadegh Sepideh38,Singer Joshua B39,Theys Kristof40,Upton Chris41,Welzel Marius15,Williams Lowri42,Marz Manja18

Affiliation:

1. Friedrich-Schiller-University Jena, Germany

2. EMBL-EBI and the Wellcome Sanger Institute, UK

3. CNRS, France

4. Biocuration and Literature Access at PIR, USA

5. Protein Sequence Resources at EMBL-EBI, UK

6. Technical University of Munich, Germany

7. Computational Biology at ETH Zurich, Switzerland

8. Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany

9. Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina

10. Pfam and InterPro databases, at the EMBL-EBI, UK

11. bioinformatics department at the Robert Koch-Institute, Germany

12. Pfam and MGnify

13. Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany

14. Bioinformatics Division at Philipps-University Marburg, Germany

15. Philipps-University Marburg, Germany

16. Data Science in Biomedicine at the Philipps-University of Marburg, Germany

17. Freie Universität Berlin, Germany

18. Friedrich Schiller University Jena, Germany

19. Biocomplexity Institute and Initiative at the University of Virginia, USA

20. Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany

21. Senior Software Developer

22. Max Planck Institute for the Science of Human History

23. Chandran Lab, Albert Einstein College of Medicine, USA

24. University of Hasselt, Belgium

25. EMBL-EBI, UK

26. Chair of Experimental Bioinformatics at TU Munich, Germany

27. Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany

28. Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA

29. Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France

30. National Center for Biotechnology Information (NCBI)

31. Rambaut group at Edinburgh University, UK

32. GLOBE Institute in the University of Copenhagen, Denmark

33. Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)

34. Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research

35. Universidad de los Andes, Colombia

36. Sequence Families team at EMBL-EBI, UK

37. MRC-University of Glasgow Centre for Virus Research, UK

38. Chair of Experimental Bioinformatics at Technical University of Munich, Germany

39. MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK

40. Rega institute of the University of Leuven, Belgium

41. Department of Biochemistry and Microbiology, University of Victoria, Canada

42. Pfam and InterPro databases, at EMBL-EBI, UK

Abstract

Abstract 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

Funder

Agencia Nacional de Promoción Científica y Tecnológica

Biotechnology and Biological Sciences Research Council

Bundesministerium für Bildung und Forschung

Carl Zeiss Foundation

Deutsche Forschungsgemeinschaft

European Commission

European Molecular Biology Laboratory

Fondation Innovations en Infectiologie

Max Planck Society

Medical Research Council

National Institutes of Health

Intramural Research Program

National Library of Medicine

Swiss Federal Government

State Secretariat for Education, Research and Innovation

Velux Foundations

Wellcome Trust

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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