Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

Erica T Prates^#^{1

2}, Michael R Garvin^#^{1

2}, Piet Jones³, J Izaak Miller^{1

2}, Kyle A Sullivan^{1

2}, Ashley Cliff³, Joao Gabriel Felipe Machado Gazolla^{1

2}, Manesh B Shah⁴, Angelica M Walker³, Matthew Lane³, Christopher T Rentsch^{5

6}, Amy Justice^{6

7}, Mirko Pavicic^{1

2}, Jonathon Romero³, Daniel Jacobson^{8

9

10

11

12}

Affiliations

¹ Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA.
² National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
³ The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
⁴ Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA.
⁵ Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
⁶ VA Connecticut Healthcare/General Internal Medicine, West Haven, CT, USA.
⁷ Yale University School of Medicine, New Haven, CT, USA.
⁸ Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA. jacobsonda@ornl.gov.
⁹ National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA. jacobsonda@ornl.gov.
¹⁰ The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.
¹¹ Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.
¹² Department of Psychology, NeuroNet Research Center, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.

^# Contributed equally.

PMID: 35554915
DOI: 10.1007/978-1-0716-2111-0_19

Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

Erica T Prates et al. Methods Mol Biol. 2022.

. 2022:2452:317-351.

doi: 10.1007/978-1-0716-2111-0_19.

Authors

Affiliations

¹ Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA.
² National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
³ The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
⁴ Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA.
⁵ Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
⁶ VA Connecticut Healthcare/General Internal Medicine, West Haven, CT, USA.
⁷ Yale University School of Medicine, New Haven, CT, USA.
⁸ Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA. jacobsonda@ornl.gov.
⁹ National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA. jacobsonda@ornl.gov.
¹⁰ The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.
¹¹ Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.
¹² Department of Psychology, NeuroNet Research Center, University of Tennessee Knoxville, Knoxville, TN, USA. jacobsonda@ornl.gov.

^# Contributed equally.

PMID: 35554915
DOI: 10.1007/978-1-0716-2111-0_19

Abstract

The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.

Keywords: Antiviral; COVID-19; Multiomics; Pandemic; SARS-CoV-2; Systems Biology.

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References

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Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

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Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

Authors

Affiliations

Abstract

References

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LinkOut - more resources

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