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

Erica T. Prates; Michael R. Garvin; Piet Jones; J. Izaak Miller; Kyle A. Sullivan; Ashley Cliff; Joao Gabriel Felipe Machado Gazolla; Manesh B. Shah; Angelica M. Walker; Matthew Lane; Christopher T. Rentsch; Amy Justice; Mirko Pavicic; Jonathon Romero; Daniel Jacobson

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

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

Erica T. Prates, Michael R. Garvin, Piet Jones, J. Izaak Miller, Kyle A. Sullivan, Ashley Cliff, Joao Gabriel Felipe Machado Gazolla, Manesh B. Shah, Angelica M. Walker, Matthew Lane, Christopher T. Rentsch, Amy Justice, Mirko Pavicic, Jonathon Romero, Daniel Jacobson

Computational and Predictive Biology

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	317-351
Number of pages	35
DOIs	https://doi.org/10.1007/978-1-0716-2111-0_19
State	Published - 2022

Publication series

Name	Methods in Molecular Biology
Volume	2452
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Funding

This research funded by the Laboratory Directed Research and Development and Seed funding programs of Oak Ridge National Laboratory (LOIS:10074,10124) and the DOE Office of Science through the National Virtual Biotechnology Laboratory (NVBL), a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) and the Compute and Data Environment for Science (CADES) at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. Figures were generated with Biorender and VMD. Erica T. Prates and Michael R. Garvin contributed equally to this work. Author Contributions: Erica Prates (Conceptualization, Investigation, Methodology, Visualization, Writing—original draft, review and editing), Michael Garvin (Conceptualization, Investigation, Methodology, Visualization, Writing——original draft, review and editing), Piet Jones (Investigation, Methodology, Writing— original draft, review and editing, visualization), J. Izaak Miller (Writing—original draft, Writing—review and editing), Kyle A. Sullivan (Investigation, Writing—original draft, Writing— review and editing), Ashley Cliff (Investigation, Methodology, Writing—original draft, Writing—review and editing), Joao Gabriel Felipe Machado Gazolla (Investigation, Methodology, Visualization, Writing—original draft, Writing—review and editing), Man-esh Shah (Investigation, Methodology, Writing—original draft, review and editing), Angelica M. Walker (Investigation, Methodology, Writing—original draft, review and editing), Matthew Lane (Investigation, Methodology, Writing—original draft, review and editing), Christopher Rentsch (Investigation, Methodology, Writing—original draft, review and editing), Amy Justice (Investigation, Methodology, Writing—original draft, review and editing), Mirko Pavicic (Writing—original draft, review and editing), Jona-thon Romero (Investigation, Methodology, Writing—original draft, review and editing), Daniel Jacobson (Conceptualization, Formal Analysis, Funding acquisition, Methodology, Supervision, Writing—original draft, Writing—review and editing). This work was also funded by the United States Government.

Funders	Funder number
Compute and Data Environment for Science
National Virtual Biotechnology Laboratory
United States Government
U.S. Department of Energy	DE-AC05-00OR22725
Office of Science
Oak Ridge National Laboratory
Laboratory Directed Research and Development

Keywords

Antiviral
COVID-19
Multiomics
Pandemic
SARS-CoV-2
Systems Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/978-1-0716-2111-0_19

Cite this

Prates, E. T., Garvin, M. R., Jones, P., Miller, J. I., Sullivan, K. A., Cliff, A., Gazolla, J. G. F. M., Shah, M. B., Walker, A. M., Lane, M., Rentsch, C. T., Justice, A., Pavicic, M., Romero, J., & Jacobson, D. (2022). Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. In Methods in Molecular Biology (pp. 317-351). (Methods in Molecular Biology; Vol. 2452). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2111-0_19

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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",

author = "Prates, {Erica T.} and Garvin, {Michael R.} and Piet Jones and Miller, {J. Izaak} and Sullivan, {Kyle A.} and Ashley Cliff and Gazolla, {Joao Gabriel Felipe Machado} and Shah, {Manesh B.} and Walker, {Angelica M.} and Matthew Lane and Rentsch, {Christopher T.} and Amy Justice and Mirko Pavicic and Jonathon Romero and Daniel Jacobson",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2022",

doi = "10.1007/978-1-0716-2111-0_19",

language = "English",

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publisher = "Humana Press Inc.",

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Prates, ET, Garvin, MR, Jones, P, Miller, JI, Sullivan, KA, Cliff, A, Gazolla, JGFM, Shah, MB, Walker, AM, Lane, M, Rentsch, CT, Justice, A, Pavicic, M, Romero, J & Jacobson, D 2022, Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2452, Humana Press Inc., pp. 317-351. https://doi.org/10.1007/978-1-0716-2111-0_19

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AU - Garvin, Michael R.

AU - Jones, Piet

AU - Miller, J. Izaak

AU - Sullivan, Kyle A.

AU - Cliff, Ashley

AU - Gazolla, Joao Gabriel Felipe Machado

AU - Shah, Manesh B.

AU - Walker, Angelica M.

AU - Lane, Matthew

AU - Rentsch, Christopher T.

AU - Justice, Amy

AU - Pavicic, Mirko

AU - Romero, Jonathon

AU - Jacobson, Daniel

PY - 2022

Y1 - 2022

N2 - 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.

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KW - Multiomics

KW - Pandemic

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ER -

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

Abstract

Publication series

Funding

Keywords

UN SDGs

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