Towards an integrative view of virus phenotypes

John P. DeLong; Maitham A. Al-Sammak; Zeina T. Al-Ameeli; David D. Dunigan; Kyle F. Edwards; Jeffry J. Fuhrmann; Jason P. Gleghorn; Hanqun Li; Kona Haramoto; Amelia O. Harrison; Marcia F. Marston; Ryan M. Moore; Shawn W. Polson; Barbra D. Ferrell; Miranda E. Salsbery; Christopher R. Schvarcz; Jasmine Shirazi; Grieg F. Steward; James L. Van Etten; K. Eric Wommack

doi:10.1038/s41579-021-00612-w

Towards an integrative view of virus phenotypes

John P. DeLong, Maitham A. Al-Sammak, Zeina T. Al-Ameeli, David D. Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack

Plant Pathology

Research output: Contribution to journal › Review article › peer-review

8 Scopus citations

Abstract

Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus’s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in the context of fitness. Such an integrated view of virus phenotype is necessary for comprehensive interpretation of viral genome sequences and will advance our understanding of viral evolution and ecology.

Original language	English (US)
Pages (from-to)	83-94
Number of pages	12
Journal	Nature Reviews Microbiology
Volume	20
Issue number	2
DOIs	https://doi.org/10.1038/s41579-021-00612-w
State	Published - Feb 2022

ASJC Scopus subject areas

Microbiology
Immunology and Microbiology(all)
Infectious Diseases

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10.1038/s41579-021-00612-w

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DeLong, J. P., Al-Sammak, M. A., Al-Ameeli, Z. T., Dunigan, D. D., Edwards, K. F., Fuhrmann, J. J., Gleghorn, J. P., Li, H., Haramoto, K., Harrison, A. O., Marston, M. F., Moore, R. M., Polson, S. W., Ferrell, B. D., Salsbery, M. E., Schvarcz, C. R., Shirazi, J., Steward, G. F., Van Etten, J. L., & Wommack, K. E. (2022). Towards an integrative view of virus phenotypes. Nature Reviews Microbiology, 20(2), 83-94. https://doi.org/10.1038/s41579-021-00612-w

DeLong, JP, Al-Sammak, MA, Al-Ameeli, ZT, Dunigan, DD, Edwards, KF, Fuhrmann, JJ, Gleghorn, JP, Li, H, Haramoto, K, Harrison, AO, Marston, MF, Moore, RM, Polson, SW, Ferrell, BD, Salsbery, ME, Schvarcz, CR, Shirazi, J, Steward, GF, Van Etten, JL & Wommack, KE 2022, 'Towards an integrative view of virus phenotypes', Nature Reviews Microbiology, vol. 20, no. 2, pp. 83-94. https://doi.org/10.1038/s41579-021-00612-w

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abstract = "Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus{\textquoteright}s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in the context of fitness. Such an integrated view of virus phenotype is necessary for comprehensive interpretation of viral genome sequences and will advance our understanding of viral evolution and ecology.",

author = "DeLong, {John P.} and Al-Sammak, {Maitham A.} and Al-Ameeli, {Zeina T.} and Dunigan, {David D.} and Edwards, {Kyle F.} and Fuhrmann, {Jeffry J.} and Gleghorn, {Jason P.} and Hanqun Li and Kona Haramoto and Harrison, {Amelia O.} and Marston, {Marcia F.} and Moore, {Ryan M.} and Polson, {Shawn W.} and Ferrell, {Barbra D.} and Salsbery, {Miranda E.} and Schvarcz, {Christopher R.} and Jasmine Shirazi and Steward, {Grieg F.} and {Van Etten}, {James L.} and Wommack, {K. Eric}",

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doi = "10.1038/s41579-021-00612-w",

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AU - Al-Sammak, Maitham A.

AU - Al-Ameeli, Zeina T.

AU - Dunigan, David D.

AU - Edwards, Kyle F.

AU - Fuhrmann, Jeffry J.

AU - Gleghorn, Jason P.

AU - Li, Hanqun

AU - Haramoto, Kona

AU - Harrison, Amelia O.

AU - Marston, Marcia F.

AU - Moore, Ryan M.

AU - Polson, Shawn W.

AU - Ferrell, Barbra D.

AU - Salsbery, Miranda E.

AU - Schvarcz, Christopher R.

AU - Shirazi, Jasmine

AU - Steward, Grieg F.

AU - Van Etten, James L.

AU - Wommack, K. Eric

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Towards an integrative view of virus phenotypes

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