Towards an integrative view of virus phenotypes

John P DeLong¹, Maitham A Al-Sammak^{2

3}, Zeina T Al-Ameeli^{3

4}, David D Dunigan^{3

5}, Kyle F Edwards⁶, Jeffry J Fuhrmann^{7

8}, Jason P Gleghorn^{8

9}, Hanqun Li^{8

10}, Kona Haramoto^{7

10}, Amelia O Harrison^{7

10}, Marcia F Marston¹¹, Ryan M Moore^{10

12}, Shawn W Polson^{7

8

10

12}, Barbra D Ferrell^{10

12}, Miranda E Salsbery¹³, Christopher R Schvarcz⁶, Jasmine Shirazi⁹, Grieg F Steward⁶, James L Van Etten^{3

5}, K Eric Wommack^{14

15

16}

Affiliations

¹ School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA. jpdelong@unl.edu.
² Tropical Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
³ Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.
⁴ Medical Technical Institutes, Middle Technical University, Baghdad, Iraq.
⁵ Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.
⁶ Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.
⁷ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
⁸ Department of Biological Sciences, University of Delaware, Newark, DE, USA.
⁹ Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.
¹⁰ Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
¹¹ Department of Biology and Marine Biology, Roger Williams University, Bristol, RI, USA.
¹² Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
¹³ School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
¹⁴ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.
¹⁵ Department of Biological Sciences, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.
¹⁶ Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.

PMID: 34522049
DOI: 10.1038/s41579-021-00612-w

Review

Towards an integrative view of virus phenotypes

John P DeLong et al. Nat Rev Microbiol. 2022 Feb.

. 2022 Feb;20(2):83-94.

doi: 10.1038/s41579-021-00612-w. Epub 2021 Sep 14.

Authors

Affiliations

¹ School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA. jpdelong@unl.edu.
² Tropical Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
³ Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.
⁴ Medical Technical Institutes, Middle Technical University, Baghdad, Iraq.
⁵ Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.
⁶ Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.
⁷ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
⁸ Department of Biological Sciences, University of Delaware, Newark, DE, USA.
⁹ Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.
¹⁰ Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
¹¹ Department of Biology and Marine Biology, Roger Williams University, Bristol, RI, USA.
¹² Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
¹³ School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
¹⁴ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.
¹⁵ Department of Biological Sciences, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.
¹⁶ Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA. wommack@dbi.udel.edu.

PMID: 34522049
DOI: 10.1038/s41579-021-00612-w

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.

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References

1. Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007). - PubMed
1. Rohwer, F. & Thurber, R. V. Viruses manipulate the marine environment. Nature 459, 207–212 (2009). - PubMed
1. Simmonds, P. et al. Virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15, 161–168 (2017). - PubMed
1. Fuhrman, J. A. Marine viruses and their biogeochemical and ecological effects. Nature 399, 541–548 (1999). - PubMed
1. Suttle, C. A. Viruses in the sea. Nature 437, 356–361 (2005). - PubMed

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Towards an integrative view of virus phenotypes

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Towards an integrative view of virus phenotypes

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Abstract

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Full Text Sources