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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This Review was inspired by discussions at a workshop supported by the US National Science Foundation under grant no. 1736030, and by the Delaware INBRE programme, with a grant from the US National Institute of General Medical Sciences (P20 GM103446) from the US National Institutes of Health and the State of Delaware.
The authors declare no competing interests.
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When genome segments from different infecting viruses combine to form a new viral genome.
A length of viral genome occurring within a host cell.
- T number
The number of sides of a virion.
A genome separated into different parts and not physically connected.
Referring to a virus with a non-segmented genome.
Referring to a virus with a genome segmented into two parts.
- Multiplicity of infection
The ratio of infecting viruses to hosts.
- G+C content
The proportion of all the nucleotides that are guanine or cytosine.
Host proteins that can inhibit virus reproduction.
- Restriction–modification systems
A tool for breaking up foreign DNA within host cells.
- CRISPR–Cas immunity
Genetic sequences that can be used to identify and destroy foreign genomes.
Cytoplasmic connections between neighbouring plant cells.
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DeLong, J.P., Al-Sammak, M.A., Al-Ameeli, Z.T. et al. Towards an integrative view of virus phenotypes. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00612-w