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.

了解表型如何从基因型中出现是生物学的一个基本目标。在考虑细胞生命时，这项任务虽然具有挑战性，但在病毒的情况下则更加复杂。在复制过程中，作为离散实体（病毒体）的病毒消失并表现为病毒和宿主（病毒细胞）之间的代谢混合物。识别明确构成病毒表型的特征对于病毒体来说很简单，而对于病毒细胞来说则不然。在这里，我们提出了一个对病毒表型进行分类的框架，该框架包括病毒体和病毒细胞阶段，并在适应度的背景下考虑病毒的功能和性能特征。