Martin Cody, Emerson Joanne B, Roux Simon, Anantharaman Karthik
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
Nat Microbiol. 2025 Aug 27. doi: 10.1038/s41564-025-02095-4.
Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes are highly compact and have limited coding capacity for accessory genes. Advances in viral (meta)genomics have expanded the detection of putative AMGs from viruses in diverse environments. However, this has also led to many instances of misannotation due to the limitations of annotation tools, resulting in misinterpretations about the roles of some viral genes. Here, we highlight studies that support claims about AMGs with more than just function predictions for guidance on best practices. We then propose the adoption of an expanded, inclusive view of all genes auxiliary to core viral functions with the term 'auxiliary viral genes' (AVGs), alongside an associated eco-evolutionary framework for considering the types of analyses that can better support claims made about AVGs.
病毒编码的辅助代谢基因（AMGs）是一类非必需基因，它们通过在感染过程中维持或操纵宿主代谢来提高病毒的适应性。从进化的角度来看，AMGs很有趣，因为大多数病毒基因组高度紧凑，辅助基因的编码能力有限。病毒（宏）基因组学的进展扩大了对不同环境中病毒推定AMGs的检测。然而，由于注释工具的局限性，这也导致了许多错误注释的情况，从而对一些病毒基因的作用产生误解。在这里，我们重点介绍了一些研究，这些研究不仅仅通过功能预测来支持关于AMGs的说法，还为最佳实践提供指导。然后，我们建议采用一种更广泛、包容性更强的观点来看待所有辅助核心病毒功能的基因，即使用“辅助病毒基因”（AVGs）这一术语，并提出一个相关的生态进化框架，以考虑能够更好地支持关于AVGs说法的分析类型。
