Reassessing Viral Origins: From Escaped Genes to Degenerated Microbes

The origin of viruses remains one of the most complex and unresolved questions in biology. Several major hypotheses have been proposed to explain their emergence: the exogenisation (escape) hypothesis, which posits that mobile genetic elements acquired infectivity and autonomy; the degeneration hypothesis, which holds that viruses are the result of gene loss from more complex, possibly cellular, organisms; and the virus-first hypothesis, which suggests that viruses are ancient, pre-cellular entities. In this review, we examine these models in light of current molecular, structural, and ecological data. Key considerations include the lack of homologues for many viral proteins, the existence of giant DNA viruses with extensive gene repertoires, the widespread conservation of capsid architecture, and the obligate dependence of all viruses on living host cells. We also discuss recent metaviromic discoveries that have uncovered the vast scale and diversity of the global virosphere—particularly in marine environments—where viruses play central roles in microbial population dynamics and major biogeochemical processes. These findings underscore the need to view viruses as integral components of biological systems, rather than as peripheral or purely parasitic entities. While no single hypothesis fully accounts for the origin of all virus types, the enormous functional and genetic complexity of viruses suggests that a unified explanation may remain out of reach. This review supports a multifaceted approach that considers both genomic features and ecological function across a wide range of viral forms.