Introduction
Virus taxonomy has undergone significant transformations in recent years, with the adoption of a comprehensive classification system by the International Committee on Taxonomy of Viruses (ICTV). The current structure includes four large realms, introduced in 2020, and two smaller realms added a year later. However, virus taxonomy is a dynamic field, continuously evolving with new discoveries and deeper evolutionary analyses. This article explores the anticipated changes in virus taxonomy driven by detailed evolutionary studies, the development of frameworks for unclassified viruses, and the discovery of novel viruses through metagenomic and metatranscriptomic research.
Evolutionary Analyses and Their Implications
Recent evolutionary analyses have revealed intriguing complexities within the realm of virus megataxonomy, especially concerning the ribovirians and monodnavirians. These findings have challenged the conventional understanding of these viral groups, suggesting a more intricate evolutionary history than previously appreciated. Despite the presence of universal virus hallmark genes (VHGs) that ostensibly unite each realm, the ribovirians and monodnavirians do not form monophyletic groups in the evolutionary tree.
The evidence points towards multiple independent founder events that have shaped the evolution of these viruses from what were likely non-viral mobile genetic elements (MGEs). This hints at a non-linear evolutionary trajectory for these viral groups, raising fundamental questions about the current taxonomy and classification of viruses.
One of the key dilemmas facing virologists and taxonomists is whether to retain the existing realm structure, which is based on shared VHGs, or to consider a more drastic reorganization. Strict adherence to the principle of monophyly, where a taxonomic group consists of all descendants of a common ancestor, appears to advocate for the splitting of these realms into independent entities to better reflect the evolutionary relationships among viruses.
This proposed realm splitting would signify a significant shift in how we categorize and understand viruses, potentially transforming kingdoms into separate realms with distinct evolutionary histories. Such a restructuring would not only redefine our classification system but also provide new insights into the origins and diversity of viruses, shedding light on their intricate relationship with other genetic elements in the microbial world.
Large-scale metatranscriptome studies have exponentially increased the diversity of ribovirians, leading to the suggestion of new phyla and classes. For example, the discovery of “hot spring riboviruses” or “Artimaviricota,” which encode a distant RNA-dependent RNA polymerase (RdRP), might warrant the creation of a new ribovirian kingdom.
Additionally, eukaryotic viruses in the Anelloviridae family, once considered unrelated to other single-stranded DNA (ssDNA) viruses, are now believed to have evolved from a shotokuviraen ancestor. This discovery suggests the potential assignment of these viruses to the realm Monodnaviria as a new phylum, “Commensaviricota.”
Unclassified Viruses and New Small Realms
Among the known but unclassified viruses, several groups are clear candidates for new small realms. Notably, archaeal viruses with unique virion architectures, such as spindles, bottles, or droplets, do not connect to other viruses through homologous VHGs. Similarly, bacterial viruses in the Plasmaviridae family could be assigned to a new realm due to their distinct characteristics.

The discovery of viroid-like viruses with ribozyme-containing circular RNA genomes through metatranscriptome mining has introduced significant novelty. These include new groups related to kolmiovirids and others that are not, suggesting a major expansion of the realm Ribozyviria. For instance, “ambiviruses,” with the largest genomes among known viroid-like viruses, display a combination of ribovirian and viroid features, indicating a chimeric origin.
Expanding Virus Realms
Metagenome mining has also expanded other large virus realms. A notable discovery is the “mirusviricots,” a group of large viruses with double-stranded DNA (dsDNA) genomes. These viruses possess structural protein VHGs characteristic of duplodnavirians and genes for replication and transcription machineries related to varidnavirian phylum Nucleocytoviricota. This discovery hints at a previously unknown evolutionary link between dsDNA virus realms.
Furthermore, the order Crassvirales of Duplodnaviria, founded by the crAssphage, exemplifies the rapid expansion of virus realms. Initially unique, subsequent metagenome mining identified thousands of related viruses, expanding our understanding of this group’s diversity.
Virus Megataxonomy and Host Ranges
Overlaying virus megataxonomy with host information reveals complex patterns. While viruses from three of the four large realms are found across Bacteria, Archaea, and Eukaryota, ribovirians have not yet been detected in archaea. This absence might be due to insufficient sampling or extreme divergence of the presumed RdRP. The abundance and diversity of viruses differ significantly among host domains, often showing non-overlapping host ranges.

Conclusion
The landscape of virus taxonomy is on the brink of significant transformation, driven by the continual evolution analyses and the unearthing of novel viruses. The existing virus megataxonomy, although thorough, is at the cusp of revisions to assimilate the newfound discoveries. The profound comprehension of the evolutionary relationships and ecological dispersion of viruses is bound to enrich our understanding of their functions in diverse ecosystems and their dynamics with hosts.
Viruses, as microscopic infectious agents, exhibit an immense genetic diversity and versatility in their interactions with hosts and environments. Ongoing evolutionary analyses are shedding light on the intricate evolutionary history of viruses, unveiling connections between different virus families and elucidating the mechanisms underlying their adaptations to various ecological niches.
The discovery of novel viruses, often through metagenomic studies and advanced sequencing technologies, has broadened our perspective on the vast virosphere that exists alongside other life forms on Earth. These discoveries not only expand the boundaries of our knowledge but also challenge existing taxonomic frameworks, necessitating a reevaluation of the classification and nomenclature of viruses.
By delving deeper into the evolutionary and ecological aspects of viruses, researchers can unravel the complexities of virus-host interactions and their impacts on ecosystems. Understanding the roles that viruses play in shaping ecological communities, influencing disease dynamics, and driving evolutionary processes is crucial for mitigating viral threats and harnessing the potential benefits that viruses may offer in biotechnological and medical advancements.
In essence, the evolving landscape of virus taxonomy presents a dynamic field of study that promises to enhance our understanding of viruses as integral components of the biosphere, while also highlighting the need for continual adaptation and innovation in taxonomy and virology research.
For the latest updates on virus taxonomy and research, visit the ICTV website.
FAQs
Q1: What is virus megataxonomy? A1: Virus megataxonomy is a comprehensive classification system that categorizes viruses into realms, kingdoms, phyla, and other ranks based on evolutionary relationships and shared virus hallmark genes (VHGs).
Q2: How do evolutionary analyses impact virus taxonomy? A2: Evolutionary analyses challenge existing classifications by revealing multiple independent origins and evolutionary paths for viruses. These insights may lead to splitting current realms or redefining taxonomic structures based on monophyly criteria.
Q3: What are some examples of unclassified viruses that may form new realms? A3: Examples include archaeal viruses with unique virion architectures and bacterial viruses in the Plasmaviridae family. These groups do not connect to other viruses through homologous VHGs, suggesting the need for new taxonomic realms.
Q4: How do metagenomics and metatranscriptomics contribute to virus taxonomy? A4: These technologies enable high-throughput sequencing of environmental and host-associated viromes, revealing a vast diversity of viruses. They play a crucial role in discovering new viruses and expanding existing taxonomic realms.