Baltimore classification

Abstract: The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

Abstract: Fifty years ago, David Baltimore published a brief conceptual paper delineating the classification of viruses by the routes of genome expression. The six "Baltimore classes" of viruses, with a subsequently added 7th class, became the conceptual framework for the development of virology during the next five decades. During this time, it became clear that the Baltimore classes, with relatively minor additions, indeed cover the diversity of virus genome expression schemes that also define the replication cycles. Here, we examine the status of the Baltimore classes 50 years after their advent and explore their links with the global ecology and biology of the respective viruses. We discuss an extension of the Baltimore scheme and why many logically admissible expression-replication schemes do not appear to be realized in nature. Recent phylogenomic analyses allow tracing the complex connections between the Baltimore classes and the monophyletic realms of viruses. The five classes of RNA viruses and reverse-transcribing viruses share an origin, whereas both the single-stranded DNA viruses and double-stranded DNA (dsDNA) viruses evolved on multiple independent occasions. Most of the Baltimore classes of viruses probably emerged during the earliest era of life evolution, at the stage of the primordial pool of diverse replicators, and before the advent of modern-like cells with large dsDNA genomes. The Baltimore classes remain an integral part of the conceptual foundation of biology, providing the essential structure for the logical space of information transfer processes, which is nontrivially connected with the routes of evolution of viruses and other replicators.

Abstract: DNA viruses contain DNA as their genetic material. DNA viruses infecting plants are classified into two groups according to the Baltimore classification of viruses: single-stranded (ssDNA) DNA viruses (e.g., Geminiviruses) and double-stranded DNA viruses (e.g., Caulimoviruses). There are fewer plant DNA viruses, but they cause a significant number of devastating diseases in numerous crops worldwide and severely reduce the crop yield. Plant DNA viruses are notably rare as compared with animal and bacterial DNA viruses. This chapter focuses on the biochemistry, replication and molecular genetics of plant DNA viruses. The ssDNA plant viruses are small, encode few proteins, and depend mainly on the host factor for their replication. Geminiviruses, a newly discovered group of plant viruses, have single-stranded circular DNA in their genome. The nucleocapsids are isometric units bonded together in pairs. Geminiviruses are among the smallest autonomously replicating viruses known so far. For this and other reasons, geminiviruses are of considerable fundamental interest in plant molecular genetics and plant pathology. The family Geminiviridae has been classified into nine genera (Begomovirus, Curtovirus, Capulavirus, Becurtovirus, Eragrovirus, Grablovirus, Topocuvirus, Mastrevirus, and Turncurtovirus) on the basis of phylogenetic analysis, genome organization (monopartitite or bipartite), vector transmission (whiteflies, treehoppers, aphids, or leafhoppers), and host range (monocots or dicots). Often, three types of circular ssDNA satellite complex (betasatellite, deltasatellite, and alphasatellite) have been associated with old-world monopartite begomoviruses. Betasatellite and deltasatellite are now classified in the genera Betasatellite and Deltasatellite in the subviral family Tolecusatellitidae. A new classification of alphasatellites in the family Alphasatellitidae is introduced. The Alphasatellitidae are further classified into the subfamilies Nanoalphasatellitinae (nanovirus-associated alphasatellites) and Geminialphasatellitinae (geminivirus-associated alphasatellites).

Abstract: The virus was first described 120 years ago as a filterable, transmissible agent that causes disease in plants and animals. A virus is a “submicroscopic and intracellular parasite” that can propagate only inside a living cell. The obligatory nature of a virus brought a debate on whether it is living or nonliving. Virology, as a discipline that studies the diverse aspects of viral infection of host cells and its consequence, became established during the early 20th century. Viruses are found in almost all living organisms on earth, ranging from bacteria, fungi, and amoeba, to plants and animals. Viruses are classified into seven groups, according to genomic features. This molecular classification, also called the “Baltimore classification,” allows us to predict precisely the mode of viral genome replication.