The Baltimore classification of viruses 50 years later: how does it stand in the light of virus evolution?

EV Koonin, M Krupovic, VI Agol - Microbiology and Molecular …, 2021 - journals.asm.org
SUMMARY 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” …

Origin of viruses: primordial replicators recruiting capsids from hosts

M Krupovic, VV Dolja, EV Koonin - Nature Reviews Microbiology, 2019 - nature.com
Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on
Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their …

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

H Bin Jang, B Bolduc, O Zablocki, JH Kuhn… - Nature …, 2019 - nature.com
Microbiomes from every environment contain a myriad of uncultivated archaeal and
bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable …

[HTML][HTML] Marine DNA viral macro-and microdiversity from pole to pole

AC Gregory, AA Zayed, N Conceição-Neto… - Cell, 2019 - cell.com
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan,
gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community …

Origins and evolution of the global RNA virome

YI Wolf, D Kazlauskas, J Iranzo, A Lucía-Sanz, JH Kuhn… - MBio, 2018 - journals.asm.org
Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in
animals and plants. The recent advances of metaviromics prompted us to perform a detailed …

ViPTree: the viral proteomic tree server

Y Nishimura, T Yoshida, M Kuronishi, H Uehara… - …, 2017 - academic.oup.com
ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for
classification of viruses based on genome-wide similarities. Users can upload viral genomes …

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes

S Roux, M Krupovic, RA Daly, AL Borges… - Nature …, 2019 - nature.com
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique
morphology, genome content and infection cycle. One of the most striking features of …

Megataxonomy and global ecology of the virosphere

EV Koonin, JH Kuhn, VV Dolja, M Krupovic - The ISME Journal, 2024 - academic.oup.com
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most
abundant biological entities in the biosphere. With recent advances in metagenomics and …

Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

E Pfeifer, JA Moura de Sousa, M Touchon… - Nucleic acids …, 2021 - academic.oup.com
Plasmids and temperate phages are key contributors to bacterial evolution. They are usually
regarded as very distinct. However, some elements, termed phage–plasmids, are known to …

Multiple origins of viral capsid proteins from cellular ancestors

M Krupovic, EV Koonin - Proceedings of the National Academy of …, 2017 - pnas.org
Viruses are the most abundant biological entities on earth and show remarkable diversity of
genome sequences, replication and expression strategies, and virion structures …