Abstract
Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.
Highlights
Viral particles: free viruses in the environment not actively infecting a host; known as virions
Reaching magnification levels as high as 1,000,000× and resolving structures measuring only a few nanometers, electron microscopy (EM) allowed individual viruses to be distinguished based on their sizes and overall viral structures [12]
In 1967 Eisenstark published morphological descriptions, including EM images, of the 111 known bacteriophages; he was followed by Ackermann, who reviewed phages as a group in a series of publications spanning several decades [13, 14]
Summary
Http://vogdb.org/ Grazziotin et al 2017 [126] Goodacre et al 2018 [127] Roux et al 2020 [41]. One possibility would be to establish genome-based phylogenies of all sequenced viral groups, encompassing both cultivated and uncultivated viruses, analogous to the Genome Taxonomy Database developed for bacteria and archaea [70] This approach could shed new light on the evolution of the virosphere and facilitate new methods for the automated taxonomic annotation of viral genomes. CRISPR matching is performed by identifying near-perfect alignments between CRISPR spacers and viral genomes, indicating a history of past infection While this approach is accurate for assigning the host at low ranks (e.g., species), CRISPR-Cas systems are only found in ∼40% of bacteria and 70% of archaea [74] and can be entirely absent from certain prokaryotic lineages [75], and CRISPR arrays can be challenging to assemble from short-read data [76]. Host–virus genomic similarity is another commonly used approach [41, 80], which is
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