RNA Phage Biology in a Metagenomic Era

Abstract

The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.

Sustained RNA virome diversity in Antarctic penguins and their ticks

“…Due to the nature of the cloacal swabs, it is impossible to accurately determine the host for these viruses, although some information can be gleaned from the families in which these virus fall. For example, the Narnaviridae are known to infect fungi and protists, while the related Leviviridae infect bacteria [58][59][60][61]. Other novel viruses fell within invertebrate associated clades of the Nodaviridae and Tombusviridae, associated with both vertebrate and invertebrate infecting viruses in the Picornavirales [36].…”

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

“…The case is well illustrated by the families Microviridae and Leviviridae, which have received relatively little attention from the ICTV (i.e., two subfamilies, six genera and 21 species versus two genera and four species, respectively). Environmental studies have indicated that the family Microviridae contains at least five unclassified subfamilies [40][41][42][43][44][45][46][47]. Recently, Callanan et al [48] predicted 331 species and 247 genera among the single-stranded RNA phages, potentially leading to a significant expansion of the family Leviviridae.…”

Carbon dots for effective photodynamic inactivation of virus

“…Generally bacteriophages use specialized surface receptor-binding proteins to interact with and adhere to their specic cognate host receptors, and then the phages use various mechanisms to breach the bacterial cell wall and inject their genome into the host bacterial cell, leaving the empty phage capsid outside the cell. 45 Once the viral genome is uncoated in Fig. 1 A cartoon illustration on the structure of CDots in general, with the carbon nanoparticle surface functionalization by EDA molecules highlighted for EDA-CDots.…”

“…Aer the synthesis of viral genome and proteins, the proteins are packaged with the newly replicated viral genomes to assemble new virions ready to be released from the host cells, resulting in the lysis of infected host cells. 45 However, in some other cases, viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specic site in the host's chromosome. 41 Many antiviral agents/drugs are designed to target either viral proteins or host factors.…”