34-514: Jingmenvirus is a group of positive-sense single-stranded RNA viruses with segmented genomes . They are primarily associated with arthropods and are one of only two known segmented RNA viruses that infect animal hosts. The first group member, the Jingmen tick virus (JMTV), was described in 2014. Another member, the Guaico Culex virus (GCXV), has a highly unusual multicomponent architecture in which
68-438: A genome and as messenger RNA ; it can be directly translated into protein in the host cell by host ribosomes . The first proteins to be expressed after infection serve genome replication functions; they recruit the positive-strand viral genome to viral replication complexes formed in association with intracellular membranes. These complexes contain proteins of both viral and host cell origin, and may be associated with
102-434: A combination of filtration, density centrifugation, and enzymatic treatments to get rid of free nucleic acids. The nucleic acids are then sequenced and analyzed using metagenomic methods. Alternatively, there are recent computational methods that use directly metagenomic assembled sequences to discover viruses. The Global Ocean Viromes (GOV) is a dataset consisting of deep sequencing from over 150 samples collected across
136-404: A single capsid. Homology has consistently been observed between the genes encoding non-structural proteins of jingmenviruses and flaviviruses, including RNA-dependent RNA polymerase . However, the genomic architecture of the homologous genes varies significantly; the canonical flavivirus genome consists of a single open reading frame (ORF) whose protein product is processed by proteases , whereas
170-553: A sister clade in relation to Lenarviricota . The third phylum that contains +ssRNA viruses is Pisuviricota , which has been informally called the "picornavirus supergroup". The phylum contains a large assemblage of eukaryotic viruses known to infect animals, plants, fungi, and protists. The phylum contains three classes, two of which contain only +ssRNA viruses: Pisoniviricetes , which contains nidoviruses , picornaviruses , and sobeliviruses , and Stelpaviricetes , which contains potyviruses and astroviruses . The third class
204-518: Is Duplopiviricetes , whose members are double-stranded RNA viruses that are descended from +ssRNA viruses. Virome Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or holobiont . The word is frequently used to describe environmental viral shotgun metagenomes . Viruses , including bacteriophages , are found in all environments, and studies of
238-649: Is a multicomponent ( multipartite ) virus in which each genome segment is enclosed in its small, enveloped viral capsid . At least three genome segments, containing genes for non-structural proteins and capsid components, must enter a cell to infect it and reproduce the virus successfully. Before the discovery of GMXV, multicomponent architecture had previously been reported only in viruses that infect plants and fungi , and had never been observed in an enveloped virus. Genetic material that likely belongs to other jingmenviruses can be identified through bioinformatics . In some cases, such sequences were not recognized as viral or
272-580: Is frequently referred to as metagenomics. In the 2000s, the Rohwer lab sequenced viromes from seawater, marine sediments, adult human stool, infant human stool, soil, and blood. This group also performed the first RNA virome with collaborators from the Genomic Institute of Singapore. From these early works, it was concluded that most of the genomic diversity is contained in the global virome and that most of this diversity remains uncharacterized. This view
306-473: Is further disrupted by viral proteases degrading components required to initiate translation of cellular mRNA. All positive-strand RNA virus genomes encode RNA-dependent RNA polymerase , a viral protein that synthesizes RNA from an RNA template. Host cell proteins recruited by +ssRNA viruses during replication include RNA-binding proteins , chaperone proteins , and membrane remodeling and lipid synthesis proteins, which collectively participate in exploiting
340-664: The Retroviridae (e.g. HIV ), genome damage appears to be avoided during reverse transcription by strand switching, a form of recombination. Recombination occurs in the Coronaviridae (e.g. SARS ). Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Recombination can also occur infrequently between +ssRNA viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans, as in
374-480: The host cell's ribosomes . Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome. Positive-strand RNA viruses are divided between the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota (specifically classes Pisoniviricetes and Stelpavirictes ) all of which are in
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#1732870065170408-616: The virome , the evolutionary mechanism underlying this structure is unclear. Likewise, It is unclear whether multicomponent architecture is a distinct evolutionary strategy or an artifact of the segmentation mechanism, possibly via the formation of defective interfering particles . Positive-sense single-stranded RNA virus Positive-strand RNA viruses ( +ssRNA viruses ) are a group of related viruses that have positive-sense , single-stranded genomes made of ribonucleic acid . The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by
442-502: The IMG/VR system -the largest interactive public virus database contained 265,000 metagenomic viral sequences and isolate viruses. This number scaled up to over 760,000 in November 2018 (IMG/VR v.2.0). The IMG/VR systems serve as a starting point for the sequence analysis of viral fragments derived from metagenomic samples. The human virome encompasses the diverse viral communities residing in
476-472: The JMTV genome have no known homologs. In addition to identification in ticks, JMTV has also been identified in low abundances in mosquitoes such as Aedes albopictus . The Guaico Culex virus (GCXV) was reported in 2016 after isolation from Culex mosquitoes found near Guaico , Trinidad. Different virus isolates have four or five genome segments, though the fifth is not essential for viral proliferation. GCXV
510-478: The apparent descendants of leviviruses, which infect eukaryotes . The phylum is divided into four classes: Leviviricetes , which contains leviviruses and their relatives, Amabiliviricetes , which contains narnaviruses and their relatives, Howeltoviricetes , which contains mitoviruses and their relatives, and Miaviricetes , which contains botourmiaviruses and their relatives. Based on phylogenetic analysis of RdRp, all other RNA viruses are considered to comprise
544-764: The body. Prior advances in high-throughput sequencing (HTS) revealed insights into their diversity, evolutionary dynamics, and genome integrations. However, due to shallow sequencing in the past, the genetic composition and diversity of tissue-resident viruses remained poorly characterized, hindering understanding of their roles in pathogenesis and viral evolution. In 2024, a study of the virome examined persistent viruses in multiple organs from individuals who died of non-viral causes, revealing that viral sequences were highly conserved within each person, indicating persistence from single dominant strains. Increased viral diversity in two cases suggested that reactivation may influence variability. The study also identified selective pressures from
578-739: The case of SARS and MERS. Positive-strand RNA viruses are common in plants. In tombusviruses and carmoviruses , RNA recombination occurs frequently during replication. The ability of the RNA-dependent RNA polymerase of these viruses to switch RNA templates suggests a copy choice model of RNA recombination that may be an adaptive mechanism for coping with damage in the viral genome. Other +ssRNA viruses of plants have also been reported to be capable of recombination, such as Brom mosaic bromovirus and Sindbis virus . Positive-strand RNA viruses are found in three phyla: Kitrinoviricota , Lenarviricota , and Pisuviricota , each of which are assigned to
612-453: The cell's secretory pathway for viral replication. Numerous positive-strand RNA viruses can undergo genetic recombination when at least two viral genomes are present in the same host cell. The capability for recombination among +ssRNA virus pathogens of humans is common. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae (e.g. poliovirus). In
646-519: The coronaviruses and rhinoviruses that cause the common cold . Positive-strand RNA virus genomes usually contain relatively few genes, usually between three and ten, including an RNA-dependent RNA polymerase. Coronaviruses have the largest known RNA genomes, between 27 and 32 kilobases in length, and likely possess replication proofreading mechanisms in the form of an exoribonuclease within nonstructural protein nsp14. Positive-strand RNA viruses have genetic material that can function both as
680-553: The genome segments are separately enclosed in different viral capsids. The group's first member was described in 2014 and named the Jingmen tick virus (JMTV) because it was isolated from a tick sampled in Jingmen , China. It is an enveloped spherical virus slightly larger than its closest viral relatives. The JMTV genome has four segments, two containing genes with sequence homology to non-structural proteins found in flaviviruses , including methyltransferase and RNA-dependent RNA polymerase . The putative structural proteins in
714-428: The host. Spacers from isolate microbial genomes with matches to metagenomic viral contigs (mVCs) were identified for 4.4% of the viral groups and 1.7% of singletons. The hypothesis was explored that viral transfer RNA (tRNA) genes originate from their host. Viral tRNAs identified in 7.6% of the mVCs were matched to isolate genomes from a single species or genus. The specificity of tRNA-based host viral assignment
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#1732870065170748-590: The kingdom Orthornavirae and realm Riboviria . They are monophyletic and descended from a common RNA virus ancestor. In the Baltimore classification system, +ssRNA viruses belong to Group IV. Positive-sense RNA viruses include pathogens such as the Hepatitis C virus , West Nile virus , dengue virus , and the MERS , SARS , and SARS-CoV-2 coronaviruses , as well as less clinically serious pathogens such as
782-423: The kingdom Orthornavirae in the realm Riboviria . In the Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, +ssRNA viruses are group IV. The first +ssRNA phylum is Kitrinoviricota . The phylum contains what have been referred to as the " alphavirus supergroup" and " flavivirus supergroup" along with various other short-genome viruses. Four classes in
816-499: The largest phage yet identified, increased the number of known viral genes by 16-fold. A suite of computational methods was used to identify putative host virus connections. The isolate viral host information was projected onto a group, resulting in host assignments for 2.4% of viral groups. Then the CRISPR –Cas prokaryotic immune system which holds a "library" of genome fragments from phages (proto-spacers) that have previously infected
850-451: The membranes of a variety of organelles —often the rough endoplasmic reticulum , but also including membranes derived from mitochondria , vacuoles , the Golgi apparatus , chloroplasts , peroxisomes , plasma membranes , autophagosomal membranes , and novel cytoplasmic compartments. The replication of the positive-sense RNA genome proceeds through double-stranded RNA intermediates, and
884-645: The non-structural jingmenvirus proteins are encoded on two genome segments, each containing one ORF. Although there are few known jingmenvirus sequences, the gene composition of the genome segments appears to be well-conserved. By contrast, the putative jingmenvirus structural proteins that likely make up its capsids have no homology to known proteins. It is striking that the segmented jingmenviruses' closest known relatives are nonsegmented. The evolutionary mechanisms underlying genome segmentation and especially multicomponent architecture are poorly understood. Although segmented genomes appear to have evolved several times in
918-451: The phylum are recognized: Alsuviricetes , the alphavirus supergroup, which contains a large number of plant viruses and arthropod viruses; Flasuviricetes , which contains flaviviruses, Magsaviricetes , which contains nodaviruses and sinhaliviruses ; and Tolucaviricetes , which primarily contains plant viruses. Lenarviricota is the second +ssRNA phylum. It contains the class Leviviricetes , which infect prokaryotes , and
952-528: The purpose of replication in these membranous invaginations may be the avoidance of cellular response to the presence of dsRNA. In many cases subgenomic RNAs are also created during replication. After infection, the entirety of the host cell's translation machinery may be diverted to the production of viral proteins as a result of the very high affinity for ribosomes by the viral genome's internal ribosome entry site (IRES) elements; in some viruses, such as poliovirus and rhinoviruses , normal protein synthesis
986-417: The segmented nature of the genome was not recognized before JMTV was described. For example, the reported genome of the dog parasite Toxocara canis was found to contain sequences with homology to JMTV, likely representing a viral infection in the parasite that was sequenced. The Mogiana tick virus , first reported in 2011, is a similar example; its segmented genome was not recognized on first publication but
1020-425: The virome have provided insights into nutrient cycling , development of immunity, and a major source of genes through lysogenic conversion . Also, the human virome has been characterized in nine organs (colon, liver, lung, heart, brain, kidney, skin, blood, hair) of 31 Finnish individuals using qPCR and NGS methodologies. The first comprehensive studies of viromes were by shotgun community sequencing, which
1054-513: The world's oceans in two survey periods by an international team. Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Over 5 Tb of metagenomic sequence data were used from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. In August 2016, over 125,000 partial DNA viral genomes, including
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1088-881: Was confirmed by CRISPR–Cas spacer matches showing a 94% agreement at the genus level. These approaches identified 9,992 putative host–virus associations enabling host assignment to 7.7% of mVCs. The majority of these connections were previously unknown, and include hosts from 16 prokaryotic phyla for which no viruses have previously been identified. Many viruses specialize in infecting related hosts. Viral generalists that infect hosts across taxonomic orders may exist. Most CRISPR spacer matches were from viral sequences to hosts within one species or genus. Some mVCs were linked to multiple hosts from higher taxa. A viral group composed of macs from human oral samples contained three distinct photo-spacers with nearly exact matches to spacers in Actionbacteria and Bacillota . In January 2017,
1122-464: Was reanalyzed and identified as a jingmenvirus in 2017. Sequences with homology to JMTV have also been isolated from a red colobus monkey , suggesting the possibility of a segmented, possibly multicomponent virus capable of infecting primates . A metagenomics study of arthropod flaviviruses identified five additional examples of likely jingmenvirus sequences. Jingmenviruses are related to flaviviruses , which have non-segmented genomes transmitted in
1156-412: Was supported by individual genomic sequencing project, particularly the mycobacterium phage. By the late 2010s advances in sequencing technologies have allowed for a deep probing of viromes. The virome of the human gut in particular has gained increased attention as a result of these advancements. In order to study the virome, virus-like particles are separated from cellular components, usually using
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