marnaviridae marnaviridae marnaviridae is a family of positive-stranded rna viruses in the order picornavirales that infect various photosynthetic marine protists. members of the family have non-enveloped, icosahedral capsids. replication occurs in the cytoplasm and causes lysis of the host cell. the first species of this family that was isolated is heterosigma akashiwo rna virus (harnav) in the genus marnavirus, which infects the toxic bloom-forming raphidophyte alga, heterosigma akashiwo. as of 2021, there are twenty species across seven genera in this family, as well as many other related virus sequences discovered through metagenomic sequencing that are currently unclassified. marnaviridae low-resolution image of a marnavirus under electron microscope virus classification (unranked): virus realm: riboviria kingdom: orthornavirae phylum: pisuviricota class: pisoniviricetes order: picornavirales family: marnaviridae genera bacillarnavirus kusarnavirus labyrnavirus locarnavirus marnavirus salisharnavirus sogarnavirus maximum-likelihood phylogeny of the picornavirales rdrp amino acid sequences. https://academic.oup.com/ve/article/5/2/vez056/5692928 phylogeny of environmental sequences of genera within the marnaviridae. https://academic.oup.com/ve/article/5/2/vez056/5692928 interactions between members of the marnaviridae family and their hosts have notable significance in marine ecology, and are also relevant within the aquaculture industry. harnav and viruses from bacillarnavirus are known to have roles in regulating dynamics and composition of their hosts’ blooms. an unclassified sequence, baishivirus, has been suggested to be the possible pathogen of glass post-larvae disease, which is prevalent in shrimp aquaculture. viruses detected in a cultured prawn species that had been affected by growth retardation disease have also been placed in marnaviridae. history the name "marnaviridae" is based on its genome type (rna virus - rnaviridae), together with the prefix "ma" being derived from the latin word mare (sea). the family was proposed following the discovery of an rna virus (harnav) that infects h. akashiwo off of the coast of british columbia, which was the first report of a single-stranded rna virus capable of causing cell lysis in phytoplankton. harnav was isolated from water collected in the strait of georgia in british columbia, canada, from a concentrated virus assemblage using the host h. akashiwo (nepcc 522). it must not be confused with two other unrelated viruses that infect this host, h. akashiwo virus 01 (hav-1, isolate: hav53) in the genus raphidovirus, and heterosigma akashiwo nuclear inclusion virus (haniv). marnaviridae existed for multiple years with marnavirus as the only genus and harnav as the only species. after the usage of metagenomic analysis on the amino acid sequences of the capsid proteins and rdrp domains on viruses under the order picornavirales, marnaviridae was discovered to have a larger variety of viruses classified under it. previously unassigned labyrnavirus and bacillarnavirus were also classified as genera under marnaviridae. further metagenomic studies have yielded 653 marnavirus-like sequences, prompting the proposal for a taxonomic reorganization to incorporate the new data into existing frameworks. taxonomy the following genera are recognised: bacillarnavirus kusarnavirus labyrnavirus locarnavirus marnavirus salisharnavirus sogarnavirus classification while marnaviridae has several characteristics that are similar to those of other viruses in the broader picornavirales order, members of marnaviridae are placed through analysis of the rdrp sequence of amino acids. the seven genera of marnaviridae are designated based on analysis of rna-dependent rna polymerase (rdrp) sequences and capsid amino acid sequences, species are listed under each genus. bacillarnavirus the bacillarnavirus species share 57.8-64.4% of rdrp and 29.1-33.4% of capsid amino acid sequences, when compared with each other within bacillarnavirus. when compared with other genera of the family, they share 23.8-47.8% of rdrp and18.3-29.4% of capsid sequences. chaetoceros socialis forma radians rna virus 1 chaetoceros tenuissimus rna virus 01 rhizosolenia setigera rna virus 01 kusarnavirus kusarnavirus shares 25.4-48.2% of rdrp and 21.7-47.9% of capsid sequences, with other genera in the family. astarnavirus labyrnavirus labyrnavirus shares 22.4-33.6% identities of rdrp and 17.1-22.5% of capsid sequences. it is a deep-branching taxon. aurantiochytrium single-strand rna virus 01 locarnavirus the locarnavirus species share 52.4-59.1% identities of rdrp and 32.2-38.3% of capsid sequences, when compared with each other within locarnavirus. when compared with other genera of the family, they share 24.0-48.2% of rdrp and 17.2-27.4% of capsid sequences. jericarnavirus b sanfarnavirus 1 sanfarnavirus 2 sanfarnavirus 3 marnavirus marnavirus shares 22.4-30.3% of amino acid sequence identity of rdrp and 18.5-26.4% of capsid sequences. it is the most divergent and deeply branched taxon within the family. heterosigma akashiwo rna virus salisharnavirus the salisharnavirus species share 35.6-63.6% of rdrp and 24.9-34.4% of capsid sequences, when compared with each other within salisharnavirus. when compared with other genera of the family, they share 24.3-47.2% of rdrp and 18.2-31.5% of capsid sequences. britarnavirus 1 britarnavirus 4 palmarnavirus 128 palmarnavirus 473 sogarnavirus the sogarnavirus species share 48.8-77.0% of rdrp and 27.6-59.0% of capsid sequences, when compared with each other within sogarnavirus. when compared with other genera of the family, they share 24.3-47.2% of rdrp and 17.1-47.9% for capsid sequences. britarnavirus 2 britarnavirus 3 chaetarnavirus 2 chaetenuissarnavirus ii jericarnavirus a palmarnavirus 156 additionally, there are 653 virus sequences that have been identified (via metagenomic analysis) as possibly belonging to the family marnaviridae. however, these sequences are not assigned under any of the existing genera. characteristics structure electron micrograph of heterosigma akashiwo rna virus (harnav) particles. scale 50 nm. genome map of marnaviridae.modified after viralzone.schematic drawing of a virion of the family marnaviridae, cross section and side view. chaetoceros tenuissimus rna virus 01, genus bacillarnavirus: the mcps are coloured in green, magenta and cyan and the mcp in yellow. virions in marnaviridae are non-enveloped, with icosahedral geometries, and t=pseudo3 symmetry. virus particles are 22-35 nm in diameter. the capsid consists of three major capsid proteins (mcps: vp1, vp2, vp3), each having a jelly roll fold. most species also encode a minor capsid protein (mcp: vp4). all vps are composed of β-sheets and α-helices. that is located around the five-fold axes on the inside of the capsid. the structures of chaetoceros socialis forma radians rna virus 1 (csfrrnav01, bacillarnavirus) and chaetoceros tenuissimus rna virus type ii (ctenrnavii, sogarnavirus) have been determined. in both species, vp1 surrounds the five-fold axes while vp2 and vp3 form the two- and three-fold axes. the jelly roll folds on the mcps are non-canonical with vp1 having nine β-strands and vp2 and vp3 having seven. vp1 also contains a unique ef-loop connected to the extra β-strand in the jelly roll fold which protrudes from the surface of the virus particle. a cd-loop is also present on vp1 which obscures the canyon structure that binds host receptors in the related picornaviridae family. unlike other species, vp4 is not present in the csfrrnav01 capsid, although the corresponding gene still exists. genome marnaviridae genomes consist of linear, non-segmented, positive-sense single-stranded rna 8.6-9.6 kb in length. the genomic rna generally contains either one or two open-reading frames (orfs) that may overlap. for species whose genomes have two orfs, orf1 encodes proteins involved in replication (rna helicase, rdrp) and a cysteine protease which cleaves the polyprotein, while orf2 encodes structural proteins. genomes also contain internal ribosome entry sites (ires) in intergenic regions and on the 5' end. the 3' end of the genome contains a poly(a) tail. one exception to the typical genome organization of marnaviridae is aurantiochytrium single-strand rna virus 01 (aurnav01) which has a third orf that encodes a protein with unknown function. in aurnav01, orfs 2 and 3 are thought to be translated from subgenomic rna rather than using an ires. host interactions life cycle various marine phytoplankton species serve as hosts for members of the family marnaviridae. entry of the virus is achieved by penetration into the host cell. ef-, cd-, and e1e2-loops are hypothesized to interact with host receptors to trigger viral entry. replication occurs in the cytoplasm and relies on the viral rdrp. the positive-sense rna genome is directly translated to produce viral proteins. after a latent period between 8–48 hours, host cells are observed to experience cytopathic symptoms such as swelling of the endoplasmic reticulum, formation of vacuoles, appearance of fibrous matter in vacuolated parts of the cell, and the deterioration of the cytoplasm. virus particles accumulate in the cytoplasm and may form crystalline arrays or random aggregates. the virus then exits the host cell by tubule-guided viral movement and virions are released by cell lysis. burst sizes differ greatly between species and range from 66 to 106. as infected cells are lysed shortly after showing signs of infection, proportions of infected cells in the environment remain low. heterosigma akashiwo rna virus (harnav) harnav is the first identified virus in the marnaviridae family. when the virus infects h. akashiwo, a toxic bloom-forming alga, it replicates inside the cytoplasm of its host, and is distributed either singly or in groups as crystalline arrays. within those that are aligned in crystalline arrays, sectioned particles show that they are either packaged completely (electron dense), or incompletely (ring-shaped). once infected, the host cells exhibit symptoms such as swelling of the endoplasmic reticulum, disintegration and vacuolation of the cytoplasm, as well as fibrous material appearing in those vacuolated areas. harnav is known to be able to infect multiple strains of h. akashiwo in the pacific ocean, namely 3 strains (nepcc 102, nepcc 522, nepcc 764) from the northeast pacific region, and 2 strains (h93616, h94608) from japan. it is noted that harnav infect different strains of h. akashiwo than other h. akashiwo viruses, suggesting co-existence, with each virus having a slightly different host range. h. akashiwo cells also demonstrate more viral resistance after its bloom has collapsed, suggesting that the h. akashiwo strains may change over the course of the algal bloom, which is regulated by the viruses. chaetoceros tenuissimus rna virus 01 ctenrnav01 infects the bloom-forming diatom chaetoceros tenussimus meunier. it was first isolated from strain 2-10 but is able to infect other strains of the same species. host cells in stationary phase are more susceptible to the virus than logarithmic phase cells. host susceptibility is also affected by temperature, with various strains being more susceptible at temperatures above 20 °c. strain 2-10, however, is more susceptible below 20 °c which is not optimal for host growth. iron-limitation has also been shown to reduce viral infection rates. stationary phase infection and virus-induced lysis of host cells is also impaired by bacteria of the genera nautella, polaribacter, and sulitobacter that coexist with the host diatom in the marine environment. this is thought to be a mechanism allowing for susceptible diatom species to survive viral infections. chaetoceros socialis forma radians rna virus 1 the diatom c. socialis is the natural host of csfrrnav01. infection with the virus induces spore formation in host cells, and the spores formed take longer to germinate than spores induced by host nutrient limitation. although viral rna is present within these spores, those that germinate are not able to produce infectious viral particles. chaetoceros tenuissimus rna virus type ii like ctenrnav01, ctenrnavii was first isolated from c. tenussimus meunier strain 2-10, however it is also able to infect at least 4 other chaetoceros species. it is the only marnaviridae species identified thus far that has demonstrated this broad of a host range. unassigned viruses given the nature of metaviromic analysis, it is difficult to determine the exact host range of these viruses. however, since the species fall under marnaviridae, as well as by comparing genetic codes in other virus groups in the yangshan assemblage, it has been inferenced that these viruses likely infect unicellular eukaryotes. echinodermata through a study aiming to investigate the diversity of the rna viruses infecting species within the phylum echinodermata, the transcriptomes and viral metagenomes of 38 echinoderm species, with representation of species from all five classes of echinoderms, were analyzed and categorized into their respective families and genera. from this analysis, it was found that of the viral contigs recovered, more than half were classified within the viral order picornavirales, with the highest number of the picornaviruses being placed in the marnaviridae family. this finding suggests the protists, such as symbionts, that are affiliated with echinoderms are infected by marnaviridae, or that members of this viral family are capable of infecting a wider range of hosts than the single-celled eukaryotes they were initially known to infect. host-specific receptor-binding mechanisms marnaviridae use a narrow range of hosts, as they lyse their host species, which is thought to connect to a receptor binding mechanism unique to the family. in tests involving the species chaetoceros socialis forma radians rna virus (csfrrnav), full and empty capsids were analyzed by their atomic structure