Quadriviridae


Quadriviridae

Chapter Contents

Posted September 2018

Quadriviridae: The Family

Quadriviridae: Member Taxa

Quadriviridae: Supporting Information

  • Authors - Corresponding author: Sotaro Chiba (chiba@agr.nagoya-u.ac.jp)
  • Resources - Sequence alignments and tree files
  • References - Literature cited

Citation

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

Chiba, S., Castón, J.R., Ghabrial, S.A., Suzuki, N., and ICTV Report Consortium, 2018, ICTV Virus Taxonomy Profile: Quadriviridae, Journal of General Virology, 99, 1480-481

Summary

The Quadriviridae is a family of non-enveloped spherical viruses with quadripartite dsRNA genomes of 3.5–5.0 kbp, comprising 16.8–17.1 kbp in total. The family includes the genus Quadrivirus to which the single species Rosellinia necatrix quadrivirus 1 has been assigned. All quadriviruses have been reported to infect filamentous fungi. Pathogenicity of the viruses has not been reported. Quadriviruses have unique features in virion structure compared to those of other known dsRNA viruses. Quadriviruses are transmitted intracellularly via anastomosis of compatible fungal hyphae. Neither vertical transmission of the viruses through sexual and asexual spores or by natural vectors has been reported, and nor is it known if viruses have an extracellular phase.

Table 1.Quadriviridae. Characteristics of the family Quadriviridae. 

Characteristic

Description

Typical member

Rosellinia necatrix quadrivirus 1-W1075, (RNA1: AB620061; RNA2: AB620062; RNA3: AB620063; RNA4: AB620064), species Rosellinia necatrix quadrivirus 1, genus Quadrivirus

Genome

Four, linear dsRNAs of 3.5–5.0 kbp, 16.8–17.1 kbp in total

Virion

Isometric, non-enveloped, 45 nm in diameter; dsRNA segments may be separately encapsidated

Replication

No information available

Translation

Presumed from monocistronic positive-sense transcripts of each genomic dsRNA

Host Range

Fungi

Taxonomy

One genus including a single species

Virion

Morphology

Quadriviruses form rigid spherical particles of 45 nm in diameter (Figure 1.Quadriviridae). Each capsid consists of 60 copies of heterodimers of two major structural proteins P2 and P4 encoded by dsRNA2 and dsRNA4, respectively (Figure 2.Quadriviridae). The P2 and P4 proteins form an asymmetric hetero-dimer subunit, and 60 of those build the T=1 capsid (Luque et al., 2016). The P2 and P4 proteins of the Rosellinia necatrix quadrivirus 1 (RnQV1) strains W1075 and W1118 are more than 80% identical. Despite a lack of sequence similarity between the two proteins, they have a similar a-helical domain, the structural signature shared with the lineage of the dsRNA viruses. While P2-P4 heterodimers are organized similarly to homodimers of other spherical dsRNA viruses, P2 and P4 have acquired domains situated on the outer surface that are hypothesized to possess actin regulatory (P2-domain) and protease (P4-domain) enzyme activities (Mata et al., 2017). Transfection competency of purified virions has not been demonstrated.

Figure 1.Quadriviridae. Transmission electron micrograph of negatively stained (top, left) and unstained and vitrified (bottom, left) virions of the W1075 isolate of Rosellinia necatrix quadrivirus 1, a member of the type species of the genus Quadrivirus in the family Quadriviridae. Bar, 50 nm. (Right) Three-dimensional cryo-electron microscopy reconstruction of RnQV1 virions at 8Å resolution.

Figure 2.Quadriviridae. Three-dimensional cryo-EM reconstruction of Rosellinia necatrix quadrivirus 1 virions (W1118 isolate) at a resolution of 3.7 Å. (Left) Cryo-EM map of the Rosellinia necatrix quadrivirus 1 capsid viewed along a twofold axis, showing P2 (blue) and P4 (yellow) proteins. (Right) Atomic model of P2 (blue) and P4 (yellow) (top view). N and C termini are indicated. Symbols indicate icosahedral symmetry axes; from (Mata et al., 2017).

Physicochemical and physical properties

Unknown.

Nucleic acid

All members of the family Quadriviridae possess four dsRNA genome segments, termed dsRNA1 to dsRNA4 in a decreasing order of length. A single large ORF is present on the positive-sense strand of each of the dsRNA genomic segments (Figure 3.Quadriviridae). The linear dsRNA segments are 3.5-5.0 kbp and are expected to be encapsidated separately (Lin et al., 2012, Lin et al., 2013). The 5′-terminal 7 and 3′-terminal 13 nucleotides for RnQV1-W1075 and the 5′-terminal 9 and 3′-terminal 12 nucleotides for RnQV1-W1075, are conserved in all the genomic segments. There is notable heterogeneity in the very terminal ends of each segment (5′-C/U--------------G/A-3′) (Lin et al., 2012, Lin et al., 2013).

Figure 3.Quadriviridae. Genomic organization of the W1075 strain of Rosellinia necatrix quadrivirus 1. dsRNA2 and dsRNA4 encode structural proteins (capsid protein, CP) while dsRNA3 encodes the replicase (RNA-dependent RNA polymerase, RdRP). dsRNA1 encodes a non-structural protein of unknown function. Double lines indicate genomic dsRNAs; boxes indicate open reading frames on the positive-sense strands which begin and end at the nucleotide positions indicated.

Genome organization and replication 

Quadrivirus genomes consist of four linear, monocistronic dsRNA segments; the largest segment/ORF (dsRNA1) encodes a hypothetical protein (P1) with unknown function. The second and fourth segments (dsRNA2 and dsRNA4) encode the capsid proteins (CP, P2 and P4 respectively), whereas the third segment (dsRNA3) encodes viral RdRP (Lin et al., 2012, Lin et al., 2013) (Figure 3.Quadriviridae). Both the 5′- and 3′- terminal sequences of the dsRNA genome are well conserved in all the segments. Transcription and replication are presumably carried out in a spherical particle by virion-associated RdRP. All the genomic segments except for dsRNA3 have (CAA)n repeats, which are presumably translational enhancers, as reported for chrysoviruses (Ghabrial et al., 2018) and some partitiviruses (Chiba et al., 2016, Tavantzis 2008).

Antigenicity 

Antibodies prepared to N- and C-terminal truncated polypeptides derived from RnQV1-W1075 P2 show cross-reactivities to RnQV-W1118 P2 (Lin et al., 2013). 

Biology 

The quadriviruses persistently infect their fungal hosts, and are stably maintained in the natural host Rosellinia necatrix (an ascomycete fungus) for a long period, despite successive subcultures. The quadriviruses are transmitted intracellularly during cell division and hyphal anastomosis (Lin et al., 2012). Horizontal transmission by hyphal fusion between fungi of different mycelial compatibility groups is blocked by programmed cell death (PCD). PCD appears to be retarded by the presence of Zn2+ cations in the media, which allows mycoviruses to be horizontally transmitted between vegetatively incompatible mycelia, as is the case for a megabirnavirus (Rosellinia necatrix megabirnavirus 1) (Ikeda et al., 2013, Kondo et al., 2013). Little is known about vertical transmission during asexual or sexual sporulation, or horizontal transmission by natural vectors. The quadrivirus RnQV1-W1075 spreads relatively slowly and shows uneven distribution in fungal colonies compared to other R. necatrix-infecting viruses (Yaegashi et al., 2011). Attempts to transfect protoplasts derived from the natural (R. necatrix) and experimental fungal hosts (Cryphonectria parasitica) with purified quadriviruses have been unsuccessful.

Derivation of names 

Quadri: from the viruses’ quadripartite genome, from the Latin quad meaning four. 

Phylogenetic relationships 

Three strains of RnQV1 have been partially or completely sequenced and compared. The exemplar virus, RnQV1 W1075 shows greater phylogenetic affinity to RnQV1 W726 than to W1118. Greater sequence similarity is observed between strains W1075 and W726 than between other combinations. Amino acid sequence deduced from the W726 dsRNA3 shows 98% and 75% identities to the corresponding portions of W1075 and W118 RdRPs, respectively. Amino acid sequence identities found between the homologues of RnQV1 W1075 and W1118 vary from 72% (P1) to 82% (P4), while those for nucleotide sequence identities vary from 67% (dsRNA1 and dsRNA3) to 70% (dsRNA2). 

Similarity with other taxa

Phylogenetic analyses show that quadriviruses are most closely related to members of the genus Totivirus in the family Totiviridae (Lin et al., 2012, Lin et al., 2013) (Figure 4.Quadriviridae). Other quadripartite dsRNA viruses such as chrysoviruses and unclassified alternaviruses show relatively distant relation to quadriviruses. It is noteworthy that members of the genus Totivirus show greater phylogenetic affinity to quadriviruses than to members of other genera within Totiviridae (Figure 4.Quadriviridae). This suggests that taxonomic reorganization of the family Totiviridae needs to be considered.

The quadripartite nature of quadrivirus dsRNA genomes resembles that of members of the family Chrysoviridae and an unclassified mycovirus Alternaria alternata virus 1 (AaV-1). However, the size range of genomic dsRNA segments are different for each of these viruses: quadriviruses, 3.5–5.0 kbp; chrysoviruses, 2.5–3.6 kbp (Ghabrial et al., 2018); AaV-1, 1.4–3.6 kbp excluding a poly(A) tract (Aoki et al., 2009). The 5′-UTRs of quadriviruses and AaV-1 are short (24–107 bp), and those of chrysoviruses are relatively long, presumably due to the possession of an internal ribosomal entry site (Chiba et al., 2018). The 3′-end of AaV-1 genomic segments are polyadenylated in the coding strand, similar to some members in the family Partitiviridae, which is not found in quadriviruses and chrysoviruses (Lin et al., 2012, Aoki et al., 2009). Chrysoviruses and AaV-1 form a capsid with a single CP, whereas quadriviruses have two CPs. A taxonomically unclassified quadripartite dsRNA virus (1.1–2.4 kbp) tentatively named tetramycovirus was reported (Kanhayuwa et al., 2015) and recently renamed as a polymycovirus upon the discoveries of similar viruses with more than 4 genomic segments (Kotta-Loizou and Coutts 2017). Although the polymycovirus genome segments are monocistronic, as are the genome segments of the abovementioned quadripartite dsRNA viruses, polymycoviruses do not form typical virions and are infectious as purified viral dsRNA (Kanhayuwa et al., 2015, Kotta-Loizou and Coutts 2017).

Figure 4.Quadriviridae. Phylogenetic tree of the RdRP of quadriviruses, chrysoviruses and some members of the family Totiviridae. Translated sequences were aligned using MUSCLE (Edgar 2004) as implemented in SSE v1.3 (Simmonds 2012), and the least divergent region (amino acid positions 679 to 1066, numbered according to the RdRP of Rosellinia necatrix quadrivirus 1 strain W1075) was used to produce a midpoint rooted maximum likelihood dendrogram in MEGA7 (Kumar et al., 2016) using the LG model with a gamma distribution of substitution rates and a proportion of invariant sites. Numbers at the nodes denote bootstrap values where these were > 70%. The scale bar represents the amino acid distances.

Related, Unclassified Viruses

Virus-like dsRNA elements with high sequence similarity to RnQV1 dsRNA1 and dsRNA3 have been reported (Lin et al., 2012, Kozlakidis et al., 2006) (Figure 4.Quadriviridae). These elements are named after Amasya cherry disease (ACD)-dsRNA1, -dsRNA2, -dsRNA3 and -dsRNA4, and occur together with a chrysovirus and a partitivirus (Coutts et al., 2004, Covelli et al., 2004). However, no CP-encoding dsRNA segments (corresponding to RnQV1 dsRNA2 and dsRNA4) have been reported. Such dsRNAs were also found in cherry chlorotic rusty spot (CCRS)-associated cherry leaves (Kozlakidis et al., 2006). ACD and CCRS are diseases presumably with a fungal etiology, but isolation of the causal pathogens has not been successful. This leaves unanswered the question of whether the origin of these dsRNA elements is from fungal or plant tissue. 

Probable viral element

RnQV1-dsRNA1 like

RnQV1-dsRNA3 like

Virus abbreviation

Amasya cherry disease L dsRNA

dsRNA1: AM085136; dsRNA2: AM085137

dsRNA3: AM085134; dsRNA4: AM085135

ACD-L

Virus names and virus abbreviations are not official ICTV designations.


Genus: Quadrivirus


Since only one genus (Quadrivirus) is currently recognized in the family Quadriviridae, the family description above corresponds to the genus description. For clarity, the additional information that can be found on the genus page is also presented below.

Distinguishing features

Since only one genus is currently recognized, the genus description corresponds to the family description. Members of the genus Quadrivirus infect ascomycetous fungi. All members have four dsRNA genomic segments with sizes ranging from 3.5 to 5.0 kbp.

Virion

See discussion under family description. 

Genome organization and replication

See discussion under family description.

Biology 

See discussion under family description.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Rosellinia necatrix quadrivirus 1Rosellinia necatrix quadrivirus 1W1075RNA1: AB620061; RNA2: AB620062; RNA3: AB620063; RNA4: AB620064RNA1: NC_016757; RNA2: NC_016759; RNA3: NC_016760; RNA4: NC_016758Complete genomeRneQV1

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.