Chrysoviridae


Chrysoviridae

Chapter Contents

Posted January 2018

Chrysoviridae: The Family

Chrysoviridae: Member Taxa

Chrysoviridae: Supporting Information

  • Authors - Corresponding author: Said A. Ghabrial (saghab00@uky.edu)
  • Resources - Sequence alignments, tree files
  • References - Literature cited

Citation

A summary of this ICTV Online (10th) 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: 

Ghabrial, S.A*., Castón, J.R., Coutts, R.H.A., Hillman, B.I., Jiang, D., Kim D-H., Moriyama, H. and ICTV Report Consortium. 2018, ICTV Virus Taxonomy Profiles: ChrysoviridaeJournal of General Virology, 99:1920.

Summary

The Chrysoviridae is a family of small non-enveloped isometric viruses (about 40 nm in diameter) with segmented dsRNA genomes (typically four segments). The dsRNA segments are individually encapsidated in separate particles and together comprise 11.5-12.8 kbp. Chrysoviruses infect ascomycetous or basidiomycetous fungi. The single genus, Chrysovirus, includes 9 species.

Table 1.Chrysoviridae. Characteristics of family Chrysoviridae.

Typical member

Penicillium chrysogenum virus ATCC 9480 (dsRNA1: AF296439; dsRNA2: AF296440; dsRNA3: AF296441; dsRNA4: AF296442), species Penicillium chrysogenum virus, genus Chrysovirus

Virion

Isometric, non-enveloped, 40 nm in diameter

Genome

A total of 11.5-12.8 kbp of dsRNA in a quadripartite genome with each segment separately encapsidated

Replication

Particles containing both dsRNA and ssRNA can be isolated from infected fungal hosts. Virions accumulate in the cytoplasm

Translation

From positive-sense transcripts of genomic dsRNAs

Host Range

Fungi

Taxonomy

One genus (Chrysovirus) including 9 species

Virion

Morphology

Virions are isometric, non-enveloped, about 40 nm in diameter. The capsid of Penicillium chrysogenum virus (PcV) comprises 60 copies of a 109 kDa polypeptide (982-aa) arranged on a T=1 icosahedral lattice (Figure 1.Chrysoviridae). The most prominent features are 12 outward-protruding pentamers. The capsid protein is formed by a repeated a-helical domain, indicative of gene duplication despite a lack of sequence similarity between the two halves (Luque et al., 2010). This domain has a fold that is conserved among dsRNA viruses (Luque et al., 2014). The capsid inner surface has highly positively charged triskelion-shaped areas that maintain the encapsidated genome in close contact with the inner capsid surface. Arrangement of dsRNA might facilitate genome mobility within the capsid for its transcription and replication. It may also have a structural role in capsid stability (Castón et al., 2013). 

Figure 1.Chrysoviridae. Three-dimensional cryo-EM reconstruction of Penicillium chrysogenum virus (PcV) virions at a resolution of 4.1 Å. (Left) Cryo-EM image of PcV (scale bar, 50 nm). (Middle) Atomic model of the PcV capsid viewed along a twofold axis. (Right) Atomic model of a PcV capsid protein (top view) showing the N-terminal domain (1–498, blue), the linker segment (499–515, red), and the C-terminal domain (516–982, yellow). Symbols indicate icosahedral symmetry axes.

Physicochemical and physical properties

Virion buoyant density in CsCl is in the range of 1.34–1.39 g cm−3and S20,w is 145-150S (Buck and Girvan 1977, Sanderlin and Ghabrial 1978, Wood and Bozarth 1972). 

Nucleic acid

Virions contain four linear, separately encapsidated, dsRNA segments. PcV segments are 2.9–3.6 kbp; Table 2.Chrysoviridae  (Jiang and Ghabrial 2004). The largest segment, dsRNA1, codes for the virion-associated RNA-dependent RNA polymerase (RdRP; P1) and dsRNA2 codes for the major CP; P2. Both dsRNAs 3 and 4 encode proteins of unknown function, designated as chryso-P3 and chryso-P4, respectively (Ghabrial 2008). Sequences at the 5′- and 3′-UTRs are highly conserved among the four-dsRNA segments (Figure 2.Chrysoviridae). The 5′-UTRs are relatively long, between 140 and 400 nt (nucleotides). In addition to the absolutely conserved 5′- and 3′-termini, a 40–75 nt region with high sequence identity is present in the 5′-UTR of all four dsRNAs (Table 1.Chrysoviridae; Figure 2.Chrysoviridae). A second region of strong sequence similarity is present immediately downstream from Box 1 and consists of 30–50 nt containing a reiteration of the sequence “CAA”. The (CAA)n repeats are similar to the enhancer elements present at the 5′-UTRs of tobamoviruses (Gallie and Walbot 1992).

Table 2. Chrysoviridae. Genome content and encoded proteins of Penicillium chrysogenum virus (PcV-ATCC9480)

Segment

bpa

Mass of encoded protein in Dab

Designation and function of encoded protein

dsRNA1

3562

128,548 (1117 aa)

P1, RdRP

dsRNA2

3200

108,806 (982 aa)

P2, CP

dsRNA3

2976

101,458 (912 aa)

Chryso-P3, unknownc

dsRNA4

2902

94,900 (847 aa)

Chryso-P4, unknownc

a Deduced from sequence of full-length cDNA clones
b Predicted from aa sequence encoded by full-length cDNA; the numbers of aa residues is given in parentheses.
c See section on genome organization and replication.

Figure 2.Chrysoviridae. Genome organization of Penicillium chrysogenum virus ATCC 9480 (PcV-ATCC9480). The genome consists of four dsRNA segments; each is monocistronic. The RdRP ORF (nt positions 145 to 3,498 on dsRNA1), the CP ORF (nt positions 158 to 3,106 on dsRNA2), the P3 ORF (nt positions 162 to 2900 on dsRNA3) and the P4 ORF (nt positions 163 to 2706 on dsRNA4) are represented by rectangular boxes. Although the functions of P3 and P4 are unknown (see below), the N-terminal region of P3 shares high sequence similarity with the corresponding N-terminal region of RdRP (P7/P-loop domain; possibly an nucleotide triphosphate hydrase [NTPase] domain). P4 is a putative cysteine protease.

Proteins

The capsids are made up of a single major polypeptide species (100–113 kDa). Virion-associated RNA-dependent RNA polymerase activity is present.

Genome organization and replication

Classified chrysoviruses have multipartite genomes comprising four linear dsRNA segments (as exemplified by PcV; Figure 2.Chrysoviridae). Each segment is monocistronic; dsRNA1 codes for the RdRP (P1) and dsRNA2 codes for the major CP (P2). Although the proteins P3 and P4 (designated chryso-P3 and chryso-P4), coded for by PcV dsRNA3 and dsRNA4, respectively, are of unknown function, protein database searches reveal that PcV-P3 sequence shares a “phytoreo S7 domain” with a protein family consisting of several phytoreovirus P7 proteins that are known to be viral core proteins (Jiang and Ghabrial 2004, Liu et al., 2012). Interestingly, the N-terminal regions of PcV-P3 (and corresponding P3 proteins of other chrysoviruses) share significant sequence similarity with comparable N-terminal regions of RdRPs encoded by chrysovirus dsRNA1s (Jiang and Ghabrial 2004, Liu et al., 2012). Furthermore, HHPred (Soding et al., 2005) predicts a separate P-loop NTPase domain near the N terminus of P1, which oserlaps the region of P1 that is represented by homologous sequences in P3. The P7/P-loop NTPase domain (Pathak et al., 2014) in P1 is independent (non-overlapping) of the RdRP domain in P1. Thus, P1 has at least two distinct enzymatic activities, RdRP and NTPase, mediated by at least two different domains. The PcV P4 (and comparable proteins of other chrysoviruses) contains the motifs that form the conserved core of the ovarian tumor gene-like superfamily of predicted cysteine proteases (Covelli et al., 2004). HHPred also shows that P4 has a region of homology with P2/CP. All of these motifs/homologies are shared by all fungal chrysoviruses with quadripartite genomes. The unclassified, chrysovirus-related viruses with tripartite genomes (see list of related, unclassified viruses), which mostly infect plants, lack a PcV P3 homolog; otherwise the virally-encoded proteins share the same motifs in the same relative positions as in the homologous proteins of fungal chrysoviruses with quadripartite genomes.

Assignment of numbers 1–4 to PcV dsRNAs was made according to their decreasing size. There is, however, some variation in the relative sizes of segments 3 and 4 among other chysoviruses. For example, dsRNA segments 3 of Amasya cherry disease associated chrysovirus (ACDACV), Cryphonectria nitschkei chrysovirus 1 (CnCV1), and Helminthosporium victoriae 145S virus (HvV145S) are shorter than their corresponding segments 4. Sequence comparisons confirmed that dsRNA3s of ACDACV, CnCV1 and HvV145S are in fact the counterparts of PcV dsRNA4 rather than dsRNA3. Likewise, dsRNA4s of these three chrysoviruses are the counterparts of PcV dsRNA3. Since PcV was the first chrysovirus to be characterized at the molecular level and to avoid confusion, the protein designations P3 and P4 as used for PcV are adopted and referred to as chryso-P3 and chryso-P4.

The virion-associated RdRP catalyzes in vitro end-to-end conservative transcription of each dsRNA to produce mRNA. Virions accumulate in the cytoplasm.

Antigenicity

High quality antisera are produced in rabbits immunized with purified virions.

Biology

Chrysoviruses are typically associated with latent infections of their fungal hosts. Chrysoviruses lack an extracellular phase to their life cycle; they are transmitted intracellularly during cell division and sporogenesis (vertical transmission) and by cell fusion following hyphal anastomosis between compatible fungal strains (horizontal transmission) (Ghabrial 2008). Unclassified, chrysovirus-related viruses with 3-segmented dsRNA genomes mostly infect plants with evidence for vertical transmission through seeds (Zhang et al., 2017, Li et al., 2013). Furthermore, some unclassified, chrysovirus-related viruses with 5 dsRNA segments cause deleterious effects in their fungal hosts (Urayama et al., 2010, Urayama et al., 2012, Urayama et al., 2014).

Derivation of names

Chryso: from the specific epithet of Penicillium chrysogenum.

Phylogenetic relationships within the family

Phylogenetic analysis based on the complete deduced amino acid sequences of RdRPs of members of family Chrysoviridae and related, unclassified viruses with 3-5 dsRNA segments (Figure 3.Chrysoviridae) leads to the identification of two distinct clusters: cluster I (shaded in blue) corresponds to classified members of the genus Chrysovirus combined with the 3-segmented chrysovirus-related unclassified viruses. Cluster II comprises chrysovirus-related, unclassified viruses with 4 or 5 genomic segments. Among the 5-segmented chrysovirus-related viruses, Magnaporthe oryzae chrysovirus 1-A  (MoCV1-A) and Magnaporthe oryzae chrysovirus 1-B  (MoCV 1-B) are most closely related to each other but form a sister sub-clade to Fusarium graminearum dsRNA mycovirus-2 (FgV2), Fusarium graminearum mycovirus-China9  (FgV-ch9), Tolypocladium cylindrosporum virus 2 (TocV2) and Aspergillus mycovirus 1816 (AmV1816). It is noteworthy that dsRNA 5 is dispensable for replication of MoCV-1-B as stable derivatives with 4 dsRNA segments can be readily obtained via sub-culturing (Urayama et al., 2014).

Table 3.Chrysoviridae. Amino acid identity between PcV RdRP/CP and proteins of classified members of genus Chrysovirus and related, unassigned chrysoviruses.

Virus name

Isolate

RdRPa

CPa

Reference

Aspergillus fumigatus chrysovirus AfCV-A56 70.2% 52.6% (Jamal et al., 2010)

Isaria javanica chrysovirus 1 

 
IjCV1- NB IFR-19 61.5% 35.0% (Herrero 2017)

Macrophomina phaseolina chrysovirus 1

 
MpCV1-TN263 55.3% 31.7%

(Marzano et al., 2016)

Cryphonectria nitschkei chrysovirus 1 CnCV1-BS122 50.7% 30.2% (Kim et al., 2010)
Verticillium dahliae chrysovirus 1 VdCV1-China 47.6% 29.2% (Cao et al., 2011)
Helminthosporium victoriae 145S virus HvV145S-A9 39.3% 28.3% (Ghabrial et al., 2013)

Fusarium oxysporum chrysovirus 1

FoCV1-Shiraz

38.5%b

 

EF152346

Amasya cherry disease associated chrysovirus

ACDACV-Turkey

37.6%

24.6%

(Covelli et al., 2004)

a Percentage amino acid identity with PcV-ATCC9480 (Jiang and Ghabrial 2004) calculated using SIM (http://web.expasy.org/sim/)
b Incomplete sequence

Similarity with other taxa

Other fungal viruses that possess four dsRNA genome segments include members of the family Quadriviridae (Lin et al., 2012) and the unclassified viruses Alternaria alternate virus 1 (Aoki et al., 2009) and Aspergillus fumigatus tetramycovirus-1 (Kanhayuwa et al., 2015). From these, however, only Quadriviridae shows any close phylogenetic relatedness to chrysoviruses in the RdRP gene, along with members of the Botybirnaviridae, Megabirnaviridae and Totiviridae. These latter viruses, however, have quite different genome organisations (2, 2 and 1 genome segment respectively). Virion structures are also distinct; the latter possessing T=1 capsids made up from 120-subunits of homodimeric or heterodimeric capsid proteins (Luque et al., 2016) instead of 60 copies of a single, internally duplicated capsid protein arranged on a T=1 icosahedral lattice (Figure 2.Chrysoviridae) (Castón et al., 2003).

Figure 3.Chrysoviridae. Phylogenetic analysis of members of the family Chrysoviridae and related, unclassified viruses based on amino acid sequences of their RdRPs. The viruses cluster into two groups; cluster I contains viruses with 4 (blue box) or 3 genome segments (green box) and include classified members of the genus Chrysovirus (indicated by bold type). Viruses in Cluster II (yellow box) have either 4 or 5 genome segments. A multiple alignment of RdRP amino acid sequences was produced using MUSCLE (Edgar 2004) within the program SSEv1 (Simmonds 2012). A neighbour-joining phylogenetic tree constructed from this alignment for distance calculated with a Poisson model and a gamma distribution of rates between sites using the program MEGA 6.0 (Tamura et al., 2013). Bootstrap percentages (1000 replicates) are shown (Figure provided by D.B.Smith).

Related, Unclassified Viruses

Unclassified, chrysoviruses-related viruses with 3 dsRNA genome segments are mostly plant viruses (Table 4.Chrysoviridae), (Zhang et al., 2017, Li et al., 2013, Zhong et al., 2016). These 3-segmented viruses lack a PcV P3 homolog but their other encoded proteins share the same motifs in the same relative positions as in the homologous proteins of classified fungal chrysoviruses. Four of the five known 3-segmented chrysovirus-related viruses infect plants. Only Colletotrichum gloeosporioides chrysovirus 1-HZ-1 (CgCV1-HZ-1) infects a plant pathogenic fungus (Zhang et al., 2017). Interestingly, CgCV1-HZ-1 clusters with the fungal 4-segmented chrysoviruses, but not with the 3-segmented plant chrysovirus-related viruses. Host preference and the number of genome segments may justify the creation of a new genus with five new species in the family Chrysoviridae to accommodate the 3-segmented chrysovirus-related viruses. Whether the 4 or 5-segmented chrysovirus-related viruses in cluster II (Figure 3.Chrysoviridae, yellow shaded clade) can be accommodated in a new genus within the family Chrysoviridae or in a separate family is not yet clear. Although the RdRPs encoded by these viruses have the P7/ P-loop NTPase domain at their N-termini as well as the RdRP conserved motifs, the other virally encoded proteins lack the motifs identified in typical chrysoviruses (e.g. motifs of predicted cysteine proteases). Furthermore, the capsids of the 5-segmented chrysovirus-related viruses appear to contain more than one structural protein. Future studies on detailed capsid structure may provide useful insights to the taxonomic placement of the 5-segmented chrysovirus-related viruses.

Table 4.Chrysoviridae. Related, unclassified viruses.

Virus name

Accession number

Virus abbreviation

Number and size of genome segments (bp)

Anthurium mosaic-associated virus-PHA

dsRNA1: FJ899675;
dsRNA2: FJ899676;
dsRNA3: FJ899677

AmAV-PHA

3 (3550, 3448, 3244)

Brassica campestris chrysovirus 1-Hubei

dsRNA1: KP782031;
dsRNA2: KP782030;
dsRNA3: KP782029

BcCV1-Hubei 

3 (3639, 3569, 3337)

Colletotrichum gloeosporioides chrysovirus 1-HZ-1

dsRNA1: KT581957;
dsRNA2: KT581958;
dsRNA3: KT581959

CgCV1- HZ-

3 (3397, 2869, 2630)

Raphanus sativus chrysovirus 1-D13

dsRNA1: JQ045335;
dsRNA2: JQ045336;
dsRNA3: JQ045337

RsCV1-D13

3 (3638, 3617, 3299)

Persea americana chrysovirus-Spain

dsRNA1: KJ418374;
dsRNA2: KJ418375;
dsRNA3: KJ418376

PaCV-Spain

3 (3421, 3335, 2857)

Botryosphaeria dothidea chrysovirus 1- LW-1

dsRNA1: KF688736;
dsRNA2: KF688737;
dsRNA3: KF688738;
dsRNA4: KF688739

BdCV1-LW-1

4 (3654, 2773, 2597, 2574)

Fusarium graminearum dsRNA mycovirus-2 

dsRNA1: HQ343295;
dsRNA2: HQ343296;
dsRNA3: HQ343297;
dsRNA4: HQ343298;
dsRNA5: HQ343299

FgV2- 98-8-60

5 (3580, 3000, 2982, 2748, 2414)

Fusarium graminearum mycovirus-China-9 

dsRNA1: HQ228213;
dsRNA2: HQ228214;
dsRNA3: HQ228215;
dsRNA4: HQ228216;
dsRNA5: HQ228217

FgV-ch-9

5 (3581, 2850, 2830, 2746, 2423)

Fusarium oxysporum f. sp.  Dianthi virus-Fod 116

dsRNA1: KP876629;
dsRNA2: KP876630;
dsRNA3: KP876631;
dsRNA4: KP876632

FodV-Fod 116

4 (3555, 2809, 2794, 2646)

Magnaporthe oryzae chrysovirus 1-A 

dsRNA1: AB560761;
dsRNA2: AB560762;
dsRNA3: AB560763;
dsRNA4: AB560764;
dsRNA5: AB700631

MoCV-1A

5 (3554, 3250, 3074, 3043, 2879)

Magnaporthe oryzae chrysovirus 1-B

dsRNA1: AB824667;
dsRNA2: AB824668;
dsRNA3: AB824669;
dsRNA4: AB824670;
dsRNA5: AB824671

MoCV-1-B

5 (3504, 3147, 2502, 2598, 2181)

Aspergillus mycovirus 1816

dsRNA1: EU289896a

AmV1816

 

Tolypocladium cylindrosporum virus 2

dsRNA1: FR750563

TocV2

4b

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

a Incomplete (Hammond et al., 2008).
b Only dsRNA1 sequenced (Herrero and Zabalgogeazcoa 2011)

 


Genus: Chrysovirus


 Since only one genus (Chrysovirus) is currently recognized in the family Chrysoviridae, 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

Members of the genus Chrysovirus infect ascomycetous or basidiomycetous fungi. All members have four dsRNA genome segments ranging from 2.5 to 3.6 kbp. The genome comprises 11.5-12.8 kbp in total. The dsRNA segments are individually encapsidated in separate particles.

Species demarcation criteria

Species demarcation criteria:

  • Host of isolation.
  • Nucleotide and deduced amino acid sequence data (≤ 70% and ≤ 53% aa sequence identity in the RdRp and CP, respectively)
  • size of dsRNA genome segments
  • length of 5′-UTR

Species demarcation considers a combination of each of the criteria listed above. While nucleotide and amino acid sequence relatedness are important criteria for species demarcation, the other listed criteria may be useful in demarcation of genetically closely related viruses that nevertheless belong to different species.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)Isolate Abbreviation
Amasya cherry disease associated chrysovirusAmasya cherry disease associated chrysovirusTurkeyRNA1: AJ781166; RNA2: AJ781165; RNA3: AJ781164; RNA4: AJ781163RNA1: NC_009947; RNA2: NC_009946; RNA3: NC_009945; RNA4: NC_009944Complete genomeACDACV
Amasya cherry disease associated chrysoviruscherry chlorotic rusty spot associated chrysovirusItalyRNA1: AJ781397; RNA2: AJ781398; RNA3: AJ781399; RNA4: AJ781400CCRSACV
Aspergillus fumigatus chrysovirusAspergillus fumigatus chrysovirusA56RNA1: FN178512; RNA2: FN178513; RNA3: FN178514; RNA4: FN178515Complete genomeAfCV
Cryphonectria nitschkei chrysovirus 1Cryphonectria nitschkei chrysovirus 1BS122RNA1: GQ290649; RNA2: GQ290645; RNA3: HM013825; RNA4: HM013826Complete coding genomeCnCV1
Fusarium oxysporum chrysovirus 1Fusarium oxysporum chrysovirus 1ShirazEF152346; EF152347; EF152348partial genomeFoCV1
Helminthosporium victoriae 145S virusHelminthosporium victoriae virus 145SA9RNA1: AF297176; RNA2: AF297177; RNA3: AF297178; RNA4: AF297179RNA1: NC_005978; RNA2: NC_005979; RNA3: NC_005980; RNA4: NC_005981Complete genomeHvV145S
Penicillium brevicompactum virusPenicillium brevicompactum virusIndianaNo entry in GenbankPbV
Penicillium chrysogenum virusPenicillium chrysogenum virusATCC9480RNA1: AF296439; RNA2: AF296440; RNA3: AF296441; RNA4: AF296442RNA1: NC_007539; RNA2: NC_007540; RNA3: NC_007541; RNA4: NC_007542Complete genomePcV
Penicillium cyaneofulvum virusPenicillium cyaneo-fulvum virusIMI58138No entry in GenbankPc
Verticillium dahliae chrysovirus 1Verticillium dahliae chrysovirus 1VdCV1/ChinaRNA1: HM004067; RNA2: HM004068; RNA3: HM004069; RNA4: HM004070Complete genomeVdCV1

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Related, Unclassified Viruses

See Table 3.Chrysoviridae and Figure 3.Chrysoviridae for further details of these viruses.

Virus Name

Accession number

Virus abbreviation and Exemplar isolate

Number and size of genome segments (bp)

Isaria javanica chrysovirus 1 

 

dsRNA1: KX898416;
dsRNA2: KX898417;
dsRNA3: KX898418;
dsRNA4: KX898419

IjCV1, NB IFR-19

4 (3593, 3175, 3165, 2874)

Macrophomina phaseolina chrysovirus 1

 

dsRNA1: KP900886;
dsRNA2: KP900887;
dsRNA3: KP900888;
dsRNA4: KP900889

MpCV1, TN263

4 (3712, 3462, 2927, 2985)

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.