ssRNA(+) Mycoviruses

Mycoviruses with positive-sense, single-stranded RNA (ssRNA(+)) genomes represent the most significant fraction of known fungal viruses. Unlike many plant and animal viruses, most ssRNA mycoviruses do not form true, rigid virions. Instead, their RNA genomes often exist as “naked” nucleocapsids within host-derived lipid vesicles. These viruses replicate entirely in the host cytoplasm or specific organelles like mitochondria.

Diversity and prevalence

The viruses listed belong to distinct families, not all of which exclusively contain mycoviruses or have a definitive ssRNA(+) genome. Some families also include plant- or animal-infecting species, and some lack a traditional capsid protein gene. Notable exceptions in the list include Flexiviridae, Togaviridae, and Tombusviridae, which are primarily classified as plant or animal virus families but share evolutionary links with mycoviruses and may include mycovirus-like relatives identified through metagenomics.

Families and characteristics

Family / Group Genome Structure Characteristics
Alphaflexiviridae Linear, monopartite, (5.4–9 kb) Flexuous filamentous virions in some genera; others are non-encapsidated. Infects plants or plant-pathogenic fungi. Encodes replicase, and sometimes a coat protein (CP) and/or movement proteins.
Botourmiaviridae Linear, monopartite (~2–5 kb) or tripartite (~2.8, 1.1, 0.97 kb) Fungal members are generally non-encapsidated and have a monopartite genome encoding an RdRp.
Deltaflexiviridae Linear, monopartite (~6.5–8 kb) Fungal viruses. Virions have not been observed; the presence of a capsid is unknown. The genome encodes a RNA-dependent RNA polymerase (RdPR) and additional ORFs in some members.
Fusariviridae Linear, mono-segmented (5.9–10.7 kb) Viruses thought to be capsidless and not associated with true virions. Genomes are usually bicistronic but can contain one to four ORFs. The largest ORF encodes a protein with RdRP and helicase domains, and the second ORF typically encodes a conserved protein of unknown function.
Gammaflexiviridae Linear, monopartite (~7–9 kb) Viruses of fungi with non-enveloped, flexuous filamentous virions. The genome is capped and polyadenylated and encodes an RdRP and a coat protein.
Hypoviridae Linear, unsegmented RNA (7.3–18.3 kb) Capsidless viruses with one or two ORFs translated by non-canonical mechanisms, including IRES-mediated initiation and stop/restart translation. They replicate in Golgi body-derived lipid vesicles containing dsRNA replicative forms, and some induce hypovirulence in fungal hosts.
Mitoviridae Linear, monopartite, (2.1–4.5 kb) Capsidless, non-virion-forming viruses with a single ORF encoding the RNA-dependent RNA polymerase (RdRp). Their replication occurs primarily in host mitochondria.
Mycoalphaviridae Linear, monopartite (6.0-8.1 kb) Viruses infecting protists and fungi.
Narnaviridae Linear, monopartite, (2.3–2.7 kb) Capsidless, non-encapsidated viruses located in the host cytoplasm; the genome encodes a single RNA-dependent RNA polymerase (RdRp).
Splipalmiviridae 2-4 linear segments (4.0-7.0 kb) Segmented ssRNA(+) viruses infecting fungi.
Tombusviridae Linear, usually monopartite (3.7–4.8 kb), but bipartite in dianthoviruses Non-enveloped plant viruses with T=3 icosahedral virions; members infect monocotyledonous or dicotyledonous plants, fungus and are often mechanically or soil transmitted.
Tymoviridae Linear, monopartite, positive-sense ssRNA (6.0–7.5 kb) Primarily plant viruses with non-enveloped, isometric virions of about 30 nm diameter; the only family in the order Tymovirales with isometric particles. Related mycotymovirus-like viruses have also been reported in fungi.
Yadokariviridae Linear, monopartite(3.6–6.3 kb) Capsidless per se; trans-encapsidated by phylogenetically distant dsRNA viruses in non-enveloped spherical virions, and infecting fungi and possibly oomycetes.

Effects on fungal host

Many mycoviruses, including several positive-sense single-stranded RNA viruses, can alter the biology of their fungal hosts. Infection may result in reduced growth, abnormal colony morphology, decreased sporulation, and reduced virulence toward plant hosts, a phenomenon known as hypovirulence. Hypovirulence-associated mycoviruses have attracted considerable interest as biological control agents against plant Botrytis cinerea, following the successful precedent use of Cryphonectria hypovirus 1 to manage chestnut blight in Europe. Certain mycoviruses, such as Botrytis cinerea hypovirus 1 (BcHV1), can significantly reduce gray mould severity. BcHV1 specifically suppresses the formation of infection cushions, which are critical for host penetration, thereby attenuating virulence without necessarily reducing the fungus's radial growth.

Ecological significance and impact

Positive-sense single-stranded RNA (+ssRNA) mycoviruses, like mycoviruses more generally, can affect the fitness, virulence, reproduction, and other phenotypic traits of their fungal hosts. Most mycoviruses are transmitted intracellularly, primarily by hyphal anastomosis (horizontal) and spore (vertical) transmission, and they typically lack an extracellular phase. In addition, phylogenetic links between fungal and plant viruses, together with documented cases of virus shuttling between fungi and plants, indicate that cross-kingdom movement can occur, although its frequency and mechanisms remain incompletely understood. These observations highlight the ecological and evolutionary significance of mycoviruses in fungus–plant systems.

Evolutionary history

The study of mycovirus evolution in Botrytis cinerea provides important insight into viral diversity and the potential use of mycoviruses in biological control through virus-induced hypovirulence. The B. cinerea virome is characterized by a significant presence of positive-sense single-stranded RNA (+ssRNA) viruses, including members of the Mitoviridae and Botourmiaviridae families. These +ssRNA mycoviruses often feature non-segmented genomes and share a common evolutionary history with plant viruses, suggesting ancestral links across phyla. Furthermore, evidence of cross-kingdom horizontal transfer between B. cinerea and its host plants highlights the role of these viruses in filling major evolutionary gaps within the global fungal virome.

Nucleotide alignment

Primary structure alignment (amino acids)

Phylogeny