ssRNA(-) Mycoviruses

Negative-sense, single-stranded RNA (ssRNA (-)) mycoviruses are viruses that can have segmented or non-segmented RNA genomes and with a characteristic mode of replication. This group of viruses must have their genome copied by an RNA replicase to form positive-sense RNA. The virus must carry the RNA replicase enzyme. The positive-sense RNA molecule is translated into proteins by the host ribosomes. ssRNA(-) virus particles package their RNA-dependent RNA polymerase (RdRp) molecules, and their nucleocapsids exhibit helical symmetry (linear symmetry).

Diversity and prevalence

In Botrytis cinerea, (−)ssRNA mycoviruses have been reported primarily within lineages related to non-segmented mononegavirus-like viruses and segmented bunyavirus-like viruses. The families listed below include established fungal virus taxa such as Mymonaviridae as well as broader virus families with many plant- and arthropod-infecting members (Phenuiviridae, Fimoviridae, Bunyaviridae, andPeribunyaviridae).

Families and characteristics

Family / Group Genome Structure Characteristics
Mymonaviridae Single molecule of linear, negative-sense RNA of about 10 kb Members of the family Mymonaviridae are mononegavirales viruses that usually infect filamentous fungi, although they have also been identified in metagenomics studies of insects, oomycetes, plants, and soil. A typical genome is about 10 kb and may contain four to seven ORFs; in the representative virus Sclerotinia sclerotiorum negative-stranded RNA virus 1, ORF II encodes the nucleoprotein (NP) and ORF V encodes the large (L) protein containing the RNA-directed RNA polymerase domain. Typical members produce filamentous, enveloped virions, but whether other members produce virions is unknown.
Phenuiviridae Segmented genome comprising 2–8 segments of negative-sense or ambisense RNA (total 8.1–25.1 kb; commonly 3 segments: L, M, S) Family of viruses with segmented negative-sense or ambisense RNA genomes. Members are ecologically diverse and infect vertebrates (including humans, livestock, and birds), invertebrates (including arthropods), plants, and fungi. Genomes typically encode four structural proteins: L (RNA-directed RNA polymerase), Gn and Gc glycoproteins, and N (nucleocapsid protein), although some members lack glycoprotein genes or encode additional non-structural proteins. Arthropods often act as biological vectors for transmission.
Fimoviridae Multipartite genome of 4–10 segments of negative-sense single-stranded RNA (total 12.3–18.5 kb) Family of plant viruses with multipartite negative-sense ssRNA genomes. Members primarily infect plant hosts (mainly dicotyledons, with some monocotyledons) and are transmitted by eriophyid mites. Each genome segment typically encodes a single protein, including RNA1 encoding the RNA-directed RNA polymerase (RdRp), RNA2 a glycoprotein precursor, RNA3 the nucleocapsid protein, and RNA4 a movement protein, while additional segments encode proteins of unknown function. Fimovirus-like sequences has been identified in Botrytis cinerea.
Bunyaviridae Segmented genome with three segments (L, M, S) of negative-sense or ambisense ssRNA (total 11–19 kb) Family of viruses with three-segmented negative-sense or ambisense ssRNA genomes (L, M, S). Virions are typically enveloped, spherical or pleomorphic, with surface glycoproteins. Members include viruses infecting vertebrates, arthropods, and plants, often transmitted by arthropod vectors. The L, M, and S segments encode the RNA-dependent RNA polymerase, glycoproteins (Gn, Gc), and nucleocapsid protein, respectively.
Peribunyaviridae Segmented genome with three negative-sense ssRNA segments (L, M, S), total 10.7–12.5 kb Family of enveloped viruses with three negative-sense RNA segments (L, M, S). The segments encode the RNA-directed RNA polymerase (L), envelope glycoproteins Gn and Gc (M), and nucleocapsid protein (N) (S). Members infect vertebrates and invertebrates and are often maintained in vertebrate–arthropod transmission cycles, although some are arthropod-specific.

Effects on fungal host

Mycovirus infections can influence fungal host biology in some cases. For example, at least one member of the family Mymonaviridae, Sclerotinia sclerotiorum negative-stranded RNA virus 1, has been reported to induce hypovirulence in its fungal host. However, information on the effects of negative-stranded RNA mycoviruses on fungal hosts is limited, and detailed descriptions of host phenotypic alterations are not broadly reported for most virus families.

Ecological significance and impact

The ecological significance of negative-stranded RNA mycoviruses is linked to their distribution across diverse hosts and environments. Viruses belonging to families such as Mymonaviridae and Phenuiviridae infect fungi and have also been detected in plants, invertebrates, and environmental samples, indicating a broad host range and ecological diversity. Some of those viruses encode proteins that facilitate interactions with their hosts, such as movement proteins that enable cell-to-cell movement in plant and fungal hosts and suppressors of RNA silencing that counteract host antiviral defence mechanisms. However, detailed mechanisms of transmission and cross-kingdom transfer have not been comprehensively described yet.

Evolutionary history

Negative-sense RNA viruses share conserved features, including a homologous RNA-dependent RNA polymerase (RdRp), encapsidated genomes, and complementary terminal sequences, but exhibit substantial diversity in genome organization, including variation in the number of genome segments. Comparative analysis of RdRp sequences is widely used to infer relationships among viruses, and has revealed extensive genetic diversity, including highly divergent lineages and potential new virus groups. Segmented genome organization in some virus groups provides the potential for genetic exchange through reassortment, which contributes to viral diversity. Negative-sense RNA viruses have been identified in a wide range of hosts, including fungi, plants, vertebrates, and invertebrates, indicating broad evolutionary diversification across ecological niches.

Nucleotide alignment

Primary structure alignment (amino acids)

Phylogeny