Hadaka Virus 1: a Capsidless Eleven-Segmented Positive-Sense Single-Stranded RNA Virus from a Phytopathogenic Fungus, Fusarium oxysporum

Abstract

The search for viruses infecting fungi, or mycoviruses, has extended our knowledge about the diversity of RNA viruses, as exemplified by the discovery of polymycoviruses, a phylogenetic group of multisegmented RNA viruses with unusual forms. The genomic RNAs of known polymycoviruses, which show a phylogenetic affinity for animal positive-sense single-stranded RNA [(+)RNA] viruses such as caliciviruses, are comprised of four conserved segments with an additional zero to four segments. The double-stranded form of polymycovirus genomic RNA is assumed to be associated with a virally encoded protein (proline-alanine-serine-rich protein [PASrp]) in either of two manners: a capsidless colloidal form or a filamentous encapsidated form. Detailed molecular characterizations of polymycoviruses, however, have been conducted for only a few strains. Here, a novel polymyco-related virus named Hadaka virus 1 (HadV1), from the phytopathogenic fungus Fusarium oxysporum, was characterized. The genomic RNA of HadV1 consisted of an 11-segmented positive-sense RNA with highly conserved terminal nucleotide sequences. HadV1 shared the three conserved segments with known polymycoviruses but lacked the PASrp-encoding segment. Unlike the known polymycoviruses and encapsidated viruses, HadV1 was not pelleted by conventional ultracentrifugation, possibly due to the lack of PASrp. This result implied that HadV1 exists only as a soluble form with naked RNA. Nevertheless, the 11 genomic segments of HadV1 have been stably maintained through host subculturing and conidiation. Taken together, the results of this study revealed a virus with a potential novel virus lifestyle, carrying many genomic segments without typical capsids or PASrp-associated forms. IMPORTANCE Fungi collectively host various RNA viruses. Examples include encapsidated double-stranded RNA (dsRNA) viruses with diverse numbers of genomic segments (from 1 to 12) and capsidless viruses with nonsegmented (+)RNA genomes. Recently, viruses with unusual intermediate features of an infectious entity between encapsidated dsRNA viruses and capsidless (+)RNA viruses were found. They are called polymycoviruses, which typically have four to eight dsRNA genomic segments associated with one of the virus-encoded proteins and are phylogenetically distantly related to animal (+)RNA caliciviruses. Here, we identified a novel virus phylogenetically related to polymycoviruses, from the phytopathogenic fungus Fusarium oxysporum. The virus, termed Hadaka virus 1 (HadV1), has 11 (+)RNA genomic segments, the largest number in known (+)RNA viruses. Nevertheless, HadV1 lacked a typical structural protein of polymycoviruses and was not pelleted by standard ultracentrifugation, implying an unusual capsidless nature of HadV1. This study reveals a potential novel lifestyle of multisegmented RNA viruses.

Molecular Characterization of a Novel Polymycovirus From Penicillium janthinellum With a Focus on Its Genome-Associated PASrp

“…Recent studies suggest that multi-segmented RNA viruses can also be capsidless, which has been shown for some polymycoviruses (Kanhayuwa et al, 2015;Zhai et al, 2016;Kotta-Loizou and Coutts, 2017;Niu et al, 2018) and one hadakavirus (Sato et al, 2020). Polymycoviruses are a group of mycoviruses belonging to the genus Polymycovirus in the family Polymycoviridae, which was established in 2020 1 .…”

“…Several polymycoviruses have additional one to four genomic segments, among which no significant sequence similarities were found (Zhai et al, 2016;Jia et al, 2017;Kotta-Loizou and Coutts, 2017;Mahillon et al, 2019). Hadakavirus is a novel (+)RNA virus that has a close phylogenetic relationship with polymycoviruses (Sato et al, 2020). In contrast to polymycoviruses, the hadakavirus has 11 dsRNA segments as its replicative form, which include three segments cognate with polymycovirus, namely -dsRNA1, -dsRNA2, and -dsRNA3 (Sato et al, 2020).…”

“…Hadakavirus is a novel (+)RNA virus that has a close phylogenetic relationship with polymycoviruses (Sato et al, 2020). In contrast to polymycoviruses, the hadakavirus has 11 dsRNA segments as its replicative form, which include three segments cognate with polymycovirus, namely -dsRNA1, -dsRNA2, and -dsRNA3 (Sato et al, 2020). Total genome size considerably varies between polymycoviruses and a hadakavirus due to the expanded genomic segment numbers ( Table 1).…”

“…Thus, despite its capsidless nature, Polymycoviridae has been classified as a dsRNA virus family by the International Committee on Taxonomy of Viruses (ICTV). In contrast to polymycoviruses, the hadakavirus lacks PASrp or its related candidate and is hypothesized to exist as a soluble RNA form, although its alternative strategies for genome protection remain unknown (Sato et al, 2020). It should be noted that proline-alanine-serine (PAS)-rich proteins, phylogenetically unrelated to polymycovirus PASrps, are also encoded in other unclassified RNA viruses with a potentially capsidless nature, including phlegiviruses (Kozlakidis et al, 2009;Kanhayuwa et al, 2015;Kotta-Loizou and Coutts, 2017).…”

Investigating the Concept and Origin of Viruses

“…Using virion or capsid to distinguish viral lineages and viruses from cells can generate similar confusions. For example, it can complicate classifications for virus-like genetic elements and viruses that either lack virions (e.g., plasmids, viroids [ 29 ]) or encode only part of the virion (e.g., polydnaviruses). For example, the genome of polydnaviruses is dispersed within the genome of parasitoid wasps.…”