Characterization and complete nucleotide sequence of Strawberry mottle virus: a tentative member of a new family of bipartite plant picorna-like viruses

Abstract

An isolate of Strawberry mottle virus (SMoV) was transferred from Fragaria vesca to Nicotiana occidentalis and Chenopodium quinoa by mechanical inoculation. Electron micrographs of infected tissues showed the presence of isometric particles of approximately 28 nm in diameter. SMoVassociated tubular structures were also conspicuous, particularly in the plasmodesmata of C. quinoa. DsRNA extraction of SMoV-infected N. occidentalis yielded two bands of 6n3 and 7n8 kbp which were cloned and sequenced. Gaps in the sequence, including the 5h and 3h ends, were filled using RT-PCR and RACE. The genome of SMoV was found to consist of RNA1 and RNA2 of 7036 and 5619 nt, respectively, excluding a poly(A) tail. Each RNA encodes one polyprotein and has a 3h noncoding region of " 1150 nt. The polyprotein of RNA1 contains regions with identities to helicase, viral genome-linked protein, protease and polymerase (RdRp), and shares its closest similarity with RNA1 of the tentative nepovirus Satsuma dwarf virus (SDV). The polyprotein of RNA2 displayed some similarity to the large coat protein domain of SDV and related viruses. Phylogenetic analysis of the RdRp region showed that SMoV falls into a separate group containing SDV, Apple latent spherical virus, Naval orange infectious mottling virus and Rice tungro spherical virus. Given the size of RNA2 and the presence of a long 3h non-coding region, SMoV is more typical of a nepovirus, although atypically for a nepovirus it is aphid transmissible. We propose that SMoV is a tentative member of an SDV-like lineage of picorna-like viruses.

Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)

“…Regarding the relationships between Cheravirus, Sadwavirus and other recognized taxa, the study group initially proposed that the two new genera should be assigned to the family Sequiviridae, mostly on the basis of sequence similarities, and to reflect the suggestion made by various authors [6,14,16,19,26,34]. In this hypothesis, the segmentation of the genome could have been considered a criterion for genus demarcation within the family Sequiviridae.…”

“…The number of CP subunits is one of the distinctive features of the ''atypical nepoviruses'' discussed here: LASV, RCSV, SDV, SLRSV have 2 CP subunits, a large one and a small one as in comoviruses and fabaviruses, while ALSV, AVB, CRLV and StPV have 3 CP subunits of similar sizes, like sequiviruses and picornaviruses [3,12,23,24]. The number of CP subunits has not been experimentally determined for SMoV and BRNV [12,34].…”

“…However, the observed patterns of spread in the field suggest soil transmission [3,14]. Black raspberry necrosis virus (BRNV) and strawberry mottle virus (SMoV) are transmitted by aphids [12,34]. Arracacha virus B (AVB) is pollen-borne.…”

“…Instead, the recent availability of full-length or partial sequences of the genomes of several ''atypical nepoviruses'' revealed that most of them if not all were closer to members of the family Sequiviridae [6,14,16,19,21,26,34].…”

Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus

“…The genus Cheravirus includes viruses that have three CPs [20], and the genus Sadwavirus includes viruses that have two CPs [21]. Originally, various studies proposed that the new genera should be included in the families Comoviridae or Sequiviridae or that a new family should be created [10,14,16,17,24,40]. However, at the time of creation of these genera, the executive committee from the International Committee for the Taxonomy of Viruses (ICTV) felt that a reevaluation of the taxonomy of plant picorna-like viruses was necessary before the two new genera could be assigned to either existing families or to a new family.…”