New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.

A novel weevil-transmitted tymovirus found in mixed infection on hollyhock

Leaves of hollyhock (Alcea rosea) exhibiting vein chlorosis and yellow mosaic symptoms were collected at public sites in Lausanne and Nyon, two cities of western Switzerland. Diagnostic methods untangled in samples from both sites the mixed infections of a novel isometric virus, tentatively named "Alcea yellow mosaic virus" (AYMV) with the carlavirus Gaillardia latent virus. A new potyvirus was also identified in samples from Nyon. A combination of Illumina, Nanopore and Sanger sequencing was necessary to assemble the full-length genome of AYMV, revealing an exceptionally high cytidine content and other features typically associated with members of the genus Tymovirus. The host range of AYMV was found to be restricted to mallows, including ornamentals as well as economically important plants. Phylogenetic analyses further showed that AYMV belongs to a Tymovirus subclade that also gathers the other mallow-infecting members. The virus was readily transmitted by sap inoculation, and the weevil species Aspidapion radiolus was evidenced as a vector. Transmission assays using another weevil or other insect species did not succeed, and seed transmission was not observed.

Pathogenicity and Relative Abundance of Dickeya and Pectobacterium Species in Switzerland: An Epidemiological Dichotomy

Pectobacterium and Dickeya species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are Dickeya dianthicola, Dickeya solani, Pectobacterium atrosepticum, Pectobacterium brasiliense, Pectobacterium carotovorum, and Pectobacterium parmentieri. Ten years ago, the most prevalent Soft Rot Pectobacteriaceae in Europe were the Dickeya species, P. atrosepticum and P. carotovorum, with some variations among countries. Since then, a drastic increase in the abundance of P. brasiliense has been observed in most European countries. This shift is difficult to explain without comparing the pathogenicity of all Dickeya and Pectobacterium species. The pathogenicity of all the above-mentioned bacterial species was assessed in field trials and in vitro tuber slice trials in Switzerland. Two isolates of each species were inoculated by soaking tubers of cv. Desiree in a suspension of 10⁵ CFU/mL, before planting in the field. For all trials, the Dickeya species were the most virulent ones, but long-term strain surveys performed in Switzerland indicate that P. brasiliense is currently the most frequent species detected. Our results show that the pathogenicity of the species is not the main factor explaining the high prevalence of P. brasiliense and P. parmentieri in the Swiss potato fields.

Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Ligustrum vulgare) in Europe

Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub Ligustrum vulgare (privet) was recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and de novo assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3'-terminal common region (CR) attached to each segment via a ∼53-71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus Hordeivirus of family Virgaviridae, which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts Chenopodium quinoa and Nicotiana benthamiana. Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3'-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.

Early Emergence of Dickeya solani Revealed by Analysis of Dickeya Diversity of Potato Blackleg and Soft Rot Causing Pathogens in Switzerland

Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya, before the large outbreak caused by D. solani in the 2000s, only D. dianthicola was isolated in Europe. The population dynamics of potato blackleg causing soft rot Pectobacteriaceae was, however, different in Switzerland as compared to that in other European countries with a high incidence (60 up to 90%) of Dickeya species (at the time called Erwinia chrysanthemi) already in the 1980s. To pinpoint what may underlie this Swiss peculiarity, we analysed the diversity present in the E. chrysanthemi Agroscope collection gathering potato isolates from 1985 to 2000s. Like elsewhere in Europe during this period, the majority of Swiss isolates belonged to D. dianthicola. However, we also identified a few isolates, such as D. chrysanthemi and D. oryzeae, two species that have not yet been reported in potatoes in Europe. Interestingly, this study allowed the characterisation of two "early" D. solani isolated in the 1990s. Genomic comparison between these early D. solani strains and strains isolated later during the large outbreak in the 2000s in Europe revealed only a few SNP and gene content differences, none of them affecting genes known to be important for virulence.

Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species

Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.