Two distinct nanovirus species infecting faba bean in Morocco

Occurrence, distribution, and genetic diversity of faba bean viruses in China

With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.

Nonconcomitant host-to-host transmission of multipartite virus genome segments may lead to complete genome reconstitution

Because multipartite viruses package their genome segments in different viral particles, they face a potentially huge cost if the entire genomic information, i.e., all genome segments, needs to be present concomitantly for the infection to function. Previous work with the octapartite faba bean necrotic stunt virus (FBNSV; family Nanoviridae, genus Nanovirus) showed that this issue can be resolved at the within-host level through a supracellular functioning; all viral segments do not need to be present within the same host cell but may complement each other through intercellular trafficking of their products (protein or messenger RNA [mRNA]). Here, we report on whether FBNSV can as well decrease the genomic integrity cost during between-host transmission. Using viable infections lacking nonessential virus segments, we show that full-genome infections can be reconstituted and function through separate acquisition and/or inoculation of complementary sets of genome segments in recipient hosts. This separate acquisition/inoculation can occur either through the transmission of different segment sets by different individual aphid vectors or by the sequential acquisition by the same aphid of complementary sets of segments from different hosts. The possibility of a separate between-host transmission of different genome segments thus offers a way to at least partially resolve the genomic maintenance problem faced by multipartite viruses.

Effects of an alphasatellite on life cycle of the nanovirus Faba bean necrotic yellows virus

Nanoviruses are plant viruses with a multipartite single-stranded DNA (ssDNA) genome. Alphasatellites are commonly associated with nanovirus infections, but their putative impact on their helper viruses is unknown. In this study, we investigated the role of subterranean clover stunt alphasatellite 1 (hereafter named SCSA 1) on various important traits of faba bean necrotic yellows virus (FBNYV) in its host plant Vicia faba and aphid vector Acyrthosiphon pisum, including disease symptoms, viral accumulation and transmission. The results indicate that SCSA 1 does not affect the symptom severity nor the overall FBNYV accumulation in V. faba, but changes the relative amounts of its different genomic segments. Moreover, the association of SCSA 1 with FBNYV increases the rate of plant-to-plant transmission by a process seemingly unrelated to simple increase of the viral accumulation in the vector. These results represent the first study on the impact of an alphasatellite on the biology of its helper nanovirus. They suggest that SCSA 1 may benefit FBNYV, but the genericity of this conclusion is discussed and questioned. Importance Alphasatellites are circular single stranded DNA molecules frequently found in association with natural isolates of nanoviruses and some geminiviruse, the two ssDNA plant infecting virus families. While the implications of alphasatellite presence in geminivirus infections are relatively well documented, comparable studies on alphasatellites associated with nanoviruses are not available. Here we confirm that subterranean clover stunt alphasatellite 1 affects different traits of its helper nanovirus, faba bean necrotic yellows virus, both in the host plant and aphid vector. We show that the frequencies of the virus segments change in the presence of alphasatellite, in both plant and vector. We also confirm that while within-plant virus load and symptom are not affected by alphasatellite, the presence of alphasatellite decreases within-aphid virus load, but significantly increases virus transmission rate, so may confer a possible evolutionary advantage for the helper virus.

Nanovirus Disease Complexes: An Emerging Threat in the Modern Era

Multipartite viruses package their genomic segments independently and mainly infect plants; few target animals. Nanoviridae is a family of multipartite single-stranded DNA plant viruses that individually encapsidate single-stranded DNAs of approximately 1 kb and transmit them through aphids without replication in the aphid vectors, thereby causing important diseases of leguminous crops and banana. Significant findings regarding nanoviruses have recently been made on important features, such as their multicellular way of life, the transmission of distinct encapsidated genome segments through the vector body, evolutionary ambiguities, mode of infection, host range and geographical distribution. This review deals with all the above-mentioned features in view of recent advances with special emphasis on the emergence of new species and recognition of new host range of nanoviruses and aims to shed light on the evolutionary linkages, the potentially devastating impact on the world economy, and the future challenges imposed by nanoviruses.

A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams (Lutraria rhynchaena)

In this study, we present an analysis of metagenome sequences obtained from a filtrate of a siphon tissue homogenate of otter clams (Lutraria rhynchaena) with swollen-siphon disease. The viral signal was mined from the metagenomic data, and a novel circular ssDNA virus was identified. Genomic features and phylogenetic analysis showed that the virus belongs to the phylum Cressdnaviricota, which consists of viruses with circular, single-stranded DNA (ssDNA) genomes. Members of this phylum have been identified in various species and in environmental samples. The newly found virus is distantly related to the currently known members of the phylum Cressdnaviricota.

Novel nanovirus and associated alphasatellites identified in milk vetch plants with chlorotic dwarf disease in Iran

Members of the family Nanoviridae are multi-component single-stranded DNA viruses that infect a variety of plant species. Using a combination of conventional PCR and high throughput sequencing-based approach, we identified a novel nanovirus infecting two symptomatic milk vetch plants (Astragalus myriacanthus Boiss.; family Fabaceae) showing marginal leaf chlorosis, little leaves and dwarfing in Iran. All eight segments (DNA-C, DNA-M, DNA-N, DNA-R, DNA-S, DNA-U1, DNA-U2 and DNAU4) were recovered and Sanger sequenced. The genome of this new nanovirus, hereby referred to as milk vetch chlorotic dwarf virus (MVCDV), shares 62.2-74.7 % nucleotide pairwise identity with the genomes of other nanoviruses. DNA-C, DNA-M, DNA-N, DNA-S components are most closely related to those of black medic leaf roll virus (BMLRV), sharing between 67.8-81.2 % identity. We also identified three nanoalphasatellites (family Alphasatellitidae) associated with the nanovirus which belong to species Faba bean necrotic yellows alphasatellite 1 (genus Subclovsatellite), Faba bean necrotic yellows alphasatellite 2 (genus Fabenesatellite) and Sophora yellow stunt alphasatellite 5 (genus Clostunsatellite). Given the significant diversity of Astragalus spp. in Iran, it is likely that there could be more nanoviruses circulating in these plants and that these may play a role in the spread of these nanovirus to cultivated fabaceous hosts.

Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range

While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

Molecular characterization of faba bean necrotic yellows viruses in Tunisia

Faba bean necrotic yellows virus (FBNYV) (genus Nanovirus; family Nanoviridae) has a genome comprising eight individually encapsidated circular single-stranded DNA components. It has frequently been found infecting faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.) in association with satellite molecules (alphasatellites). Genome sequences of FBNYV from Azerbaijan, Egypt, Iran, Morocco, Spain and Syria have been determined previously and we now report the first five genome sequences of FBNYV and associated alphasatellites from faba bean sampled in Tunisia. In addition, we have determined the genome sequences of two additional FBNYV isolates from chickpea plants sampled in Syria and Iran. All individual FBNYV genome component sequences that were determined here share > 84% nucleotide sequence identity with FBNYV sequences available in public databases, with the DNA-M component displaying the highest degree of diversity. As with other studied nanoviruses, recombination and genome component reassortment occurs frequently both between FBNYV genomes and between genomes of nanoviruses belonging to other species.

Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe

The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.

Three Distinct Nanoviruses, One of Which Represents a New Species, Infect Faba Bean in Ethiopia

In all, 70 of 296 leaf samples (23.6%) collected from faba bean (Vicia faba) plants showing leaf yellowing and stunting in Ethiopia gave nanovirus-positive reactions when studied by triple-antibody sandwich enzyme-linked immunosorbent assay using broad-spectrum monoclonal antibodies (MAbs) specific to nanoviruses. Further analysis of these samples with seven discriminating MAbs revealed contrasting epitope profiles that were categorized into roughly three serogroups, designated A, B, and C. Serogroup A was found in 89% of the nanovirus-positive samples whereas serogroups B and C were infrequently encountered. Sequence analysis of DNA-S and DNA-U1 of serogroup A, B, and C isolates suggested that each represents a distinct nanovirus species. Serogroup A comprised isolates of Faba bean necrotic stunt virus reported earlier only from Ethiopia and Morocco. The DNA-R, -S, -U1, and -U2 sequences of a serogroup B isolate closely resembled those of Faba bean necrotic yellows virus, providing first molecular evidence for its occurrence in Ethiopia. Sequence analysis of the eight genomic DNAs of a representative serogroup C isolate (Eth-231) showed that it shared overall nucleotide and amino acid sequence identities of only ≤70 and ≤74%, respectively, with other nanoviruses. This suggests that Eth-231 represents a new nanovirus species, for which the name faba bean yellow leaf virus is proposed.

High variability and rapid evolution of a nanovirus

Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 x 10(-4) substitutions per nucleotide in a field population of the virus and 5.07 x 10(-4) substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 x 10(-3) substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.

Advances in Small Isometric Multicomponent ssDNA Viruses Infecting Plants

Multicomponent ssDNA plant viruses were discovered during 1990s. They are associated with bunchy top, yellowing and dwarfing diseases of several economic plants under family Musaceae, Leguminosae and Zingiberaceae. In the current plant virus taxonomy, these viruses are classified under the family Nanoviridae containing two genera, Nanovirus and Babuvirus. The family Nanoviridae was created with five members in 2005 and by 2010, it has expanded with four additional members. The viruses are distributed in the tropical and subtropical regions of Asia, Australia, Europe and Africa. The viruses are not sap or seed transmissible and are naturally transmitted by aphid vector in a persistent manner. The genome is consisted of several circular ssDNAs of about 1 kb each. Up to 12 DNA components have been isolated from the diseased plant. The major viral proteins encoded by these components are replication initiator protein (Rep), coat protein, cell-cycle link protein, movement protein and a nuclear shuttle protein. Each ssDNA contains a single gene and a noncoding region with a stable stem and loop structure. Several Rep encoding components have been reported from each virus, only one of them designated as master Rep has ability to control replication of the other genomic components. Infectivity of the genomic DNAs was demonstrated only for two nanoviruses, Faba bean necrotic yellows virus and Faba bean necrotic stunt virus (FBNSV). A group of eight ssDNA components of FBNSV were necessary for producing disease and biologically active progeny viruses. So far, infectivity of genomic components of Babuvirus has not been demonstrated.