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Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.

Viruses are among the most abundant biological entities in the ocean, largely responsible of modulating nutrients fluxes and influencing microbial composition and functioning. In marine invertebrate holobionts like sponges and their associated microbiomes, little is known about virome composition. Here, we characterized the Haliclona fulva hologenome, an encrusting low-microbial abundance sponge found across the Western Mediterranean Sea (35–40 m of depth) producer of a large metabolic repertoire of bioactive compounds and harboring a distinct and stable associated microbiome. Assembled contigs from shotgun metagenome sequences obtained from H. fulva specimens were comprehensively analyzed regarding taxonomic and functional content revealing its remarkable and abundant viral community dominated by single-stranded DNA (ssDNA) virus. Viral families consistently detected in contigs are Circoviridae, Phycodnaviridae, Poxviridae, Herelleviridae, Mimiviridae, Microviridae, and notably the first reported encounter of Nanoviridae and Genomoviridae in Porifera, expanding their known host range. The relative abundance of inferred bacteriophages/prophages was low, suggesting that the prokaryotic community in this sponge has a limited host range and susceptibility. H. fulva showed a distinct viral composition supporting the general proposition of specific and coevolving viromes in marine holobionts.

International audience; Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (similar to 1-1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. The taxonomic update includes the establishment of the new subfamily Petromoalphasatellitinae. This new subfamily includes three new genera as well as the genus Babusatellite, which previously belonged to the subfamily Nanoalphasatellitinae. Additionally, three new genera and 14 new species have been established in the subfamily Geminialphasatellitinae, as well as five new species in the subfamily Nanoalphasatellitinae.

The families of viruses possessing single-stranded (ss) circular genome employ a dedicated replication initiator protein (Rep) for making copies of their genome through the process of rolling circle replication. The replication begins at conserved nonanucleotide sequence at the intergenic region. The Rep protein seems to be the most conserved amongst the available proteins of the nanovirids and comprises of the N-terminal endonuclease domain and the C-terminal helicase domain. The structural studies of Faba bean necrotic yellows virus endonuclease domain suggests a α + β fold comprising of central β sheet built from five antiparallel β strands surrounded by outer short α helices. The catalysis is mediated by a conserved Tyr residue and employs divalent metal ions (Mn2+). On one hand, the Reps associate with each other and oligomerize and on the other hand interact with varied host and vector associated proteins for successful infection. The sequence analysis of Reps from previously known nanovirids and the newly found ones from metagenomics data shed light on the evolutionary pattern of nanovirids in comparison to other plant infecting ssDNA viruses.

Nanoviridae is a family of plant viruses (nanovirids) whose members have small isometric virions and multipartite, circular, single-stranded (css) DNA genomes. Each of the six (genus Babuvirus) or eight (genus Nanovirus) genomic DNAs is 0.9–1.1 kb and is separately encapsidated. Many isolates are associated with satellite-like cssDNAs (alphasatellites) of 1.0–1.1 kb. Hosts are eudicots, predominantly legumes (genus Nanovirus), and monocotyledons, predominantly in the order Zingiberales (genus Babuvirus). Nanovirids require a virus-encoded helper factor for transmission by aphids in a circulative, non-propagative manner. This is a summary of the ICTV Report on the family Nanoviridae, which is available at ictv.global/report/nanoviridae.

International audience; Of the approximately 1,200 plant virus species that have been described to date, nearly one-third are single-stranded DNA (ssDNA) viruses, and all are transmitted by insect vectors. However, most studies of vector transmission of plant viruses have focused on RNA viruses. All known plant ssDNA viruses belong to two economically important families, Geminiviridae and Nanoviridae, and in recent years, there have been increased efforts to understand whether they have evolved similar relationships with their respective insect vectors. This review describes the current understanding of ssDNA virus-vector interactions, including how these viruses cross insect vector cellular barriers, the responses of vectors to virus circulation, the possible existence of viral replication within insect vectors, and the three-way virus-vector-plant interactions. Despite recent breakthroughs in our understanding of these viruses, many aspects of plant ssDNA virus transmission remain elusive. More effort is needed to identify insect proteins that mediate the transmission of plant ssDNA viruses and to understand the complex virus-insect-plant three-way interactions in the field during natural infection.

Banana bunchy top virus (BBTV, genus Babuvirus, family Nanoviridae) causes the most destructive viral disease of banana worldwide but is restricted to some countries in Africa and the Asia-Pacific region. Hosts of the virus are predominantly restricted to the plant family Musaceae, and it is transmitted through vegetative planting material and in a circulative, non-propagative manner by the banana aphid (Pentalonia nigronervosa) and P. caladii. In banana, disease symptoms include stunting, leaf chlorosis and rosetting, and a cessation of fruiting, and no natural source of immunity has been confirmed. Cytopathological effects and virus replication are restricted to the phloem tissue. The virus has isometric virions, 18–20 nm in diameter, separately encapsidating each of the six integral circular ssDNA genome components. All components are monocistronic, except for DNA-R, which encodes the master replication initiation protein, and a smaller internal ORF of unknown function. Replication is via a rolling circle mechanism, and the genome components share two conserved areas in their respective untranslated regions; the stem loop common region that contains the origin of replication and the major common region which binds a heterogeneous population of DNA primers, around 80 nucleotides in length, that prime complementary strand synthesis. Some virus isolates also support alphasatellite molecules.

Nanoviridae is a family of plant viruses (nanovirids) whose members have small isometric virions and multipartite, circular, single-stranded (css) DNA genomes. Each of the six (genus Babuvirus) or eight (genus Nanovirus) genomic DNAs is 0.9–1.1 kb and is separately encapsidated. Many isolates are associated with satellite-like cssDNAs (alphasatellites) of 1.0–1.1 kb. Hosts are eudicots, predominantly legumes (genus Nanovirus), and monocotyledons, predominantly in the order Zingiberales (genus Babuvirus). Nanovirids require a virus-encoded helper factor for transmission by aphids in a circulative, non-propagative manner. This is a summary of the ICTV Report on the family Nanoviridae, which is available at ictv.global/report/nanoviridae.

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.

International audience; Letter to the Editor

BGPI : Equipe 2 : Interactions Virus Insecte Plante (VIP); International audience; Vector transmission plays a primary role in the life cycle of viruses, and insects are the most common vectors. An important mode of vector transmission, reported only for plant viruses, is circulative nonpropagative transmission whereby the virus cycles within the body of its insect vector, from gut to salivary glands and saliva, without replicating. This mode of transmission has been extensively studied in the viral families Luteoviridae and Geminiviridae and is also reported for Nanoviridae. The biology of viruses within these three families is different, and whether the viruses have evolved similar molecular/cellular virus-vector interactions is unclear. In particular, nanoviruses have a multipartite genome organization, and how the distinct genome segments encapsidated individually transit through the insect body is unknown. Here, using a combination of fluorescent in situ hybridization and immunofluorescence, we monitor distinct proteins and genome segments of the nanovirus Faba bean necrotic stunt virus (FBNSV) during transcytosis through the gut and salivary gland cells of its aphid vector Acyrthosiphon pisum. FBNSV specifically transits through cells of the anterior midgut and principal salivary gland cells, a route similar to that of geminiviruses but distinct from that of luteoviruses. Our results further demonstrate that a large number of virus particles enter every single susceptible cell so that distinct genome segments always remain together. Finally, we confirm that the success of nanovirus-vector interaction depends on a nonstructural helper component, the viral protein nuclear shuttle protein (NSP), which is shown to be mandatory for viral accumulation within gut cells.IMPORTANCE An intriguing mode of vector transmission described only for plant viruses is circulative nonpropagative transmission, whereby the virus passes through the gut and salivary glands of the insect vector without replicating. Three plant virus families are transmitted this way, but details of the molecular/cellular mechanisms of the virus-vector interaction are missing. This is striking for nanoviruses that are believed to interact with aphid vectors in ways similar to those of luteoviruses or geminiviruses but for which empirical evidence is scarce. We here confirm that nanoviruses follow a within-vector route similar to that of geminiviruses but distinct from that of luteoviruses. We show that they produce a nonstructural protein mandatory for viral entry into gut cells, a unique phenomenon for this mode of transmission. Finally, noting that nanoviruses are multipartite viruses, we demonstrate that a large number of viral particles penetrate susceptible cells of the vector, allowing distinct genome segments to remain together.

The family Geminiviridae is the first group of plant viruses in terms of number and economic importance. They have circular single-stranded (css) DNA genomes and are transmitted in a circulative non-propagative (cnp) manner by leafhoppers, whiteflies, treehoppers and aphids (Hemiptera). While diseases induced by geminiviruses were reported for more than a century, aphid transmitted geminiviruses were discovered only recently by metagenomics. This delayed discovery is puzzling because aphids are the hemipterans that transmit the most plant viruses including the viruses of families Nanoviridae and Luteoviridae, transmitted in a cnp manner. Aphid transmission was detected among a group of 4 diverging geminiviruses exhibiting a typical genome organization and for which the genus Capulavirus was created. Aphid transmission was shown only for 2 of them, the Alfalfa leaf curl virus (ALCV) transmitted by Aphis craccivora and the Plantago latent virus (PlLV) transmitted by Dysaphis plantaginae. By demonstrating aphid transmission of a third capulavirus, Euphorbia caput-medusae latent virus (EcmLV), aphid transmission was validated as a generic taxonomic criterion. The population of A. craccivora that transmits EcmLV does not transmit ALCV, which reflect high transmission specificity among capulaviruses. ALCV was selected to investigate further geminivirus transmission by aphids because it was isolated on cultivated plants in France and associated with symptoms. Its localization in plant tissues (FISH) and the accurate analysis of the feeding behavior of the vector by electropenetrography (EPG) revealed that ALCV is phloem restricted and that its distribution is heterogeneous. Transmission tests and estimations of virus contents (qPCR) show that 12% of aphids, at maximum, transmit ALCV and that transmission is dependent on a critical threshold of virus content. We also show that ALCV accumulates and persist efficiently in the digestive tract of the vector aphid, with amounts that are similar to those of geminiviruses in their leafhopper of whitefly vectors. On the contrary, the amount and persistence of ALCV in hemolymph and heads are low, consistently with the low detection of ALCV by FISH in the salivary glands unlike in the digestive tract. These results may explain the low individual transmission rate of ALCV by A. craccivora, much lower than the 90% rate observed with geminiviruses transmitted by whiteflies and leafhoppers. Thanks to a broad bean nanovirus transmitted by A. craccivora, Faba bean necrotic stunt virus (FbNSV), we showed that the low transmission of ALCV is not imputable to the aphid. Indeed the comparisons carried out with the same A. craccivora population show that the transmission rate of FbNSV is 2 to 5 times higher than that of ALCV and FbNSV was excreted much more efficiently. FISH observations show that ALCV and FbNSV do not colocalize in midgut cells, which is consistent with distinct pathways. While nanoviruses and capulaviruses have both a circular single-stranded DNA genome, only nanoviruses encode a helper component for transmission (NSP). In geminiviruses, only CP is determining vector transmission. A yeast two-hybrid analysis carried out against the CP of ALCV identified three proteins of the digestive tract of A. craccivora. Their role in ALCV transmission will have to be validated with transmission and complementary interaction tests. Together with a similar study carried out in parallel by another Ph.D. student with the CP and the NSP of FbNSV, we expect to validate the hypothesis of distinct pathways with molecular data. The generalization of the low transmission efficiency of ALCV to all capulaviruses may explain both their late discovery and their preferential adaptation to perennial hosts. This hypothesis is discussed according to some rare descriptions of capulaviruses in natural conditions and in comparison with viruses of families Nanoviridae and Luteoviridae., Les virus de la famille Geminiviridae sont des virus à ADN simple brin circulaire (ADNsbc), transmis selon le mode circulant non-multipliant (snm) par cicadelle, aleurode, membracide et puceron (Hemiptera). Des maladies causées par des géminivirus sont décrites depuis plus d'un siècle, mais ce n'est que récemment que des geminivirus transmis par puceron ont été découverts. Cette découverte tardive est paradoxale car les pucerons sont les hémiptères qui transmettent le plus de virus de plante, y compris ceux des familles Nanoviridae et Luteoviridae, transmis selon le mode snm. La transmission par puceron a été détectée au sein d'un groupe de 4 géminivirus qui se distinguent par leurs séquences et organisations génomiques, et pour lesquels le genre Capulavirus a été créé. La transmission par puceron n'avait été démontrée que pour 2 d'entre eux, l'Alfalfa leaf curl virus (ALCV) transmis par Aphis craccivora et le Plantago latent virus (PlLV) par Dysaphis plantaginea. En démontrant la transmissibilité d'un 3e capulavirus par puceron, l'Euphorbia caput medusae latent virus (EcmLV), la transmission par puceron est validée comme critère taxonomique générique. La population de A. craccivora qui transmet l'EcmLV, ne transmet pas l'ALCV, ce qui témoigne d'une grande spécificité de transmission au sein des capulavirus. La circulation de l'ALCV a été suivi dans son puceron vecteur par des approches complémentaires. La localisation de l'ALCV dans les tissus de plante (FISH) et des analyses fines du comportement alimentaire du vecteur par électropénétrographie (EPG) montrent que l'ALCV est restreint au phloème et que sa distribution est hétérogène. Des tests de transmission et des mesures de teneurs virales (qPCR) montrent qu'au maximum 12% des pucerons transmettent l'ALCV et que la transmission est tributaire d'un seuil critique de teneur viral. Nous montrons aussi que l'ALCV s'accumule et persiste efficacement dans le tube digestif du puceron vecteur, comme d'autres géminivirus dans leurs vecteurs aleurode et cicadelle. Par contre, la teneur et la persistance de l'ALCV dans l'hémolymphe et dans la tête est faible, en cohérence avec les traces infimes d'ALCV détectées par FISH dans les glandes salivaires, contrairement au tube digestif. Ces résultats pourraient expliquer que le taux de transmission de l'ALCV par A craccivora est bien inférieur à celui de géminivirus transmis par aleurode ou cicadelle (90%). Grâce à un nanovirus de fève, le Faba bean necrotic stunt virus (FbNSV), nous avons vu que la faible transmission de l'ALCV n'est pas imputable au puceron. Avec une même population de A. craccivora, nous montrons que le taux de transmission du FbNSV est 2 à 5 fois plus élevé que celui de l'ALCV, et que le FbNSV est excrété beaucoup plus efficacement. Des observations en FISH montrent que l'ALCV et le FbNSV ne colocalisent pas dans les cellules de l'intestin moyen, suggérant des routes de circulation distinctes. Alors que dans les deux familles virales les génomes sont des ADNsbc, seuls les nanovirus ont une protéine assistante de la transmission (NSP). La transmission des géminivirus est déterminée uniquement par la CP. Un criblage double-hybride en levure contre la CP de l'ALCV a permis d'identifier 3 protéines du tube digestif de A. craccivora. Leur rôle dans la transmission devra être validé par des tests d'interaction complémentaires et de transmission. Un travail parallèle réalisé avec la CP et la NSP du FbNSV dans le cadre d'une autre thèse devrait permettre à terme de valider l'hypothèse de parcours propre à chaque virus sur une base moléculaire. La généralisation du faible taux de transmission de l'ALCV à l'ensemble des capulavirus pourrait expliquer à la fois leur découverte tardive, et leur adaptation préférentielle à des hôtes pérennes. Cette hypothèse est discutée par rapport à quelques observations de terrain et en comparaison avec des virus des familles Nanoviridae et Luteoviridae.

To understand diversity of ssDNA viruses in surface seawater of Yangshan Deep-Water Harbor, Shanghai, China, viral particles were concentrated and purified from environmental samples, and their DNA was extracted and subjected to amplification by using multiple displacement amplification. The amplicons were sequenced through high-throughput sequencing technique. Metagenomic analysis reveals that most of the sequences in the virome (91.7%, 28,935/31,560 reads) have no hits in comparison to NCBI non-redundant protein databases, indicating that the majority of potential ssDNA viruses in the surface seawater remain unknown. Among the sequences that were assigned to known ssDNA viruses, the animal Circoviridae-related sequences (79.2%) are the most dominant ones; 50 sequences (7%) are affiliated to the plant Nanoviridae and Gemiviridae; 14 sequences (2%) to Microviridae infecting bacteria. Meanwhile, 24 circular sequences were assembled, and 20 of them show no significant similarity to sequences in public databases and possibly represent novel ssDNA viruses. The results indicate unusual diversity of the ssDNA viruses in the marine environments, which awaits further exploration.

Due to their nutritional value and function as soil nitrogen fixers, production of pulses has been increasing markedly in the United States, notably in the dryland areas of the Northern Plains and the Pacific Northwest United States (NP&PNW).There are several insect-transmitted viruses that are prevalent and periodically injurious to pulse crops in the NP&PNW and elsewhere in North America. Others are currently of minor concern, occurring over limited areas or sporadically. Others are serious constraints for pulses elsewhere in the world and are not currently known in North America, but have the potential to be introduced with significant economic consequences. Managing plant viruses and the diseases they cause requires effective diagnostics, knowledge of virus vectors, virus transmission biology and ecology. A comprehensive compendium to inform producers and researchers about viruses currently and potentially affecting pulses in North America is needed. Here we provide an overview of insect transmitted viruses and their biology, followed by descriptions of the structure, infection biology, host ranges, symptoms, interspecific interactions, and current management options including host plant resistance and vector control for 33 viruses affecting or potentially affecting pulses in the United States and Canada. These are organized based on their transmission biology into persistently transmitted (families Geminiviridae, Luteoviridae and Nanoviridae), semi-persistantly transmitted (Secoviridae), and nonpersistantly transmitted (Betaflexiviridae, Bromoviridae and Potyviridae) viruses. We conclude with an overview of the principles of managing insect-transmitted viruses and an outline of areas requiring further research to improve management of viruses in pulses currently and into the future.

Stress granules (SGs) are structures within cells that regulate gene expression during stress response, e.g. viral infection. In mammalian cells assembly of SGs is dependent on the Ras-GAP SH3-domain-binding protein (G3BP). The C-terminal domain of the viral nonstructural protein 3 (nsP3) of Semliki Forest virus (SFV) forms a complex with mammalian G3BP and sequesters it into viral RNA replication complexes in a manner that inhibits the formation of SGs. The binding domain of nsP3 to HsG3BP was mapped to two tandem 'FGDF' repeat motifs close to the C-terminus of the viral proteins. It was speculated that plant viruses employ a similar strategy to inhibit SG function. This study identifies an Arabidopsis thaliana NTF2-RRM domain-containing protein as a G3BP-like protein (AtG3BP), which localizes to plant SGs. Moreover, the nuclear shuttle protein (NSP) of the begomovirus abutilon mosaic virus (AbMV), which harbors a 'FVSF'-motif at its C-terminal end, interacts with the AtG3BP-like protein, as does the 'FNGSF'-motif containing NSP of pea necrotic yellow dwarf virus (PNYDV), a member of the Nanoviridae family. We therefore propose that SG formation upon stress is conserved between mammalian and plant cells and that plant viruses may follow a similar strategy to inhibit plant SG function as it has been shown for their mammalian counterparts.

Abundant novel circular Rep-encoding ssDNA viruses (CRESS DNA viruses) have been discovered in the past decade, prompting a new appreciation for the ubiquity and genomic diversity of this group of viruses. Although highly divergent in the hosts they infect or are associated with, CRESS DNA viruses are united by the homologous replication-associated protein (Rep). An accurate genealogy of Rep can therefore provide insights into how these diverse families are related to each other. We used a dataset of eukaryote-associated CRESS DNA RefSeq genomes (n=926), which included representatives from all six established families and unclassified species. To assure an optimal Rep genealogy, we derived and tested a bespoke amino acid substitution model (named CRESS), which outperformed existing protein matrices in describing the evolution of Rep. The CRESS model-estimated Rep genealogy resolved the monophyly of Bacilladnaviridae and the reciprocal monophyly of Nanoviridae and the alpha-satellites when trees estimated with general matrices like LG did not. The most intriguing, previously unobserved result is a likely single origin of intron-containing Reps, which causes several geminivirus genera to group with Genomoviridae (bootstrap support 55%, aLRT SH-like support 0.997, 0.91-0.997 in trees estimated with established matrices). This grouping, which eliminates the monophyly of Geminiviridae, is supported by both domains of Rep, and appears to be related to our use of all RefSeq Reps instead of subsampling to get a smaller dataset. In addition to producing a trustworthy Rep genealogy, the derived CRESS matrix is proving useful for other analyses; it best fit alignments of capsid protein sequences from several CRESS DNA families and parvovirus NS1/Rep sequences.

Over the last decade, arthropods have been shown to harbour a rich diversity of viruses. Through viral metagenomics a large diversity of single-stranded (ss) DNA viruses have been identified. Here we examine the ssDNA virome of the hematophagous New Zealand blackfly using viral metagenomics. Our investigation reveals a plethora of novel ssDNA viral genomes, some of which cluster in the viral families Genomoviridae (n = 9), Circoviridae (n = 1), and Microviridae (n = 108), others in putative families that, at present, remain unclassified (n = 20) and one DNA molecule that only encodes a replication associated protein. Among these novel viruses, two putative multi-component virus genomes were recovered, and these are most closely related to a Tongan flying fox faeces-associated multi-component virus. Given that the only other known multi-component circular replication-associated (Rep) protein encoding single-stranded (CRESS) DNA viruses infecting plants are in the families Geminiviridae (members of the genus Begomovirus) and Nanoviridae, it appears these are likely a new multi-component virus group which may be associated with animals. This study reiterates the diversity of ssDNA viruses in nature and in particular with the New Zealand blackflies.

Single-stranded DNA (ssDNA) plant viruses belong to the families Geminiviridae and Nanoviridae. They are transmitted by Hemipteran insects in a circulative, mostly non-propagative, manner. While geminiviruses are transmitted by leafhoppers, treehoppers, whiteflies and aphids, nanoviruses are transmitted exclusively by aphids. Circulative transmission involves complex virus&ndash, vector interactions in which epithelial cells have to be crossed and defense mechanisms counteracted. Vector taxa are considered a relevant taxonomic criterion for virus classification, indicating that viruses can evolve specific interactions with their vectors. Thus, we predicted that, although nanoviruses and geminiviruses represent related viral families, they have evolved distinct interactions with their vector. This prediction is also supported by the non-structural Nuclear Shuttle Protein (NSP) that is involved in vector transmission in nanoviruses but has no similar function in geminiviruses. Thanks to the recent discovery of aphid-transmitted geminiviruses, this prediction could be tested for the geminivirus alfalfa leaf curl virus (ALCV) and the nanovirus faba bean necrotic stunt virus (FBNSV) in their common vector, Aphis craccivora. Estimations of viral load in midgut and head of aphids, precise localization of viral DNA in cells of insect vectors and host plants, and virus transmission tests revealed that the pathway of the two viruses across the body of their common vector differs both quantitatively and qualitatively.

Banana bunchy top disease (BBT) is one of the most economically serious viral diseases of banana caused by banana bunchy top virus (BBTV: Nanoviridae: Babuvirus). BBTV is a circular, ssDNA virus which is suitable in the phloem tissue and currently only being transmitted by the banana aphid (Pentalonia nigronervosa) in a persistent, non-propagative, circulative manner. Interaction of BBTV and banana aphid had been studied in several ways, such as transmission and translocation of BBTV inside the banana aphid body at cellular level. However, the molecular mechanism underlying the interaction between BBTV and banana aphid have been poorly understood. Therefore, this transcriptomic study was conducted to obtain the raw data for differential genes expression study in BBTV viruliferous (Vr) and non-viruliferous (NVr) banana aphid. Here, we present two data sets of RNA seq raw reads which is available in GenBank Sequence Read Archive (SRA) database with accession number of SRX6918251 and SRX6918252 for the Vr and NVr banana aphid respectively.

International audience; Numerous metagenomic studies have uncovered a remarkable diversity of circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses, the majority of which are uncultured and unclassified. Unlike capsid proteins, the Reps show significant similarity across different groups of CRESS DNA viruses and have conserved domain organization with the N-terminal nuclease and the C-terminal helicase domain. Consequently, Rep is widely used as a marker for identification, classification and assessment of the diversity of CRESS DNA viruses. However, it has been shown that in certain viruses the Rep nuclease and helicase domains display incongruent evolutionary histories. Here, we systematically evaluated the co-evolutionary patterns of the two Rep domains across classified and unclassified CRESS DNA viruses. Our analysis indicates that the Reps encoded by members of the families Bacilladnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Nanoviridae and Smacoviridae display largely congruent evolutionary patterns in the two domains. By contrast, among the unclassified CRESS DNA viruses, 71% appear to have chimeric Reps. Such massive chimerism suggests that unclassified CRESS DNA viruses represent a dynamic population in which exchange of gene fragments encoding the nuclease and helicase domains is extremely common. Furthermore, purging of the chimeric sequences uncovered six monophyletic Rep groups that may represent new families of CRESS DNA viruses.

BGPI : équipe 2 / 7; International audience; Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhône region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nanovirus genomes. The two associated alphasatellites share 62% identity with each other and < 81% identity will all other nanovirus-associated alphasatellites.

Grapevine red blotch disease has been recognized since 2008 as affecting North American grape production. The presence of the newly described Grapevine red blotch-associated virus (GRBaV) is highly correlated with the disease. To more effectively detect and monitor the presence of the virus, a sample processing strategy and multiplex polymerase chain reaction assay were developed. A total of 42 of 113 vine samples collected in or received from seven of the United States were shown to harbor the virus, demonstrating the virus is widely distributed across North America. Phylogenetic analyses of a viral replication-associated protein (Rep) gene fragment from the 42 isolates of GRBaV demonstrated distinct clades of the virus (1 and 2), with clade 1 showing the greatest variability. The full-length genome of six virus isolates was sequenced, and phylogenetic analyses of 14 whole genomes recapitulated results seen for the Rep gene. A comparison of GRBaV genomes revealed evidence of recombination underlying some of the variation seen among GRBaV genomes within clade 1. Phylogenetic analyses of coat and replicase-associated protein sequences among single-stranded DNA viruses showed GRBaV to group within the family Geminiviridae. This grouping is distinct from members of the families Nanoviridae and Circoviridae, with limited significant affinities to both recognized genera and novel plant-infecting, gemini-like viruses.

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.

The application of viral metagenomic techniques and a series of PCRs in a human fecal sample enabled the detection of two novel circular unisense DNA viral genomes with 92% nucleotide similarity. The viruses were tentatively named circo-like virus-Brazil (CLV-BR) strains hs1 and hs2 and have genome lengths of 2526 and 2533 nucleotides, respectively. Four major open reading frames (ORFs) were identified in each of the genomes, and differences between the two genomes were primarily observed in ORF 2. Only ORF 3 showed significant amino acid similarities to a putative rolling circle replication initiator protein (Rep), although with low identity (36%). Our phylogenetic analysis, based on the Rep protein, demonstrated that the CLV-BRs do not cluster with members of the Circoviridae, Nanoviridae or Geminiviridae families and are more closely related to circo-like genomes previously identified in reclaimed water and feces of a wild rodent and of a bat. The CLV-BRs are members of a putative new family of circular Rep-encoding ssDNA viruses. Electron microscopy revealed icosahedral (~23 nm) structures, likely reflecting the novel viruses, and rod-shaped viral particles (~65-460 × 21 × 10 nm in length, diameter, and axial canal, respectively). Circo-like viruses have been detected in stool samples from humans and other mammals (bats, rodents, chimpanzees and bovines), cerebrospinal fluid and sera from humans, as well as samples from many other sources, e.g., insects, meat and the environment. Further studies are needed to classify all novel circular DNA viruses and elucidate their hosts, pathogenicity and evolutionary history.

Foorkey disease is a serious constraint to the production of large cardamom ( Amomum subulatum , family Zingiberaceae). The disease is characterized by profuse proliferation of excessive stunted shoots, which makes the clump totally unproductive. The disease has been known in India since 1936 but the complete genome of the virus had not yet been characterized. In a preliminary study, an associated virus tentatively named as Cardamom bushy dwarf virus (CBDV) was identified based on the partial sequence of a single DNA component (DNA-R). In the present study, a high incidence (37.2–39.3%) of foorkey was recorded in certain plantations in the Darjeeling hills located at lower altitudes (300–1380 m) and CBDV was detected in several field samples by PCR. Nine novel DNA components were isolated and characterized from foorkey affected plants. CBDV contained six major DNA components (DNA-R, -S, -M, -C, -N and -U3) similar to the integral genome components known for the members of the genus Babuvirus in the family Nanoviridae . Additional components, satellite Rep (DNA-sRep1) and unknown components (DNA-Uf1 and -Uf2) were also identified. The size of the genome components ranged from 1028 to 1127. The sequence identity and phylogeny based on the individual components as well as overall genome (59.8–62% identity) distinguished CBDV from the two existing babuvirus species, Banana bunchy top virus and Abaca bunchy top virus. CBDV is the first distinct babuvirus species that affects plant species outside family Musaceae. This study shows further diversity in the genu s Babuvirus .

Plants infected with DNA viruses produce massive quantities of virus-derived, 24-nucleotide short interfering RNAs (siRNAs), which can potentially direct viral DNA methylation and transcriptional silencing. However, growing evidence indicates that the circular double-stranded DNA accumulating in the nucleus for Pol II-mediated transcription of viral genes is not methylated. Hence, DNA viruses most likely evade or suppress RNA-directed DNA methylation. This review describes the specialized mechanisms of replication and silencing evasion evolved by geminiviruses and pararetoviruses, which rescue viral DNA from repressive methylation and interfere with transcriptional and post-transcriptional silencing of viral genes.

Plant viruses of the families Luteoviridae and Geminiviridae rely on hemipteran vectors for the infection of their hosts. Several lines of evidence have revealed that these viruses are transmitted by competent vectors in a circulative manner, involving entry into the vector’s body and the crossing of epithelial tissues forming the alimentary tract and the salivary glands. Similar to luteovirids and geminiviruses, a third family of plant viruses, the family Nanoviridae, have also been reported to be transmitted by aphids in a circulative manner. However, there is limited direct evidence of a possible path of translocation through the aphid vectors. Here, we used time-course experiments and transmission assays coupled with real-time PCR and immunofluorescence assays on dissected tissues to examine the translocation, compartmentalization and retention of banana bunchy top virus (BBTV) into the aphid vector Pentalonia nigronervosa. Our results indicate that BBTV translocates rapidly through the aphid vector; it is internalized into the anterior midgut in which it accumulates and is retained at concentrations higher than either the haemolymph or the principal salivary glands. Despite the large increase in viral concentration, we have failed to detect BBTV transcripts with RT-PCR. When tissues were not permeabilized, BBTV localized as distinct puncta in the proximity of the basal surface of the cells forming the anterior midgut and principal salivary glands, suggesting an on-going process of virion escape and internalization, respectively. Interestingly, we document that those organs can have direct contact within the aphid body, suggesting a possible haemolymph-independent translocation path.