Strawberry chlorotic fleck: identification and characterization of a novel Closterovirus associated with the disease

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

To protect New Zealand's unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies.

Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons

To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses.

Pest categorisation of non-EU viruses of Fragaria L

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Fragaria L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of strawberry latent virus and strawberry latent C virus for which very limited information exists, the pest categorisation was completed for 12 viruses having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Fragaria seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Strawberry chlorotic fleck‐associated virus, strawberry leaf curl virus, strawberry necrotic shock virus, strawberry pallidosis‐associated virus, strawberry vein banding virus (SVBV) and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). For SVBV, the Panel considered that following its entry and establishment into the EU territory, an impact of uncertain magnitude is expected mainly because a synergistic effect may occur in strawberry in case of mixed infections with viruses already present in the EU. Strawberry crinivirus 3, strawberry crinivirus 4 and strawberry polerovirus 1 meet all criteria for being considered as potential Union QPs, except for the impact in the EU territory, on which the Panel was unable to conclude. Fragaria chiloensis cryptic virus, Fragaria chiloensis latent virus and strawberry pseudo mild yellow edge virus do not meet the criterion of having potential negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general, these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests.

This publication is linked to the following EFSA Journal articles: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5501/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5590/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5735/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5769/full

Molecular and Biological Characterization of a New Strawberry Cytorhabdovirus

Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-inoculated to N. benthamiana, N. benthamiana DCL2/4i, N.occidentalis 37B, and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae, and A. ruborum were shown to transmit StrV-1 under experimental conditions.

Functional diversification upon leader protease domain duplication in the Citrus tristeza virus genome: Role of RNA sequences and the encoded proteins

Viruses from the family Closteroviridae show an example of intra-genome duplications of more than one gene. In addition to the hallmark coat protein gene duplication, several members possess a tandem duplication of papain-like leader proteases. In this study, we demonstrate that domains encoding the L1 and L2 proteases in the Citrus tristeza virus genome underwent a significant functional divergence at the RNA and protein levels. We show that the L1 protease is crucial for viral accumulation and establishment of initial infection, whereas its coding region is vital for virus transport. On the other hand, the second protease is indispensable for virus infection of its natural citrus host, suggesting that L2 has evolved an important adaptive function that mediates virus interaction with the woody host.

Self-interaction of Citrus tristeza virus p33 protein via N-terminal helix

Citrus tristeza virus (CTV), the most economically important viral pathogen of citrus, encodes a unique protein, p33. CTV p33 shows no similarity with other known proteins, yet plays an important role in viral pathogenesis: it extends the virus host range and mediates virus ability to exclude superinfection by other variants of the virus. Previously we demonstrated that p33 is an integral membrane protein and appears to share characteristics of viral movement proteins. In this study, we show that the p33 protein self-interacts in vitro and in vivo using co-immunoprecipitation, yeast two hybrid, and bimolecular fluorescence complementation assays. Furthermore, a helix located at the N-terminus of the protein is required and sufficient for the protein self-interaction.

Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes.

Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease

A bizarre virus-like symptom of a leaf rosette formed by dense small leaves on branches of wild roses (Rosa multiflora Thunb.), designated as 'wild rose leaf rosette disease' (WRLRD), was observed in China. To investigate the presumed causal virus, a wild rose sample affected by WRLRD was subjected to deep sequencing of small interfering RNAs (siRNAs) for a complete survey of the infecting viruses and viroids. The assembly of siRNAs led to the reconstruction of the complete genomes of three known viruses, namely Apple stem grooving virus (ASGV), Blackberry chlorotic ringspot virus (BCRV) and Prunus necrotic ringspot virus (PNRSV), and of a novel virus provisionally named 'rose leaf rosette-associated virus' (RLRaV). Phylogenetic analysis clearly placed RLRaV alongside members of the genus Closterovirus, family Closteroviridae. Genome organization of RLRaV RNA (17,653 nucleotides) showed 13 open reading frames (ORFs), except ORF1 and the quintuple gene block, most of which showed no significant similarities with known viral proteins, but, instead, had detectable identities to fungal or bacterial proteins. Additional novel molecular features indicated that RLRaV seems to be the most complex virus among the known genus members. To our knowledge, this is the first report of WRLRD and its associated closterovirus, as well as two ilarviruses and one capilovirus, infecting wild roses. Our findings present novel information about the closterovirus and the aetiology of this rose disease which should facilitate its control. More importantly, the novel features of RLRaV help to clarify the molecular and evolutionary features of the closterovirus.

Membrane association of a nonconserved viral protein confers virus ability to extend its host range

Citrus tristeza virus (CTV), the largest and most complex member of the family Closteroviridae, encodes a unique protein, p33, which shows no homology with other known proteins, however, plays an important role in virus pathogenesis. In this study, we examined some of the characteristics of p33. We show that p33 is a membrane-associated protein that is inserted into the membrane via a transmembrane helix formed by hydrophobic amino acid residues at the C-terminal end of the protein. Removal of this transmembrane domain (TMD) dramatically altered the intracellular localization of p33. Moreover, the TMD alone was sufficient to confer membrane localization of an unrelated protein. Finally, a CTV variant that produced a truncated p33 lacking the TMD was unable to infect sour orange, one of the selected virus hosts, which infection requires p33, suggesting that membrane association of p33 is important for the ability of CTV to extend its host range.

Virus testing by PCR and RT-PCR amplification in berry fruit

Berry fruit crops are prone to infection by a wide range of viruses, with the list expanding every year, primarily because of the expansion of the crops to new geographic regions. Although some methods allow for virus detection in a nonspecific manner, the advent of cheap and effective nucleic acid sequencing technologies has allowed for the development of species-specific tests. This chapter describes methods for extraction of nucleic acids for molecular testing from a range of different berry fruit crops and lists oligonucleotide primers that have been developed for amplification of a large number of berry fruit viruses.

High Risk Strawberry Viruses by Region in the United States and Canada: Implications for Certification, Nurseries, and Fruit Production

There is limited information about the distribution of strawberry viruses in North America and around the world. Since the turn of the century, there has been a concerted effort to develop sensitive tests for many of the previously uncharacterized, graft-transmissible agents infecting strawberry. These tests were employed to determine the presence of strawberry viruses in major strawberry production and nursery areas of North America. The viruses evaluated in this study were Apple mosaic, Beet pseudo-yellows, Fragaria chiloensis latent, Strawberry chlorotic fleck, Strawberry crinkle, Strawberry latent ring spot, Strawberry mild yellow edge, Strawberry mottle, Strawberry necrotic shock, Strawberry pallidosis, Strawberry vein banding, and Tobacco streak. The aphid-borne viruses were predominant in the Pacific Northwest whereas the whitefly-borne viruses were prevalent in California, the Midwest, and the Southeast. In the Northeast, the aphid-transmitted Strawberry mottle and Strawberry mild yellow edge viruses along with the whitefly-transmitted viruses were most common. The incidence of pollen-borne viruses was low in most areas, with Strawberry necrotic shock being the most prevalent virus of this group. These results indicate that there are hotspots for individual virus groups that normally coincide with the presence of the vectors. The information presented highlights the high-risk viruses for nursery production, where efforts are made to control all viruses, and fruit production, where efforts are made to control virus diseases.

Gene duplication is infrequent in the recent evolutionary history of RNA viruses

Gene duplication generates genetic novelty and redundancy and is a major mechanism of evolutionary change in bacteria and eukaryotes. To date, however, gene duplication has been reported only rarely in RNA viruses. Using a conservative BLAST approach we systematically screened for the presence of duplicated (i.e., paralogous) proteins in all RNA viruses for which full genome sequences are publicly available. Strikingly, we found only nine significantly supported cases of gene duplication, two of which are newly described here--in the 25 and 26 kDa proteins of Beet necrotic yellow vein virus (genus Benyvirus) and in the U1 and U2 proteins of Wongabel virus (family Rhabdoviridae). Hence, gene duplication has occurred at a far lower frequency in the recent evolutionary history of RNA viruses than in other organisms. Although the rapidity of RNA virus evolution means that older gene duplication events will be difficult to detect through sequence-based analyses alone, it is likely that specific features of RNA virus biology, and particularly intrinsic constraints on genome size, reduce the likelihood of the fixation and maintenance of duplicated genes.

Genomic and biological analysis of Grapevine leafroll-associated virus 7 reveals a possible new genus within the family Closteroviridae

Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the most prominently represented sequence in the analysis. Graft-inoculation of the infection to another grape variety confirmed the lack of the leafroll disease symptoms, even though GLRaV-7 could be detected in the inoculated indicator plants. A 16,496 nucleotide-long genomic sequence of this virus was determined from the deep sequencing data. Its genome architecture and the sequences encoding its nine predicted proteins were compared with those of other closteroviruses. The comparison revealed that two other viruses, Little cherry virus-1 and Cordyline virus-1 formed a well supported phylogenetic cluster with GLRaV-7.

Genomic analysis of grapevine leafroll associated virus-5 and related viruses

The grapevine leafroll-associated viruses (GLRaVs) (Closteroviridae) represent an emerging threat to world grape production. One group of GLRaVs within the genus Ampelovirus, the GLRaV-4-like viruses (GLRaV-4LVs), contains a fragmented collection of seven viruses only two of which (GLRaV-Pr and GLRaCV) are fully sequenced. Here in reporting the sequence of GLRaV-5, a member of GLRaV-4LVs, we identify genomic elements common to the GLRaV-4LV group. Exclusive properties include a highly conserved p5 gene product and phylogenies for complete genes that, except for the p23 gene, are reliably monophyletic. In comparison with other members of the genus Ampelovirus, GLRaV-4LVs form a tight cluster for all genes analyzed. In addition, they all possess a conserved AlkB domain which is most similar to the more distantly related GLRaV-3, suggesting recombination. In silico RNA structural analyses revealed a conserved five stem-loop structure at the 3' untranslated region that extends to all GLRaV-4LVs, and the ampeloviruses Pineapple mealybug wilt-associated virus 1 and Pineapple mealybug wilt-associated virus 3. A conserved G-U rich stem loop was also found upstream of the ORF1a stop and 1b start codons. Taken together, this work allows for a more thorough contextualization of GLRaV-5 and the GLRaV-4LVs as a group within the genus Ampelovirus.

Further complexity of the genus Crinivirus revealed by the complete genome sequence of Lettuce chlorosis virus (LCV) and the similar temporal accumulation of LCV genomic RNAs 1 and 2

The sequence of Lettuce chlorosis virus (LCV) (genus Crinivirus) was determined and found to contain unique open reading frames (ORFs) and ORFs similar to those of other criniviruses, as well as 3' non-coding regions that shared a high degree of identity. Northern blot analysis of RNA extracted from LCV-infected plants identified subgenomic RNAs corresponding to six prominent internal ORFs and detected several novel LCV-single stranded RNA species. Virus replication in tobacco protoplasts was investigated and results indicated that LCV replication proceeded with novel crinivirus RNA accumulation kinetics, wherein viral genomic RNAs exhibited a temporally similar expression pattern early in the infection. This was noticeably distinct from the asynchronous RNA accumulation pattern previously observed for Lettuce infectious yellows virus (LIYV), the type member of the genus, suggesting that replication of the two viruses likely operate via dissimilar mechanisms.

Molecular characterization of a closterovirus from carrot and its identification as a German isolate of Carrot yellow leaf virus

A high-molecular-weight dsRNA (approximately 15 kbp) was isolated from chlorotic leaves of a carrot plant and used for determining the entire nucleotide sequence of a closterovirus. The complete genome of this carrot closterovirus (CCV) was 16.4 kb in length and contained ten open reading frames (ORFs). The genome organization of CCV resembled that of beet yellow stunt virus, but ORF2 and ORF3 were in a reversed order. Based on Hsp70h sequences, CCV is most closely related to carnation necrotic fleck virus and mint virus 1, two viruses of the genus Closterovirus (family Closteroviridae). The major coat protein gene of CCV was expressed in Escherichia coli for raising an antiserum. This permitted routine detection of CYLV by DAS-ELISA and immunoelectron microscopy and was used for demonstrating the bipolar nature of the CCV virion. Moreover, the antiserum gave a Western blot reaction with a reference sample of a Carrot yellow leaf virus (CYLV) isolate from the Netherlands, suggesting that CCV is a German isolate of CYLV.

Tandem leader proteases of Grapevine leafroll-associated virus-2: host-specific functions in the infection cycle

Several viruses in the genus Closterovirus including Grapevine leafroll-associated virus-2 (GLRaV-2), encode a tandem of papain-like leader proteases (L1 and L2) whose functional profiles remained largely uncharacterized. We generated a series of the full-length, reporter-tagged, clones of GLRaV-2 and demonstrated that they are systemically infectious upon agroinfection of an experimental host plant Nicotiana benthamiana. These clones and corresponding minireplicon derivatives were used to address L1 and L2 functions in GLRaV-2 infection cycle. It was found that the deletion of genome region encoding the entire L1-L2 tandem resulted in a ~100-fold reduction in minireplicon RNA accumulation. Five-fold reduction in RNA level was observed upon deletion of L1 coding region. In contrast, deletion of L2 coding region did not affect RNA accumulation. It was also found that the autocatalytic cleavage by L2 but not by L1 is essential for genome replication. Analysis of the corresponding mutants in the context of N. benthamiana infection launched by the full-length GLRaV-2 clone revealed that L1 or its coding region is essential for virus ability to establish infection, while L2 plays an accessory role in the viral systemic transport. Strikingly, when tagged minireplicon variants were used for the leaf agroinfiltration of the GLRaV-2 natural host, Vitis vinifera, deletion of either L1 or L2 resulted in a dramatic reduction of minireplicon ability to establish infection attesting to a host-specific requirement for tandem proteases in the virus infection cycle.

Production of antibodies to Little cherry virus 1 coat protein by DNA prime and protein boost immunization

Little cherry, an economically important disease of cherry is caused by at least two different viruses. One of these is Little cherry virus 1 (LChV-1) for the detection of which no efficient serological tools are available, so that diagnosis is based on molecular methods. In this study, different immunization strategies for producing antibodies against the viral coat protein of LChV-1 were tried, using either purified virus preparations, or bacterially expressed protein, or a DNA vector that expressed the cloned coat protein (CP) gene in vivo. Effective induction of specific antibodies to LChV-1 CP was obtained using DNA intramuscular immunization followed by a single boost with the recombinant protein. The entire coat protein sequence was cloned in a mammalian expression vector and, after being coated by an amphiphilic non-toxic reagent was delivered into rabbit. A protein boost increased the specific immune response against the virus protein. The sensitivity of this antiserum is lower if compared with that of antisera raised conventionally against other viruses, thus it requires improvements for use for diagnostic purposes.

Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae

Raspberry mosaic is one of the most important viral diseases of raspberry. Four virus and virus-like agents, two of which are poorly characterized, have been implicated in the disease complex based on symptom development in Rubus indicators. Three novel viruses were identified in a red raspberry plant that caused typical raspberry mosaic symptoms when grafted onto indicators. This communication focuses on one of these viruses, Raspberry mottle virus (RMoV), a new member of the family Closteroviridae. The complete nucleotide sequence of RMoV has been determined and exceeds 17 kilobases encoding 10 genes. The genome organization of RMoV is similar to that of Beet yellows virus, the type member of the Closterovirus genus, and phylogenetic analysis using the polymerase conserved motifs and the heat shock protein 70 homolog revealed a close relationship of RMoV with Strawberry chlorotic fleck associated virus and Citrus tristeza virus, which suggests the possibility of an aphid vector. The virus was detected in symptomatic raspberry plants in production areas in mixed infections with several other viruses, indicating that RMoV may impact raspberry production.