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A new virus with sequence similarities to members of the genus Cavemovirus in the family Caulimoviridae was identified in an Epiphyllum hybrid. The complete genome of the virus, tentatively named "epiphyllum virus 4" (EpV-4), was determined to be 7,296 nucleotides long. Its circular genome organization is typical of cavemoviruses, containing four open reading frames. This virus and the two known cavemoviruses share 67-69% and 72-75% overall nucleotide sequence identity in the replicase gene. Phylogenetic analysis placed EpV-4 in a same cluster with the two recognized cavemoviruses. Thus, EpV-4 should be considered a representative of a third species of the genus Cavemovirus. The virus was transmitted by grafting.

One large contig with high sequence similarity to Asian prunus virus 2 was identified by high-throughput sequencing from a camellia (Camellia japonica) tree with ringspot symptoms. The complete genome of this new virus was determined to be 8829 nucleotides long, excluding the 3' poly(A) tail. Its genome organization resembles that of known foveaviruses but contains an additional open reading frame in the 3'-terminal region. Phylogenetic analysis also places this virus with members of the genus Foveavirus in the family Betaflexiviridae in the same subgroup. The virus, which is provisionally named "camellia ringspot-associated virus 4″, shares 50-56% nucleotide sequence identity with other foveaviruses and should represent a new species in the genus.

Contigs with the highest sequence similarity (73%) to Apricot pseudo-chlorotic leaf spot virus (genus Trichovirus, family Betaflexiviridae) were identified by high-throughput sequencing from a symptomless sweet cherry accession. The complete genome sequence of this new virus is 7460 nucleotides, excluding the 3' poly(A) tail. Its genome organization is very similar to several trichoviruses infecting fruit trees, with three open reading frames encoding putative replicase, movement protein and coat protein (CP). The virus shares amino acid sequence identities of 60-73% at replicase and 53-76% at CP with other trichoviruses. Phylogenetic analyses group it and other trichoviruses in a cluster. These results support that this virus, which is tentatively named cherry latent virus 1, should be considered a new member in the genus Trichovirus.

A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

Cucumber green mottle mosaic virus (CGMMV), an emerging tobamovirus, has caused serious disease outbreaks to cucurbit crops in several countries, including the United States. Although CGMMV is seed-borne, the mechanism of its transmission from a contaminated seed to germinating seedling is still not fully understood, and the most suitable seed health assay method has not been well established. To evaluate the mechanism of seed transmissibility, using highly contaminated watermelon seeds collected from CGMMV-infected experimental plants, bioassays were conducted in a greenhouse through seedling grow-out and by mechanical inoculation. Through natural seedling grow-out, we did not observe seed transmission of CGMMV to germinating seedlings. However, efficient transmission of CGMMV was observed using bioassays on melon plants through mechanical inoculation of seed extract prepared from CGMMV-contaminated seeds. Understanding the seed-borne property and the ease of mechanical transmission of CGMMV from a contaminated seed to seedling is an important finding. In comparative evaluation of various laboratory techniques for seed health assays, we found that enzyme-linked immunosorbent assay and loop-mediated isothermal amplification were the most sensitive and reliable methods to detect CGMMV on cucurbit seeds. Because CGMMV is a seed-borne and highly contagious virus, a new infection might not result in a natural seedling grow-out; it could occur through mechanical transmission from contaminated seeds. Therefore, a sensitive seed health test is necessary to ensure CGMMV-free seed lots are used for planting.

A novel positive-stranded RNA virus provisionally named "citrus virus C" (CVC) was discovered in citrus trees displaying mottling symptoms. Its genome comprises 7,215 nucleotides (nt), excluding the 3' poly(A) tail, and contains two open reading frames (ORFs) that encode a replication-associated polyprotein (RP) and a putative coat protein (CP). The CVC genome contains a 16-nt 'marafibox', which is highly conserved in most viruses belonging to the genus Marafivirus of the same family. Sequence analysis suggested that the virus is most closely related to grapevine Red Globe virus (GRGV), which is yet to be officially classified in the family Tymoviridae. The sequence identities between CVC and GRGV in the whole genome (50.7%, nt) and CP (49.4% for amino acid, and 53.9% for nt) are lower than the thresholds (80% in the genome and 90% in the CP) for species demarcation in the family. Therefore, it is legitimate to propose that CVC is a member of new species in the family Tymoviridae.

In 2009, a new viral disease of citrus caused by citrus yellow vein clearing virus (CYVCV) was first discovered in China. CYVCV is considered to be the most serious pathogen affecting lemon production. In this study, a sensitive and reliable reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay was developed to detect and quantify CYVCV without references. The specificity of the assay was demonstrated by its failure to amplify other relevant citrus viruses. The quantitative linearity, sensitivity and accuracy of RT-ddPCR for detecting CYVCV were compared to those of real-time RT-PCR. The results showed that both methods had a high degree of linearity (R2 = 0.9776) and quantitative correlation. Furthermore, RT-ddPCR was found to be 100 times more sensitive than real-time RT-PCR, and it can therefore be used to detect CYVCV in individual arthropods. In summary, the results demonstrated that the RT-ddPCR assay is a promising approach for quantitative detection of CYVCV with high precision and accuracy.

A multiplex TaqMan real time RT-PCR was developed for detection and differentiation of Sweet potato virus G , Sweet potato latent virus and Sweet potato mild mottle virus in one tube. Amplification and detection of a fluorogenic cytochrome oxidase gene was included as an internal control. The assay was compared with a multiplex RT-PCR developed in the initial study for the detection and differentiation of the three viruses and host 18S rRNA. Primers and/or probes of the two assays were designed from conserved regions of each virus. The two assays were optimized for primers/probes and primer concentrations and thermal cycling conditions. Sensitivity and specificity of the assays were compared each other and with other assay. Both assays were evaluated by 74 field samples original from five different provinces of China. Results showed that the TaqMan real time RT-PCR offered rapid, sensitive, effective and reliable for the simultaneous detection and differentiation of the three viruses in sweet potato plants. The assay will be useful to quarantine and certification programs and virus surveys when large numbers of samples are tested.

A large contig with sequence similarities to several nucleorhabdoviruses was identified by high-throughput sequencing analysis from a black currant (Ribes nigrum L.) cultivar. The complete genome sequence of this new nucleorhabdovirus is 14,432 nucleotides long. Its genomic organization is very similar to those of unsegmented plant rhabdoviruses, containing six open reading frames in the order 3'-N-P-P3-M-G-L-5. The virus, which is provisionally named "black currant-associated rhabdovirus", is 41-52% identical in its genome nucleotide sequence to other nucleorhabdoviruses and may represent a new species in the genus Nucleorhabdovirus.

The complete genomic sequence of a novel potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9,660 nucleotides (nt) excluding the 3'-terminal poly (A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3030 amino acids. The virus shares 53.9-70.1% nt sequence identity and 43.9-73.2% amino acid sequence identity with other viruses classified within the genus Potyvirus. Proteolytic cleavage sites and conserved motifs of the potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus is most closely related to members of the BCMV subgroup. The results suggest that the virus should be classified as a novel species within the genus Potyvirus, which we tentatively name "Paris mosaic necrosis virus".

A new single-stranded positive-sense RNA virus, which shares the highest nucleotide (nt) sequence identity of 53.4% with the genome sequence of cherry-associated luteovirus South Korean isolate (ChALV-SK, genus Luteovirus), was discovered in this work. It is provisionally named apple-associated luteovirus (AaLV). The complete genome sequence of AaLV comprises 5,890 nt and contains eight open reading frames (ORFs), in a very similar arrangement that is typical of members of the genus Luteovirus. When compared with other members of the family Luteoviridae, ORF1 of AaLV was found to encompass another ORF, ORF1a, which encodes a putative 32.9-kDa protein. The ORF1-ORF2 region (RNA-dependent RNA polymerase, RdRP) showed the greatest amino acid (aa) sequence identity (59.7%) to that of cherry-associated luteovirus Czech Republic isolate (ChALV-CZ, genus Luteovirus). The results of genome sequence comparisons and phylogenetic analysis, suggest that AaLV should be a member of a novel species in the genus Luteovirus. To our knowledge, it is the sixth member of the genus Luteovirus reported to naturally infect rosaceous plants.

A new badnavirus was identified in an ornamental camellia tree with yellow mottle symptom. The complete circular double-stranded DNA genome of this virus was found to consist of 8,203 bp. Its genome organization is typical of badnaviruses, containing three open reading frames (ORFs). ORFs 1 and 2 encode putative proteins with unknown functions. ORF3 encodes a large polyprotein that contains almost all of the conserved domains of badnaviruses. The virus shares 55-62% nucleotide sequence identities with other badnaviruses in the RT+RNase H region. Phylogenetic analyses placed it in group I of the genus Badnavirus. Therefore, this virus, which is tentatively named "camellia Lemon Glow virus", should represent a new species of the genus Badnavirus. This virus was found to be present in approximately a quarter of camellia trees tested.

A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named “green Sichuan pepper vein clearing-associated virus” (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.

Foliar chlorotic and necrotic ringspots of different sizes were observed in many ornamental camellia (Camellia spp.) species and cultivars with or without variegation symptoms. In this study, flexuous, filamentous virions of approximately 680–780 nm long were observed by electron microscopy in sap of camellia trees with chlorotic ringspots. Five large viral contigs were identified by high-throughput sequencing technology, and complete genome sequences of them were determined. Sequence analyses show that these five isolates represent three novel viruses, two in the genus Prunevirus, one in the genus Capillovirus. The genome organization of the two camellia pruneviruses resembles that of pruneviruses but does not contain the nucleic acid-binding protein (NABP) at the 3′-terminal region. They share 66.5–66.8% with each other and 51.9–58.6% with the known pruneviruses at the genome sequence level. The genome of the camellia capillovirus contains an additional NABP at the 3′-terminus when compared to those of Capillovirus. The genomes of the two capillovirus variants are 72.7% identical to each other and 42.1–48.4% to the known capilloviruses. Phylogenetic analyses support these viruses are new members of either Prunevirus or Capillovirus. The two pruneviruses are tentatively named as camellia ringspot associated virus 1 (CRSaV-1) and CRSaV-2, and the capillovirus is named as CRSaV-3. Infections of these viruses were common in camellia species, cultivars and hybrids. The viruses were also detected in seedlings from seeds collected from two camellia trees, indicating that they are seed transmissible.

A novel positive-strand RNA virus infecting citrus with the tentative name "citrus leaf blotch virus 2" (CLBV-2), was identified in the present work. The complete genome sequence of CLBV-2 comprises 8,697 nucleotides (nt) excluding a poly(A) tail and three open reading frames (ORFs), showing the highest nucleotide sequence identity with the Actinidia strain (JN983456) of citrus leaf blotch virus (CLBV). The putative movement protein (ORF2), coat protein (ORF3), and 3' untranslated region (UTR) shared high sequence similarity with those of the extant CLBV isolates. In contrast, only low sequence similarity was observed in the 5' UTR and putative replicase polyprotein (ORF1) regions. The distant phylogenetic relationship between CLBV-2 and CLBV was deduced based on whole-genome nucleotide and whole-ORF1 amino acid sequence comparisons. Sequence comparisons suggest that CLBV-2 acquired an ORF2-ORF3-3' UTR region homologous to CLBV by recombination with of an unknown citrivirus. In view of the fact that this genomic recombination event appears to have occurred between members of different species in the genus Citrivirus, we propose that CLBV-2 should be considered a member of a distinct species.

A generic RT-PCR assay was developed for the universal detection of viruses of the genus Tobamovirus using a novel pair of degenerate primers designed based on conserved regions on replicase genes of 32 tobamoviruses. The assay detected nine tobamoviruses, including six Solanaceae-infecting subgroup tobamoviruses of Tobacco mosaic virus (TMV), Tomato mosaic virus (ToMV), Tomato mottle mosaic virus (ToMMV), Tobacco mottle green mosaic virus (TMGMV), Pepper mild mottle virus (PMMoV), Paprika mild mottle virus (PaMMV), one Orchidaceae-infecting tobamovirus of Odontoglossum ringspot virus (ORSV) and two Cucurbitaceae-infecting subgroup tobamoviruses of Cucumber green mottle mosaic virus (CGMMV) and Zucchini green mottle mosaic virus (ZGMMV), with high amplification efficiency, specificity and sensitivity. The assay was applied to detect tobamoviruses in pepper and tomato fields. Five tobamoviruses, PMMoV, TMV, ToMV, ToMMV and TMGMV, were detected from the pepper fields in single and mixed infections. Single infections of PMMoV, ToMV and ToMMV and mix-infection of ToMV + PMMoV were detected from the tomato fields. Among these viruses, PMMoV was first detected from tomato worldwide, while ToMMV was first detected from tomato plants in China. This generic assay is simple, cost-effective and has great potential to detect more tobamoviruses in the field.

The complete genome sequence of a novel member of the genus Macluravirus was determined from yam plants with chlorotic and necrotic symptoms in China. The genomic RNA consists of 8,261 nucleotides (nt) excluding the 3’-terminal poly(A) tail, containing one long open reading frame (ORF) encoding a large putative polyprotein of 2,627 amino acids. Its genomic structure is typical of macluraviruses, which lack the P1 protein, N-terminal HC-Pro, and D-A-G motif for aphid transmission that are found in potyviruses. The virus shares 56.3-63.8% sequence identity at the genome sequence level and 49.7-63.9% at the polyprotein sequence level with other members of the genus Macluravirus. Phylogenetic analysis based on the complete polyprotein sequence of representative members of the family Potyviridae clearly places the virus within the genus Macluravirus. These results suggest that the virus, tentatively named “yam chlorotic necrosis virus” (YCNV), should be considered a member of a novel species in the genus Macluravirus.

Background ‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. Methods Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5′/3’ RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus. Results Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards. Conclusions A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role. Electronic supplementary material The online version of this article (10.1186/s12985-018-0998-3) contains supplementary material, which is available to authorized users.

Tobacco bushy top disease is a complex disease caused by mixed infection of Tobacco bushy top virus (TBTV), Tobacco vein distorting virus (TVDV), satellite RNA of TBTV (Sat-TBTV) and Tobacco vein distorting virus associate RNA (TVDVaRNA). A one-tube multiplex reverse transcription-PCR (RT-PCR) assay was developed for simultaneous detection of the four causal agents of the disease. Four pairs of specific primers based on the conserved regions of each of the four disease agents were used in the one-tube RT-PCR. The RT-PCR products consisted of fragments of 1049 base pairs (bp) for TBTV, 792bp for TVDVaRNA, 598bp for Sat-TBTV and 357bp for TVDV, and their origins were confirmed by sequencing. Primer concentrations and cycling condition were optimized for the multiplex RT-PCR. The detection limit of the assay was up to 10(-4) dilution. The assay was evaluated using tobacco plants infected naturally with one to four target viruses, transmission vector of aphids and field samples collected from Yunnan, Hunan, and Guizhou province, China. The results show that the multiplex RT-PCR is reliable and sensitive as a simple, rapid and cost-effective method to detect these pathogens in tobacco and aphid. This assay will be useful for virus surveys when large numbers of samples are tested.

In this study, the real-time PCR assays were combined with high resolution melting (HRM) analysis for the simultaneous detection of Cherry necrotic rusty mottle virus (CNRMV) and Cherry green ring mottle virus (CGRMV) infection in sweet cherry trees. Detection of CNRMV and CGRMV was performed in a real-time PCR using a primer set for both of them or duplex real-time PCR that included one specific primer set for each virus. These two strategies allowed us to confirmed virus infection in all tested samples. In 17 field samples the technique revealed samples positive for CNRMV or CGRMV as well as positive for both viruses. In addition, the HRM analysis made it possible to differentiate clearly between CNRMV and CGRMV. Sequence variations among CNRMV and CGRMV isolates observed from the HRM peaks were confirmed by sequencing. To test the capability to use this method in field, forty one sweet cherry samples were examined by HRM analysis. The HRM data showed that seven samples were positive for CNRMV and three were infected with CGRMV. The results presented in this study indicated that real-time PCR followed by HRM analysis provides sensitive, automated and rapid tool to detect and differentiate between CNRMV and CGRMV isolates.

A simple and sensitive dot blot hybridization assay using a digoxigenin-labeled cRNA polyprobe was developed for the simultaneous detection of six viroids that infect pome and stone fruit trees. The polyprobe was constructed by cloning sequentially partial sequences of each viroid into a single vector, with run-off transcription driven by the T7 promoter. All six viroids were detectable within a dilution range of 5−3 to 5−4 in total nucleic acid extracts from infected trees. Individual trees were co-inoculated to create mixed infections and all four pome fruit viroids and both stone fruit viroids could be detected in pear and peach trees, respectively, using the polyprobe. The results of the assays using the polyprobe were comparable to those using single probes. The methods were validated by testing geographically diverse isolates of viroids, as well as field samples from several collections in the US. The assay offers a rapid, reliable and cost-effective approach to the simultaneous detection of six fruit trees viroids and has the potential for routine use in quarantine, certification, and plant genebank programs where many samples are tested and distributed worldwide.

A celery isolate of Apium virus Y (ApVY-Ce) from diseased plants in a commercial field in California was characterized. The experimental host range of the virus included 13 plant species in the families Apiaceae , Chenopodiaceae and Solanaceae . Almost all infected plant species showed foliar chlorosis and distortion or severe stunting and systemic chlorosis. ApVY-Ce was transmitted to all 10 host species in the Apiaceae by green peach aphids. It reacted with the potyvirus group antibody and Celery mosaic virus (CeMV) antiserum. The complete genomic sequence of ApVY-Ce was determined to be 9917 nucleotides, excluding the 3′ poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3184 amino acid residues. Its genomic organization is typical of potyviruses, and contains conserved motifs found in the genus Potyvirus . Comparisons with available genomic sequences of other potyviruses indicate that ApVY-Ce shares 26.1–52.9% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Extensive phylogenetic analysis based on the 3′-partial sequences confirms that ApVY-Ce is most closely related to CeMV and is a distinct species of the genus Potyvirus .

Sugarcane mosaic disease (SMD) caused by the Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV) and Sugarcane streak mosaic virus (SCSMV) and sugarcane yellow leaf disease (SYLD) caused by the Sugarcane yellow leaf virus (SCYLV) are the two most prevalent and economically important viral diseases of sugarcane. In this study, a one-step quadruplex reverse transcription (RT)-PCR method that employed virus-specific primers was developed for the simultaneous detection and differentiation of SCMV, SrMV, SCSMV and SCYLV. Several sets of primers for each target virus were evaluated for their sensitivity and specificity by simplex and quadruplex RT-PCR. The optimum primer combinations and concentrations, RT temperature and time, and PCR annealing temperature and extension time were determined for the quadruplex RT-PCR. The assay was then validated using sugarcane samples affected with SMD and/or SYLD collected from sugarcane breeding fields and farmers' fields in southern China.

A reliable extraction method is described for the preparation of total nucleic acids from at least ten plant genera for subsequent detection of plant pathogens by PCR-based techniques. The method combined a modified CTAB (cetyltrimethylammonium bromide) extraction protocol with a semi-automatic homogenizer (FastPrep) instrument) for rapid sample processing and low potential of cross contamination. The method was applied to sample preparation for PCR-based detection of 28 different RNA and DNA viruses, six viroids, two phytoplasmas and two bacterial pathogens from a range of infected host plants including sweet potato, small fruits and fruit trees. The procedure is cost-effective and the qualities of the nucleic acid preparations are comparable to those prepared by commonly used commercial kits. The efficiency of the procedure permits processing of numerous samples and the use of a single nucleic acid preparation for testing both RNA and DNA genomes by PCR, making this an appealing method for testing multiple pathogens in certification and quarantine programs.

The host range and complete nucleotide sequences of two Cherry necrotic rusty mottle virus (CNRMV) isolates (FC4 and FC5) infecting flowering cherry accessions imported from Japan are described. Of the plants tested, cherry, peach, apricot and almond became infected, but only sweet cherry cv. 'Canindex', Nanking cherry and apricot cv. 'Tilton' showed a mild foliar mottle. The genomic sequences of CNRMV-FC4 and CNRMV-FC5 are 8,430 and 8,429 nt in length, excluding the 3' poly (A) tail. They contain seven open reading frames encoding for a putative virus replicase, "triple gene block" proteins, a coat protein and two proteins with unknown functions. The two CNRMV-FC isolates share 96% identity in the genomic sequences, and their genome organizations are virtually identical to that of a German CNRMV isolate (CNRMV-GER). However, they differ from CNRMV-GER by 14% in the overall nucleotide sequence and 2% (ORF2) to 30% (ORF5a) in the derived amino acid sequences of individual gene products.

A one-step reverse transcription-polymerase chain reaction (RT-PCR) procedure was developed to detect Cherry green ring mottle virus (CGRMV) and Cherry necrotic rusty mottle virus (CNRMV) in woody indicators and naturally infected Prunus spp. Viral RNA suitable for RT-PCR was obtained by a simple trapping method that did not require either extraction of double-stranded RNA (dsRNA) or total RNA, availability of virus antibodies, or purification of viral particles. Consensus primers, degenerate primers and virus-specific primers, whose designs were based on alignments of available cherry flexivirus sequences, were tested to amplify viral genomic fragments of six CGRMV isolates and one CNRMV isolate. RT-PCR allowed CGRMV detection in total RNA and viral RNA preparations equivalent to 400mug and 4mug of infected leaf tissue, respectively. CGRMV was detected in tender shoots, leaves, bark and root tips, and the strongest bands were obtained using young leaves. Detection was less consistent in summer when the temperature was elevated and plant tissues were old. A direct comparison of the RT-PCR and grafting assays indicated that the RT-PCR assay is sensitive, rapid and reliable. The method will improve the routine diagnosis of cherry flexiviruses in Prunus spp.

A novel strain of Japanese yam mosaic virus (JYMV-CN) was identified in a yam plant with foliar mottle symptoms in China. The complete genomic sequence of JYMV-CN was determined. Its genomic sequence of 9701 nucleotides encodes a polyprotein of 3247 amino acids. Its organization is virtually identical to that of two JYMV isolates from Japan. With the latter, it shares nucleotide sequence identities of only 74.7–74.8 %, indicating it might be a member of a new species. However, sequence analysis of the polyprotein and individual proteins suggested that the Chinese isolate is a divergent JYMV strain in the process of speciation.

Four closely related potyviruses, Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG) and/or Sweet potato virus 2 (SPV2), are involved in sweet potato virus disease complexes worldwide. Identification and detection of these viruses are complicated by high similarity among their genomic sequences, frequent occurrence as mixed infections and low titer in many sweet potato cultivars. A one-tube multiplex reverse transcription-PCR (mRT-PCR) assay was developed for simultaneous detection and differentiation of SPFMV, SPVC, SPVG and SPV2. Four specific forward primers unique to each virus and one reverse primer based on the region conserved in all four viruses were selected and used in the assay. The mRT-PCR assay was optimized for primer concentration and cycling conditions. It was tested using sweet potato plants infected naturally with one to four target viruses and then evaluated using field samples collected from southwestern China. The mRT-PCR assay is reliable and sensitive as a simple, rapid and cost-effective method to detect these pathogens in sweet potato. This assay will be useful to quarantine and certification programs and virus surveys when large numbers of samples are tested.

The complete genomic sequences of two isolates of pokeweed mosaic virus (PkMV) were determined to be 9512 nucleotides long, excluding the poly(A) tail. Their genomic organization is typical of potyviruses and contains conserved motifs found in members of the genus Potyvirus. Pairwise comparisons showed that PkMV and other members of the genus Potyvirus share 51.0-57.5 % sequence identity at the genome sequence level and 39.8-53.0 % at the polyprotein sequence level. Phylogenetic analysis indicated that PkMV is most closely related to several viruses in the PVY group of the genus Potyvirus. The genomic information obtained for PkMV suggests that this virus is a distinct potyvirus.

Complete nucleotide sequences of Sweet potato virus G (SPVG) and Sweet potato virus 2 (SPV2) were determined to be 10,800 and 10,731 nucleotides, respectively, excluding the 3′-poly(A) tail. Their genomic organizations are typical of potyviruses, encoding a polyprotein which is likely cleaved into 10 mature proteins by three viral proteinases. Conserved motifs of orthologous proteins of viruses in the genus Potyvirus are found in corresponding positions of both viruses. Pairwise comparisons of individual protein sequences of the two viruses with those of 78 other potyviruses show that P1 protein and coat protein (CP) of both viruses are significantly large, with the SPVG CP as the largest among the all the known species of the genus Potyvirus. The extended N-terminal region of the P1 protein is conserved in the potyviruses and ipomovirus infecting sweet potato. A novel ORF, PISPO, is identified within the P1 region of SPVG, SPV2, Sweet potato feathery mottle virus (SPFMV), and Sweet potato virus C (SPVC). The C-terminal half of CP is highly conserved among SPFMV, SPVC, SPVG, SPV2, and Sweet potato virus-Zimbabwe. Phylogenetic analysis based on the deduced CP amino acid sequences supports the view that these five viruses are grouped together in a SPFMV lineage. The analysis also reveals that Sweet potato virus Y and Ipomoea vein mosaic virus are grouped with SPV2 as one species, and these two viruses should be consolidated with SPV2.

The presence of Gooseberry vein banding associated virus (GVBaV), a badnavirus in the family Caulimoviridae, is strongly correlated with gooseberry vein banding disease in Ribes spp. In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649-7663 nucleotides. These isolates share identities of 96.4-97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1-3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNA(met)-binding site is also present in the 935-bp intergenic region of GVBaV. The identities of the genomic sequences of GVBaV and other badnaviruses range from 49.1% (Sugarcane bacilliform Mor virus) to 51.7% (Pelargonium vein banding virus, PVBV). Phylogenetic analysis using the amino acid sequence of the ORF 3 putative protein shows that GVBaV groups most closely to Dioscorea bacilliform virus, PVBV, and Taro bacilliform virus. These results confirm that GVBaV is a pararetrovirus of the genus Badnavirus in the family Caulimoviridae.

The complete genomic sequence of a Pakistani isolate of Sugarcane streak mosaic virus (SCSMV-PAK) is determined to be 9782 nucleotides in length, excluding the 3' poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3130 amino acid residues. The deduced polyprotein is likely to be cleaved at nine putative protease sites by three viral proteases to ten mature proteins. Conserved motifs of orthologous proteins of other potyviruses are identified in corresponding positions of SCSMV-PAK. The genomic organization is virtually identical to the genera Ipomovirus, Potyvirus, Rymovirus, and Tritimovirus in the family Potyviridae. Sequence analyses indicate that the SCSMV-PAK genomic sequence is different from those of Sugarcane mosaic virus and Sorghum mosaic virus, two viruses with very similar symptoms and host range to SCSMV-PAK. SCSMV-PAK shares 52.7% identity with Triticum mosaic virus (TriMV) and 26.4-31.5% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Phylogenetic analyses of the polyprotein and deduced mature protein amino acid sequences reveal that SCSMV, together with TriMV, forms a distinct group in the family at the genus level. Therefore, SCSMV should represent a new genus, Susmovirus, in the Potyviridae.

The complete nucleotide sequence of tomato infectious chlorosis virus (TICV) was determined and compared with those of other members of the genus Crinivirus. RNA 1 is 8,271 nucleotides long with three open reading frames and encodes proteins involved in replication. RNA 2 is 7,913 nucleotides long and encodes eight proteins common within the genus Crinivirus that are involved in genome protection, movement and other functions yet to be identified. Similarity between TICV and other criniviruses varies throughout the genome but TICV is related more closely to lettuce infectious yellows virus than to any other crinivirus, thus identifying a third group within the genus.

A one-step reverse transcription-polymerase chain reaction (RT-PCR) is used to detect two cherry flexiviruses, Cherry green ring mottle virus (CGRMV) and Cherry necrotic rusty mottle virus (CNRMV), in Prunus species. This unit presents procedures for collection of plant samples, preparation of total nucleic acids, viral RNA-rich or total RNA extracts from plant tissues, and subsequent amplification of the viral targets by one-step RT-PCR using a pair of consensus primers. The PCR amplicons are visualized by electrophoresis in a 1% agarose gel containing ethidium bromide in TAE buffer and viewed under ultraviolet light. This procedure is rapid, sensitive, reliable, and cost-effective and is generally useful on a wide variety of plant/virus systems. The use of a semi-automatic homogenizer for sample preparation and one-tube RT-PCR for virus detection makes this approach ideal for screening large numbers of samples.

Triticum mosaic virus (TriMV) is the type species of the newly established Poacevirus genus in the family Potyviridae. In this study, we demonstrate that in contrast to the helper component-proteinase (HC-Pro) of Potyvirus species, the P1 proteins of TriMV and Sugarcane streak mosaic poacevirus function in suppression of RNA silencing (SRS). TriMV P1 effectively suppressed silencing induced by single- or double-stranded RNAs (ss/ds RNAs), and disrupted the systemic spread of silencing signals at a step after silencing signal production. Interestingly, contrary to enhanced SRS activity of potyviral HC-Pro by co-expression with P1, the presence of TriMV HC-Pro reduced SRS activity of TriMV P1. Furthermore, TriMV P1 suppressed systemic silencing triggered by dsRNA more efficiently than the HC-Pro of Turnip mosaic potyvirus. Furthermore, TriMV P1 enhanced the pathogenicity of a heterologous virus. Our results established poaceviral P1 as a potent RNA silencing suppressor that probably employs a novel mechanism to suppress RNA silencing-based antiviral defense.