Vector transmission of parsley yellow leaf curl virus by the leafhopper Austroagallia sinuata

Parsley yellow leaf curl virus (PYLCV) is a new member of the family Geminiviridae that has not yet been assigned to an established genus due to limited information about its biological properties. In this study, the ability of Austroagallia leafhoppers, which are commonly found on vegetable farms in Kerman province (Iran), to transmit this virus was studied. After a two-day acquisition access period, Austroagallia sp. successfully transmitted the virus from PYLCV-infected parsley to healthy seedlings. On the basis of male genitalia morphology, the species of leafhopper was identified as A. sinuata. This is the first report of a transmission of plant virus by a member of the genus Austroagallia.

Genome characterization of parsley severe stunt-associated virus in Iran

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.

Isolation and characterization of a novel geminivirus from parsley

Fresh leaf vegetables are a significant part of the Persian food. Following a survey for identification of nanoviruses and geminivirus infecting leaf vegetables, a novel geminivirus was identified in a diseased parsley sample showing upward marginal leaf curling, marginal leaf yellowing, dwarfing and reduced leaf size in south-eastern Iran. The genome was identified through combination of rolling circle amplification (RCA) and high throughput sequencing (HTS) approaches. The full-length genome (2779 nts) of the cloned geminivirus, parsley yellow leaf curl virus (PYLCV), shares <66 % genome-wide pairwise identity with all other known geminiviruses. The PYLCV genome has six open reading frames (ORFs) and appears to be a hybrid with the virion sense encoded proteins being most similar to those of becurtoviruses and curtoviruses, whereas the complementary sense encoded proteins are most similar to those of begomoviruses. In comparison with other geminivirus encoded capsid proteins (CPs) and replication associated proteins (Reps), the CP of PYLCV shares <56 % amino acid pairwise identity whereas the Rep shares <73 % amino acid pairwise identity. To demonstrate the pathogenicity of the geminivirus, a partial dimer infectious clone was constructed and used to agro-infect parsley as well as Nicotiana benthamiana, turnip, radish and tomato. The agro-inoculation resulted in infection with symptoms in 83.7 % (82/98) of the tested plant. Based on the similarity of the CP encoded by PYLCV to those of becurtoviruses and curtoviruses, it is likely that leafhoppers may be the primary transmission vector.

Identification of the wild and cultivated hosts of wheat dwarf virus and oat dwarf virus in Iran

In the last decade two mastreviruses, Wheat dwarf virus (WDV) and Oat dwarf virus (ODV) have been reported from cereal farms in Iran. In a survey, wild and cultivated hosts of these mastreviruses were studied during 2015 to 2017. Symptomatic small grain cereal samples and weed species were collected and assayed for WDV and/or ODV infection by PCR. While WDV which was detected in 139/284 (49%) of total symptomatic samples, low incidence (2%) was recorded for ODV which was detected only in slender wild oat (Avena barbata Pott ex Link) and red brome (Bromus rubens L.). In agroinfection studies, the clone of ODV infected common oat (A. sativa) and slender wild oat (A. barbata) with the low efficiency and did not infect wheat or barley. ODV was transmitted by the leafhopper Psammotettix alienus, from agroinfected common oat to healthy seedlings. The results show that, in contrast to WDV, ODV has a low incidence and a narrow host range in gramineous plants.

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

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

Identification of a Nanovirus-Alphasatellite Complex in Sophora alopecuroides

Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had similarities to nanovirus genome components. From this plant, the nanovirus-like molecules DNA-R (n=4), DNA-C (n=2), DNA-S (n=1), DNA-M (n=1), DNA-N (n=1), DNA-U1 (n=1), DNA-U2 (n=1) and DNA-U4 (n=1) were amplified, cloned and sequenced. Other than for the DNA-R, these components share less than 71% identity with those of other known nanoviruses. The four DNA-R molecules were highly diverse, sharing only 65-71% identity with each other and 64-86% identity with those of other nanoviruses. In the S. alopecuroides plant 14 molecules sharing 57.7-84.6% identity with previously determined sequences of nanovirus-associated alphasatellites were also identified. Given the research activity in the nanovirus field during the last five years coupled with high-throughput sequence technologies, many more diverse nanoviruses and nanovirus-associated satellites are likely to be identified.

Analysis of watermelon chlorotic stunt virus and tomato leaf curl Palampur virus mixed and pseudo-recombination infections

Watermelon chlorotic stunt virus (WmCSV) and tomato leaf curl Palampur virus (ToLCPMV) are limiting factors for cucurbit production in south and southeastern Iran. ToLCPMV infects all cucurbit crops (except watermelons) whereas WmCSV is somewhat limited to watermelon, causing detrimental effects on fruit production. In a survey, we detected WmCSV in all watermelon growing farms in Fars province (southern Iran). Given that WmCSV and ToLCPMV are present in the same geographical location in Iran, we studied the interaction of two viruses. Co-infection using agroinfectious clones of WmCSV and ToLCPMV caused severe symptoms in watermelon and zucchini in comparison to symptoms observed from individual infections. Interestingly, inoculation of zucchini with WmCSV DNA-A and ToLCPMV DNA-B agroinfectious clones or vice versa produced a viable pseudo-recombinant and induced systemic symptoms. This demonstrates that replication-associated protein of DNA-A of each virus is able to bind to cis elements of the DNA-B molecules of another virus.

Molecular characterization and field survey of Iranian potato virus X isolates

Six hundred and one symptomatic potato samples were collected from nine provinces in Iran. Screening by double-antibody sandwich enzyme linked immunosorbent assay using a potato virus X (PVX) together with a few potyviruses polyclonal antibodies, produced positive reactions in 4.3 % of samples against PVX. Based on symptoms on different test plant, the isolates were divided into two groups: the first groups causing blistering and malformation of leaves and the second showed mild mosaic and vein clearing in Nicotiana glutinosa. The almost complete nucleotide sequence of two isolates as a representative of severe and a mild isolates were determined. Genomes of two PVX Iranian isolates are identical to that of the most PVX isolates comprise 6435 nucleotides in length excluding 101 nucleotide in the 5' end of the genome and shares 94.8-96.7 % identities with European and Asian, and 77-96.1 % with American isolates. Furthermore, the 3'-terminal sequences, including the coat protein coding region of other 13 Iranian isolates were determined and compared with the GenBank sequences. Phylogenetic analysis of the cp gene of 13 Iranian isolates together all those available in public databases indicated that the 13 Iranian isolates all belong to low diversity clade I.

Incidence and characterization of Potato virus V infections in Iran

A survey was carried out to determine the extent of Potato virus V (PVV) infection, together with other potyviruses, in Iran in both commercial and local potato varieties. We found a low incidence of PVV in commercial varieties compared to a local potato cultivar Zardi, in which we noted a PVV infection up to ~32.9 %. We determined the genomic sequence 9,812 nucleotides of one isolate (KER.LAL.P) from cultivar Agria and the 3'-terminal sequence including coat protein (CP) gene of four additional isolates from cultivar Zardi. The Iranian isolate PVV KER.LAL.P was found to share 91 % sequence identity with the Scottish isolate DV-42 (AJ243766) of PVV. The CP gene sequences of the PVV isolates from Iran shared 96.5 to 99.3 % pairwise nucleotide identity and they shared <97.5 % pairwise identity with the CP sequences of all other PVV isolates available in public databases. Our host studies indicated that the Iranian PVV isolate had a narrower host range and infected Nicotiana debneyi and N. glutinosa test plants. Within the commercial varieties of potato in Iran, we noted a significant amount of mixed potyvirus infection. This study is the first report of occurrence and complete genome of PVV in Iran.

Genetic diversity and host range studies of turnip curly top virus

Turnip curly top virus (TCTV) is a unique geminivirus that has recently been characterised as infecting turnips in Iran. The genome of TCTV shares <68 % pairwise identity with other geminiviruses and has a genome organisation similar to that of curtoviruses and topocuvirus. The replication-associated protein (Rep) bears the highest similarity to curtovirus Reps (48.5-69.0 %); however, in the case of the capsid protein (CP), the extent of similarity is only 39.5-44.5 %. We constructed an agroinfectious clone of TCTV and undertook host range studies on ten plant species; in three species (turnip, sugar beet and cowpea), we detected infection which presents curly top symptoms in turnip and sugar beet. The efficiency of TCTV infection in agroinoculated turnip plants was 71.7 %, and the infection was successfully transmitted to 80 % of the healthy turnip plants used in the insect transmission studies by Circulifer haematoceps under greenhouse conditions. We also determined the genome sequence of 14 new TCTV isolates from southern Iran isolated from turnips. We observed ~13 % diversity amongst all the TCTV isolates and found evidence of recombination in the CP- and Rep-coding regions of the genomes.

Fulfilling Koch's postulates for beet curly top Iran virus and proposal for consideration of new genus in the family Geminiviridae

Beet curly top Iran virus (BCTIV) is a divergent geminivirus with biological properties similar to those of curtoviruses; however, the virus is distinct from curtoviruses phylogenetically and in its genome organisation. The replication-associated protein is phylogenetically more closely related to those of mastreviruses than to those of curtoviruses whereas the capsid protein shares high amino acid sequence identity (77-83 %) with those of curtoviruses. The 17 BCTIV genomes from Iran share ~77 % pairwise nucleotide sequence identity with spinach curly top Arizona virus (SCTAV) from Arizona, USA, which was characterised recently. To demonstrate the infectivity of the monopartite BCTIV genome and to fulfil Koch's postulates, an infectious clone was constructed using a dimer of the full-length genome of an isolate from this study - BCTIV-[IR:Neg:B33P:Sug:08]. Agroinoculation with the cloned DNA resulted in the efficient infection of 74 % of sugar beet plants, which resulted in curly top symptoms. The curly top infection of agroinoculated plants was successfully transmitted to 80 % of healthy sugar beet plants by the natural BCTIV vector, Circulifer haematoceps. Since BCTIV and SCTAV share <62 % pairwise nucleotide sequence identity with all other geminiviruses and have unique genome architectures and properties, and since this is coupled with phylogenetic support at the full-genome level and that of it proteins, we propose that they should be re-classified as members of a new genus, "Becurtovirus", in the family Geminiviridae.

Turnip curly top virus, a highly divergent geminivirus infecting turnip in Iran

From 2006 onwards turnip crops in Fars province, Iran, have been noted with unusual leaf curling and vein swelling symptoms which are characteristic of the leafhopper-transmitted viruses of the genus Curtovirus (family Geminiviridae). Rolling circle amplification was used to clone viruses from five turnip isolates exhibiting leaf curl symptoms. Analysis of the sequences showed them to have >93% sequence identity and to be distinct from all other geminiviruses previously characterised. Analysis of the sequence of this virus, for which we propose the name Turnip curly top virus (TCTV), showed it to have a genome arrangement in the complementary-sense similar to that of curtoviruses (consisting of four overlapping genes) but only two open reading frames in the virion-sense (the curtoviruses encode three). The complementary-sense genes are homologous to those of curtoviruses but show little sequence identity to their curtovirus homologs, with the exception of the product of the C4 open reading frame (ORF) which shows approximately 70.6% amino acid sequence identity to the C4 of the North American curtoviruses, Pepper curly top virus and Beet mild curly top virus. For curtoviruses the C4 protein is a symptom determinant, which likely explains the similarity of TCTV symptoms to those of curtoviruses. In the virion-sense the predicted product of the V2 ORF of TCTV shows no significant similarity with any proteins in the databases whereas the product of the V1 ORF (encoding the coat protein [CP] of geminiviruses) shows low levels of sequence identity to the CPs of curtoviruses. These findings show TCTV to be a highly divergent geminivirus with similarities to viruses of the genus curtovirus. The significance of these findings, particularly the taxonomic implications are discussed.

Incidence of Viruses Infecting Tomato and Their Natural Hosts in the Southeast and Central Regions of Iran

A survey was conducted to determine the incidence of Cucumber mosaic virus (CMV), Beet curly top virus (BCTV), Tomato yellow leaf curl virus (TYLCV), Tomato chlorotic spot virus (TcSV), Potato virus Y (PVY), Potato virus S (PVS), Tomato spotted wilt virus (TSWV), Tomato ringspot virus (TRSV), Tomato aspermy virus (TAV), Arabis mosaic virus (ArMV), Tobacco streak virus (TSV), Tomato bushy stunt virus (TBSV), Tobacco mosaic virus (TMV), and Tomato mosaic virus (ToMV) on tomato (Solanum lycopersicum) in the major horticultural crop growing areas in the southeast and central regions of Iran. A total of 1,307 symptomatic leaf samples from fields and 603 samples from greenhouses were collected from January 2003 to July 2005 in five southeastern and central provinces of Iran. Samples of symptomatic plants were analyzed for virus infection by enzyme-linked immunosorbent assay (ELISA) using specific polyclonal antibodies. ArMV and CMV were the most frequently found viruses, accounting for 25.6 and 23.4%, respectively, of the collected samples. BCTV, TSWV, TMV, PVY, ToMV, and TYLCV were detected in 6.1, 5.8, 5.6, 5, 4.8, and 1.6% of the samples, respectively. TBSV, TAV, TSV, PVS, and TRSV were not detected in any of the samples tested. Double and triple infections involving different combination of viruses were found in 13.9 and 1.7% of samples, respectively. This is the first report of PVY and ArMV as viruses naturally infecting tomato in Iran. Infection of tomato plants with PVY and ArMV was confirmed. Six out of 20 plant species belonging to six genera, growing in tomato fields or in the nearby areas, were found infected with TSWV, TMV, PVY, and CMV.

Analysis of the biological and molecular variability of Watermelon mosaic virus isolates from Iran

Watermelon mosaic virus (WMV) is one of the most important viruses that causes different symptoms in Cucurbitaceae. WMV is a potyvirus with a worldwide distribution, but occurs most commonly in temperate and Mediterranean regions. Cucurbit species grown in Yazd, Esfahan, West Azerbaijan, Hormozgan, and Kerman provinces were surveyed for the relative incidence of WMV in 2004-2005. A total of 757 symptomatic cucurbit and 31 weed species were collected and assayed for infection with WMV. Of 788 leaf samples from cucurbit and weed plants, 190 samples were positive by double antibody sandwich ELISA (DAS-ELISA) using specific polyclonal antibody. Among the weed species tested only colocynth (Citrullus colocynthis) was found to be infected with WMV. The coat protein (CP) gene from 18 representative isolates was PCR amplified, cloned, sequenced, and compared with the sequences available in GeneBank. Phylogenetic analysis using 778 nucleotide long sequences of the coat protein gene showed that these isolates fell into two; groups I and II. Only one isolates (KER.JI.1) was classified in the group II. This isolate had a wider host range and infected Nicotiana debneyii and Datura metel. None of the other 17 isolates could infect these two species. Members of group I were divided into three subgroups; A, B, and C. The subgroup I(B) appears to be a new subgroup comprising only of the Iranian isolates. Phylogenetic analysis based on 200 nucleotides coding for the N-terminal segment of the CP showed that all Iranian isolates except KER.JI.1 clustered with the previously reported WMV strains. All Iranian isolates had a DAG amino acid triplet which is involved in aphid transmissibility. This is the first report on sequence analysis of the nearly full-length CP cDNA clones of WMV isolates from Iran.

Genome characterization and genetic diversity of beet curly top Iran virus: a geminivirus with a novel nonanucleotide

Beet curly top Iran virus (BCTIV) was previously reported as a distinct curtovirus in Iran. Complete nucleotide sequences of three BCTIV isolates, one each from central, southern, and south eastern Iran were determined to be 2844, 2844, and 2845 nt long, respectively. BCTIV shared highest nucleotide sequence identity (52.3%) with Spinach curly top virus (SpCTV) and lowest identity (46.6%) with Horseradish curly top virus (HrCTV). The BCTIV genome comprises three virion-sense (V1, V2, and V3) and two complementary-sense (C1 and C2) ORFs. ORFs C3 and C4 were not found in BCTIV genome. Based on a comparison of nucleotide sequence identity of individual genes, the three virion-sense ORFs were 72.7-79.9% related to the corresponding ORFs of curtoviruses, whereas no significant relationship was found between the C1 and C2 ORFs of BCTIV and curtoviruses. These two ORFs, however, were only distantly related with those of mastreviruses. Similar to the latter viruses, the BCTIV genome comprises two intergenic regions. The BCTIV large intergenic region included a sequence capable of forming a stem loop structure and a novel nonanucleotide (TAAGATT/CC) with a unique nick site. Phylogenetic analysis using deduced amino acid sequence of individual ORFs revealed that the V2 and V3 ORFs are monophyletic and the V1 ORF is classified with the related ORF of curtoviruses. Whereas the two complementary-sense ORFs are grouped with those of mastreviruses. Computer-based prediction suggested that BCTIV has a chimeric genome which may have arisen by a recombination event involving curto- and mastrevirus ancestors. Percent nucleotide sequence identities of the coat protein gene of ten isolates of BCTIV, collected from a wide range of geographical regions in Iran, varied from 87.1 to 99.9, with the isolates being distributed between two subgroups. Based on biological and molecular properties, BCTIV is proposed as a new member of the genus Curtovirus.

Occurrence, Distribution, and Relative Incidence of Seven Viruses Infecting Greenhouse-Grown Cucurbits in Iran

Greenhouse-grown cucurbit crops in several Iranian regions were surveyed for the incidence of Cucumber mosaic virus (CMV), Squash mosaic virus (SqMV), Papaya ring spot virus-type W (PRSV-W), Watermelon mosaic virus-2 (WMV-2), Zucchini yellow mosaic virus (ZYMV), Cucumber necrosis virus (CuNV) and Tomato spotted wilt virus (TSWV) from September 2002 to June 2004. In all, 1,304 random and 1,085 symptomatic leaf or fruit samples were collected. Samples were analyzed for virus infection by enzyme-linked immunosorbent assay. CMV and ZYMV were the viruses most frequently detected, accounting for 21.2 and 18% of the infected plants, respectively. WMV-2 was detected with 4.3% incidence in 15 regions and TSWV with 1.25% incidence only in 2 regions. CuNV, SqMV, and PRSV-W were not detected in any samples. Double and triple infections involving different combinations of CMV, ZYMV, WMV-2, and TSWV were noted in 117 and 4 samples, respectively. Natural infection of cucumber with TSWV and ZYMV is reported for the first time from Iran. Of 16 plant species from 14 genera, growing in or around greenhouse facilities, 6 were found infected with ZYMV, TSWV, WMV-2, and CMV and may act as reservoirs of the viruses. Four species are reported as new hosts of these viruses.