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Beet curly top Iran virus (BCTIV) (Becurtovirus, Geminiviridae) is a destructive virus in crop growing farms in Iran. In this study, BCTIV infected eggplant and chili and bell pepper plants showing typical geminivirus symptoms were collected in north-eastern Iran and investigated. PCR and sequence of the resulting amplicons showed that the samples are infected with the BCTIV. A bell pepper isolate was chosen and BCTIV full-length genome was amplified using rolling circle amplification (RCA) method. An infectious clone containing a partial dimer of the BCTIV genome was constructed and used for agroinoculation tests. Results indicated that inoculated eggplant and bell pepper seedlings with BCTIV infectious construct are efficiently infected and resulted in 60 and 47% infection. Based on the results of this study, eggplant and chili and bell peppers are the BCTIV hosts in north-eastern Iran and therefore, eggplant is reported as new natural host of BCTIV. This finding confirms broad host range of the virus.

In this research, to identify natural wild hosts of TYLCV, 44 symptomatic samples were collected in or around harvested tomato fields in south-eastern Iran and tested for the TYLCV infectio...

Alfalfa mosaic virus (AMV) is one of the most important viruses that cause significant losses to alfalfa worldwide. A total of 1066 symptomatic alfalfa, 143 weeds and other secondary hosts were collected and assayed for AMV infection. The virus was detected in 360 samples (33.8% incidence) of alfalfa by plate-trapped antigen (PTA)-ELISA. Among the weed species and the other plants tested, potato, pepper and seven weed species were infected with AMV. The coat protein (CP) gene sequences from 59 Iranian isolates were PCR amplified, cloned, sequenced, and compared with the sequences available in GenBank. Sequence analysis of the amplified regions showed that 55 of the Iranian CP sequences share >98% pairwise identity with each other. The remaining four share between 89 and 96% identity. Our host studies indicated that the Iranian AMV isolates were classified into two groups. Only four Iranian isolates were clustered in the symptom-group B and caused relatively milder symptoms compared to those found in symptom-group A.

A handful of geminiviruses have been associated with turnip leaf curl disease. As part of our turnip surveys in Kerman province (south-eastern Iran), turnip samples showing mild leaf curl disease were collected and screened for turncurto- and begomoviruses by PCR. In four out of seven samples, we identified co-infection with begomoviruses of the species Tomato yellow leaf curl virus and Watermelon chlorotic stunt virus. Neither of these two begomovirus species have been described to be associated with turnip leaf curl disease in Iran. Using infectious clones and agroinoculation of turnip, tomato and watermelon seedlings, our results indicated that single and/or co-agroinoculation of plants with the two begomovirus constructs result in symptoms with different severity in turnip, tomato and watermelon.

Phyllody disease is a threat to sesame production in Kerman province, southeastern Iran. RFLP analysis of PCR products of phytoplasma-specific 16S rRNA gene (1.8 kb) and phylogenetic analyses of 16S-23S rDNA spacer region (SR) sequence indicated that the predominant agent associated with sesame phyllody in Kerman province is a phytoplasma with 100% similarity with eggplant big bud, and peanut witches’-broom phytoplasmas, members of “Candidatus Phytoplasma aurantifolia” from Iran and China, respectively. Among the samples tested, only one strain (SPhSr1), had a unique RFLP profile and its SR was 100% similar in nucleotide sequence with the phytoplasma carried by Orosius albicinctus and Helianthus annus witches’-broom phytoplasma from Iran, members of “Ca. Phytoplasma trifolii”. Virtual RFLP patterns of SPhJ2 (representative of the predominant PCR-RFLP profiles) SR sequence were identical to those of peanut witches’-broom phytoplasma (16SrII-A, JX871467). However, SPhSr1 SR sequence patterns resembl...

Three isolates of Tomato aspermy virus (TAV) were identified from two ornamental plants, Petunia hybrida and Chrysanthemum morifolium, sampled in Kerman province in the southeastern region of Iran. The complete genome of one isolate (Ker.Mah.P) and three open reading frames (ORFs), encoding coat protein (CP), movement protein (MP) and 2b protein of the three isolates were sequenced. The three genome segments of the Ker.Mah.P isolate (RNA-1, −2 and −3) are comprised of 3351, 3035 and 2194 nts, respectively. The nucleotide sequences of the three Iranian isolates were compared with other available sequences in GenBank, and the genome of Ker.Mah.P showed >96% sequence identity with sequences of TAV isolates. In a host range study, the three Iranian isolates induced chlorotic and necrotic symptoms on the true leaves of Cucumis sativus cv. Maximum F4 and systemic mottle and necrotic local lesions on Chenopodium amaranticolor, whereas other isolates whose sequences are deposited in GenBank cause only necrotic local lesions on these test plants. Sequences of the 2b gene of the three Iranian and one Chinese isolate have an additional 27 nt insert and it is possible that this domain, which adds nine amino acids to the 2b protein, may affect the biological properties of the virus. To the best of our knowledge, this is the first report of a TAV isolate from the Middle East whose genome has been sequenced, as well as the first global report of the natural occurrence of TAV in P. hybrida.

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.

Massumi, H., Shaabanian, M., Hosseini Pour, A., Heydarnejad, J., and Rahimian, H. 2009. Incidence of viruses infecting tomato and their natural hosts in the southeast and central regions of Iran. Plant Dis. 93:67-72. 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.

Yellow dwarf disease is a major problem in most parsley growing farms in Iran. In December 2018, parsley in fields (Petroselinum crispum) in the Kerman province of Iran showed dwarfing and general yellowing symptoms (Fig. 1). Twelve…

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.

Turncurtoviruses (family: Geminiviridae; genus: Turncurtovirus) appear to have a high degree of genetic variation in Iran. Leafhoppers of the species Circulifer haematoceps (Mulsant and Rey, 1855) (family: Cicadellidae) were collected in 2014 from three geographical regions in south-eastern Iran (Orzoeyeh, Jiroft and Sirjan; Kerman province) and screened for the presence of turncurtoviruses using a combination of PCR and rolling circle amplification (RCA) methods. Eleven genomes of turncurtovirus were recovered and sequenced. Leafhoppers were sampled off sesame (S. indicum L.) and turnip (Brassica rapa sub sp. rapa). Thus, we identified three symptomatic sesame plants (yellowing, boat-shaped leaf curling, vein swelling on the lower leaf surfaces) from sesame farms in Jiroft. In these samples, we identified the same turncurtovirus as in the leafhoppers and have named it sesame curly top virus (SeCTV). Collectively, these SeCTV share > 98% genome-wide pairwise identity and ~ 87.3% to a recently identified turncurtovirus (sesame yellow mosaic virus; SeYMV) from sesame in Pakistan (GenBank accession MF344550). The SeCTV and SeYMV sequences share

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.

Alfalfa cultivars grown in 14 provinces in Iran were surveyed for the relative incidence of peanut stunt virus (PSV) during 2013-2016. PSV were detected in 41.89% of symptomatic alfalfa samples and a few alternate hosts by plate-trapped antigen ELISA. Among other hosts tested only Chenopodium album, Robinia pseudoacacia and Arachis hypogaea were found naturally infected with PSV. Twenty five isolates of PSV were chosen for biological and molecular characterizations based on their geographical distributions. There was not any differences in experimental host range of these isolates; however, variation in systemic symptoms observed on Nicotiana glutinosa. Total RNA from 25 of viral isolates were subjected to reverse transcription polymerase chain reaction analysis using primers directed against coat protein (CP) gene. The CP genes of 25 Iranian PSV isolates were either 651 or 666 nucleotides long. The nucleotide and amino acid identities for CP gene among Iranian PSV isolates were 79.3-99.7 and 72-100%, respectively. They also shared between 67.4 and 82.4% pairwise nucleotide identity with other PSV isolates reported elsewhere in the world. Phylogenetic analyses of CP gene sequences showed formation of a new subgroup comprising only the Iranian isolates. Natural infection of a few alternate hosts with PSV is reported for the first time from Iran.

Implementation of a vector-enabled metagenomics approach resulted in the identification of various geminiviruses. We identified the genome sequences of Beet curly top Iran virus , Turnip curly top viruses , Oat dwarf viruses , the first from Iran, and Wheat dwarf virus from leafhoppers feeding on beet, parsley, pumpkin, and turnip plants.

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.

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

Beet curly top Iran virus (BCTIV) is a distinct geminivirus which has been reported from sugar-beet-growing farms in Iran. In this study, the role of the splicing in expression of complementary-sense genes of BCTIV was studied. Total RNA was extracted from BCTIV-infected tissue, and the predicted intron position of complementary-sense mRNA transcripts was amplified by RT-PCR followed by cloning of the amplicons. Sequence confirmed that both spliced and unspliced mRNAs are synthesized by the same transcription unit. Sequence comparison showed that a 155-nt segment (intron) corresponding to nucleotides 1890-2044 of the viral genome has been removed from the latter transcript and therefore fusion of the C1:C2 genes resulted creation of a continuous reading frame for potential production of intact replication initiator protein (Rep). BCTIV intron comprises of most consensus splicing signals required for splicing in eukaryotes and several plant viruses including mastre- and capulaviruses.

Among the reported begomoviruses which cause tomato leaf curl disease (TLCD) in Iran, Tomato leaf curl Palampur virus (ToLCPMV) was the first bipartite begomovirus to be detected in tomato in 2006 in Hormozgan Province (southern Iran). Following this, the ToLCPMV incidence has progressively increased amongst several cultivated plants and to new geographical regions within Iran. We detected ToLCPMV by PCR in six crop species—tomato, cucumber, three different local cultivars of melon, squash, watermelon and bean in commercial greenhouses, plastic tunnels and/or open farms. Squash, watermelon, bean and two weed species, Chenopodium sp. and Heliotropium europaeum, represent new natural hosts of ToLPMV globally. The ToLCPMV epidemic has been particularly devastating on cucumber, melon, and squash crops. Infections rates of between 50 and 100 % were identified amongst greenhouse grown cucumbers and melons farms. However, the rate of infection in watermelon and bean were negligible. Full-length genome characterization of ten ToLCPMV isolates from cucumber, melon, squash, watermelon and bean showed a minimum 95 % sequence identity with previously characterized ToLCPMV isolates (DNA-A). The movement of ToLCPMV from south-eastern Iran to south, northeast and central regions with warm climatic conditions threatens the cultivation of cucurbits and tomato in these regions, which are the major production areas for these crops.

Two hundred forty potato samples with one or more symptoms of leaf mosaic, distortion, mottling and yellowing were collected between 2005 and 2008 from seven Iranian provinces. Forty-four of these samples tested positive with double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) using a Potato virus S (PVS) polyclonal antibody. Of these 12 isolates of PVS were selected based on the geographical location for biological and molecular characterization. The full coat protein (CP) and 11K genes from 12 PVS isolates were PCR amplified, cloned and sequenced. All 12 PVS isolates showed mosaic symptoms on Nicotiana debneyii and N. tabacum cv. Whiteburly and local lesion on Chenopodium amaranticolor, C. quinoa and C. album. The Iranian isolates share between 93 and 100% pairwise nucleotide identity with other PVS(O) isolates. Based on maximum likelihood phylogenetic analysis coupled with pairwise identity analysis, we propose 15 genotypes for the PVS(O) strain and 3 genotypes for the PVS(A) strain.

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.

Kerman Province is a major agricultural centre in south-eastern Iran and an increase in agricultural activities results in an increase in disease. We report phytoplasmal infections in Iran of five plant species; spinach (Spinacia oleracea L.), sunflower (Helianthus annuus L.), canola (Brassica napus L.), cucumber (Cucumis sativus L.) and Aegean wallflower (Erysimum cheiri (L.) Crantz; Family Brassicaceae) using in silico restriction fragment length polymorphism and sequence analysis. Amplicons of approximately 300 bp were amplified using polymerase chain reaction amplification with universal P3 ⁄ P7 primer pair. The amplified products were cloned and sequenced. On the basis of in silico restriction analysis of the amplicon digested with 17 distinct restriction enzymes and 16 ⁄ 23S spacer region sequence, Erysimum and cucumber phyllodies (EPh and CuPh2, respectively) were 100% identical and showed closest similarity with members of the peanut witches-broom group (16SrII). Whereas spinach yellows (SpY) and canola phyllody (CaPh) revealed closest homology with phytoplasmas of the aster yellows group (AY) 16SrI. Mixed infections of the SuWB sample were confirmed in which two different phytoplasmas belonging to 16SrII and 16SrVI groups were found. This is the first report of phytoplasmal infection of Aegean wallflower (EPh) caused by a phytoplasma belonging to the 16SrII group. While spinach phytoplasmas have been isolated in the past; however, our isolate from spinach belonging to the 16SrI group is the first spinach isolate from Iran.

Potato leafroll virus (PLRV) is one of the most prevalent potato viruses in Iran. This report describes the distribution of PLRV in four Provinces from south-eastern, southern, north-eastern and north-western Iran and phylogenic relationships of Iranian PLRV to other previously reported PLRV isolates. PLRV was detected in c.15% (126 of 836) of symptomatic potato samples (showing yellowing and leaf roll) by double antibody sandwich enzyme-linked immunosorbent assay. The coat protein (CP) gene of four isolates was amplified by reverse transcription-polymerase chain reaction using specific primers. The nucleotide sequence showed a high degree of sequence identities between all PLRV isolates. Three of the four Iranian isolates were 100°% identical at the amino acid level (for the domain sequenced), but the fourth isolate differed by an amino acid. For isolate PLRV-Ke, we amplified the open reading frame (ORFO) (which overlaps the 5' end of the ORF1) and the sequence analysis indicated that the amino acid sequences of the ORFO and the 5' end of the ORF1 showed identity of 92.7-100% and 90.2-99% with that of the GenBank PLRV isolates, respectively. In contrast to the amino acid sequence of the CP, a constructed phylogenetic tree using the amino acid sequence of the ORFO differentiated the Iranian isolate (PLRV-Ke) from some European and African isolates.

The incidence of curly top disease on cultivated plants and weeds was investigated in Kerman Province (southeastern Iran) from October 2003 to November 2004. A total of 1186 samples were collected in fields of sugar beet and other crops as well as within commercial plastic houses. Curtovirus infection of four field crops, three vegetables and 11 weeds was verified by indirect enzyme-linked immunosorbent assay (ELISA) using a polyclonal antibody. An undescribed curtovirus, tentatively designated Iranian beet curly top virus (IBCTV), was isolated from three symptomatic beet samples collected randomly in widely separated regions of south-eastern, southern and central Iran and used for molecular studies. A 672 bp segment of the coat protein (CP) gene of each isolate was amplified by PCR and sequenced. The results showed that the three isolates shared 98.5-98.7% nucleotide homology with each other but only 72.1-76.5% with other members of the genus Curtovirus. IBCTV was also detected by PCR using specific primers in other samples of sugar beet, tomato, spinach, turnip and several weed species collected in different parts of Iran. These results indicated that IBCTV is the dominant curtovirus in Iran.

Turnip curly top virus (TCTV) is the only member of the newly established genus Turncurtovirus (family Geminiviridae). As part of an ongoing study to identify additional plant hosts and the diversity of turncurtoviruses, between 2012 and 2014, we sampled symptomatic turnip plants and other crops in the provinces Fars and Khorasan Razavi (southern and northeastern Iran, respectively). Infection by turncurtoviruses was tested by PCR and/or rolling-circle amplification (RCA) coupled with restriction enzyme digests. Turncurtoviruses were identified in turnip as well as seven other field crops, including eggplant, basil, radish, lettuce, sugar beet, red beet and spinach. Full turncurtovirus genomes were recovered from 25 of these samples, leading to the identification of TCTV and a new putative turncurtovirus, turnip leaf roll virus (TLRV; 13 isolates), which shares

Almond witches' broom (AlmWB) is a destructive dis ease in several provinces in Iran. Association of phytoplasma with the disease has been establishec previously. In the present work two phytoplasmas from Khafr (KAlmWB) and Neyriz (NAlmWB) in the Fars Province were compared by biological and molecular analysis. Both infected bitter almond, wild almond, peach and nectarine but not apple and pear. by grafting. In bitter almond the symptoms induced by KAlmWB consisted of severe proliferation, internode shortening and leaf size reduction. In contrast, NA1-mWB caused leaf necrosis, dieback and death. KAlmWB was transmitted to periwinkle and eggplant and from experimentally infected periwinkle to almond by dodder. It was also transmitted from eggplant to eggplant, ornamental eggplant and tomato by grafting. Under similar test conditions, NAlmWB was not transmitted to herbaceous plants by dodder. Phylogenetic analysis of 16S-23S rDNA spacer region (SR) sequences placed both strains in the pigeon pea witches' broom (PPWB) group. However, based on phylogenetic and putative restriction site analyses and sequence homology, NAlmWB was identical with the Lebanese AlmWB phytoplasma, while KAlmWB was closer to the Knautia arvensis phyllody (KAP) agent. Clustering of KAlmWB with KAP was confirmed by analysis of full length 16S rDNA sequence. On the basis of host range, dodder transmission, host range, symptomatology and molecular analyses of 16S rDNA and SR, two different phytoplasmas related to PPWB group were associated with AlmWB disease in Iran. KAlmWB phytoplasma is being reported as a new phytoplasma of AlmWB disease.

The full lengths of three genome segments of Iranian wheat stripe virus (IWSV) were amplified by reverse transcription (RT) followed by polymerase chain reaction (PCR) using a primer complementary to tenuivirus conserved terminal sequences. The segments were sequenced and found to comprise 3469, 2337, and 1831 nt, respectively. The gene organization of these segments is similar to that of other known tenuiviruses, each displaying an ambisense coding strategy. IWSV segments, however, are different from those of other viruses with respect to the number of nucleotides and deduced amino acid sequence for each ORF. Depending on the segment, the first 16-22 nt at the 5' end and the first 16 nt at the 3' end are highly conserved among IWSV and rice hoja blanca virus (RHBV), rice stripe virus (RSV) and maize stripe virus ( MStV). In addition, the first 15-18 nt at the 5' end are complementary to the first 16-18 nt at the 3' end. Phylogenetic analyses showed close similarity and a common ancestor for IWSV, RHBV, and Echinochloa hoja blanca virus (EHBV). These findings confirm the position of IWSV as a distinct species in the genus Tenuivirus.

Beet curly top Iran virus (BCTIV) is a major pathogen of sugar beet in Iran. In order to study diversity of BCTIV, we sampled 68 plants in Iran during the summer of 2010 with curly top disease symptoms on beans (Phaseolus vulgaris), cowpeas (Vigna unguiculata), tomatoes (Solanum lycopersicum L.), sea beets (Beta vulgaris subsp. maritima), and sugar beets (Beta vulgaris). Plant samples showing leaf curling, yellowing, and/or swelling of veins on the lower leaf surfaces were collected from various fields in Khorasan Razavi, Northern Khorasan (north-eastern Iran), East Azarbayejan, West Azarbayejan (north-western Iran), and Fars (southern Iran) provinces. Using rolling circle amplification coupled with restriction digests, cloning, and Sanger sequencing, we determined the genomes of nine new BCTIV isolates from bean, cowpea, tomato, sea beet, and sugar beet in Iran. Our analysis reveals ~11 % diversity amongst BCTIV isolates and we detect evidence of recombination within these genomes.

Turnip curly top virus (TCTV) is a unique geminivirus that has recently been characterised as infecting turnips in Iran. The genome of TCTV shares

A survey of Potato virus Y (PVY) was conducted in cultivated fields in six Iranian provinces between January 2005 to July 2007. Two hundred samples from potato and tomato were collected and analyzed by enzyme-linked immunosorbent assay (ELISA) for potyviruses. Almost one fourth of the samples were found to be infected by PVY. Analysis of these PVY-positive samples using three monoclonal antibodies (MAbs) facilitating the simultaneous detection of three main strains namely the ordinary (PVY(O)), strain (PVY(N)) and C (PVY(C)) strains. However, the fourth strain (PVY(NTN)) and some others recombinant isolates were also identified by molecular methods. Host range and symptoms analysis using sap inoculation of four different strains of PVY onto a range of plants revealed that the four strains showed biological properties that seemed to be consistent with their molecular grouping. Fourteen isolates of PVY were chosen based on the host and geographical location, primer specificity and serology for further biological and molecular characterisation. The coat protein (CP) and P1 genes and 3'-non-translated region (3'NTR) from 14 representative isolates were sequenced and analysed with the sequences available in GenBank. Composite analysis of the P1, CP and 3'-UTR sequences with all full genome sequences of PVY revealed that there are three potential strains of PVY in Iran, PVY(O), PVY(N)-W and PVY(NTN). Isolate KER.SA(N) was the most divergent of all the 14 isolates reacted with PVY(N) specific MAbs but grouped with PVY(O) strains in maximum likelihood phylogentic analysis. The PVY(NTN) isolates from Iran more closely related to the European than North American PVY(NTN) isolates.

The incidence and severity of tomato leaf curl disease (TLCD) is increasing worldwide. Here we assess the diversity and distribution within tomato producing areas of Iran of begomoviruses that cause this disease. Tomato with typical TLCD symptoms and asymptomatic weeds were collected in 2005 and 2006 and tested for the presence of begomovirus DNA using polymerase chain reaction (PCR). Analysis of cloned and sequenced PCR products revealed that both mono- and bipartite begomoviruses are associated with TLCD in Iran. Furthermore, our results confirmed the symptomless infection with mono- and bipartite begomoviruses of two weed species, Chrozophora hierosolymitana Spreng (Euphobiaceae) and Herniaria sp. (Caryophyllaceae). Eighteen Iranian begomovirus isolates were classified into two major groups and two or three subgroups according to the 5′-proximal 200 nucleotides of the coat protein (CP) gene or the N-terminal 600 nucleotides of the Rep gene. Whereas most of the monopartite isolates showed closest similarity to tomato yellow leaf curl virus-Gezira (TYLCV-Ge), the three bipartite isolates were most similar to Tomato leaf curl New Delhi virus (ToLCNDV). Mixed mono- and a bipartite begomovirus infections were detected in both tomato and C. hierosolymitana. Our results indicate that the tomato producing areas in central, southern, and southeastern Iran are threatened by begomoviruses originating from both the Mediterranean basin and the Indian subcontinent.

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.

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.

Transmission properties of Iranian wheat stripe virus (IWSV), a tentative member of the genus Tenuivirus, were studied. Results showed that similar to other tenuiviruses, IWSV multiplies in its vector, Unkanodes tanasijevici. In bioassay experiments, IWSV transmission rate by individual U. tanasijevici showed an increase with time after acquisition. IWSV was transovarially transmitted to 88–100% of progeny. The nymphs continued to be infective in the adult stage but with decreased efficiency. Males and females transmitted the virus with equal efficiency. Transmission properties of IWSV confirm the position of the virus in the genus Tenuivirus.