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In this study, the RT-PCR method was used to detect the Y virus in potato tubers and leaves. Samples suspicious of virus infection with symptoms of virus infection were gathered from farms in Kermanshah and placed in plastic bags and kept at -80 degrees C temperature in order to maintain the RNA of the virus until extraction. The extraction and purification of RNA were carried out using Tri-Reagent kit. One of the virus genes is the P1 protease gene which codes a proteinase enzyme. This enzyme plays a role in breaking the initial polyprotein. For amplification of this gene three primer, including primer-1, primer-2 and primer-3, were designed and used. Using primer 1 and reverse transcriptase enzyme, cDNA was synthesized and then PCR was performed using the primers 1, 2 and 3. The PCR products were examined by agarose gel electrophoresis (1%). Consequently, two pieces of DNA (400 and 800 bp) were yielded which were identical to the genome DNA sequencing. Thus, the proposed technique is a convenient method for quick and accurate detection of viruses and, therefore, the application of this method for detecting Potato Y virus in potato farms is recommended.

During a growing season in 2004, 231 leaf samples of virus infected and mosaic and dwarf mosaic symptoms showing maize (Zea mays L.) plants and 258 leaf samples of mosaic showing johnsongrass (Sorghum halepens L.) plants from various corn fields in Tehran province were collected. Serological tests of DAS-ELISA and DIBA were performed on samples using antisera of sugarcane mosaic virus (SCMV), maize dwarf mosaic virus (MDMV), sorghum mosaic virus (SrMV) and johnsongrasss mosaic virus (JGMV). In both tests performed on leaf samples extractions, all samples reacted strongly with SCMV antiserum and no reaction was seen with other 3 potyviruses antisera. 0.1 M potassium phosphate buffer (pH = 7) containing 2% polyvinyl pyrrolidon (PVP) was used for mechanical inoculation and all isolates were inoculated and propagated on sweet corn cv. Pars 403 and grain sorghum cv. Kimia. In serological tests on the inoculated plants samples also only SCMV was detected. Purification of virus was done using a modified "minipurification" method and the concentration of purified virus was 11.45 mg/ml and ratio of A260/280 = 1.2 was calculated for it. Electron microscopic study using ISEM and decoration method with SCMV antiserum revealed filamentous flexuous particles of SCMV. In SDS-polyachrylamide gel electrophoresis and Western blot test using SCMV antiserum that were performed on infected samples and purified viruses, the molecular weight of the virus coat protein was approximately 37-38 KDa and a difference among the CP weights of various SCMV isolates was not found. Reverse transcription-polymerase chain reaction (RT-PCR) was done using SCMV F3 and SCMV R3 primers and amplified fragments of approximately 900 bp in size were as in expected. The host range study with selected isolates of SCMV showed that the virus isolates were not transmitted by mechanical inoculation on Avena sativa, Panicum miliaceum, Setaria italica, Pennisetum americanum, Hordeum vulgare and Triticum aestivum. The isolates produced red-brown necrotic streaks on sudangrass (Sorghum sudanense) that lately changed in systemic necrosis. In host reaction studies on sorghum (Sorghum bicolor) cultivars, the virus isolates caused severe necrotic and killer reaction on sorghum cultivars Payam, Sepideh and Speed feed, but caused systemic mosaic and non-killer reaction on sorghum cultivars Kimia, KFS2, KFS3 and Jumbo. The present study showed that SCMV is the prevalent potyvirus and the main causal agent of mosaic and dwarf mosaic on maize plants in province. Since the virus is prevalent on johnsongrass plants in marginal areas of corn fields too, it seems that the origin of the virus on corn is from johnsongrass and the virus is a special strain of sugarcane mosaic virus that infects johnsongrass too.

During the growing season of 2018, several field-grown cucurbit plants in different parts of Iraq and Iran were surveyed for the presence of zucchini yellow mosaic virus (ZYMV), using two degenerate primer pairs (CIF/Rev and NIb2F/3R) targeting the two separated partial regions of the potyvirus genome (CI and NIb respectively). 7 out of 20 samples were confirmed to be infected with ZYMV. Phylogenetic analyses based on the CI gene grouped all Iranian and two Iraqi (ZYMV1 and ZYMV2) isolates together with isolates from the Middle East in the subgroup (AI), whereas the other Iraqi (ZYMV3 and ZYMV4) isolates were clustered in the subgroup (DI), which was only consisted of American isolates. The highest and lowest identity between the studied isolates and the GenBank isolates showed that the two genes (CI, NIb) of each isolate particularly the Iraqi isolates were more similar to a specific and geographically scattered mosaic of worldwide isolates, suggestive of mixed infection might have occurred between different worldwide isolates in Iraq. Furthermore, the first complete nucleotide sequence of an Iraqi ZYMV (ZYMV-Iq) isolate was done, using the Illumina sequencing technique. The complete nucleotide sequence of ZYMV-Iq isolate was 9650 nt, excluding the 3'poly (A) tail. ZYMV-Iq isolate shared the highest nt identity of 98.8% with an American (KC665630) isolate. Phylogenetic analysis based on the full genome sequence placed ZYMV-Iq in subgroup A of group I alongside 18 isolates from the US and two isolates from Australia. In addition, recombination analysis detected lone significant recombination between ZYMV-Iq and South Korean (AY279000) isolate. Moreover, the results showed that symptom intensity was varied across experimental host plants., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Maize dwarf mosaic virus (MDMV) and bermuda grass southern mosaic virus (BgSMV) is the most important cereal potyvirus in Iran. Expression of some key genes in maize plants susceptible and tolerant to MDMV or BgSMV and gene expression profile of MDMV and BgSMV compatible or incompatible to Johnson grass plants were studied. Time points of 1, 9, 24 and 72 h after inoculation with both viruses were investigated as well. By analyzing the expression of the genes, it was identified that in maize infected by MDMV and BgSMV, the transcript levels of the peroxiredoxin, GLP, SAM, NPR1 and chlorophyll a-b binding genes were significantly higher in the tolerant than in susceptible plants during the entire experiment. In the BgSMV inoculated Johnson grass plants, some of the genes related to plant defense responses including NPR1, peroxiredoxin and SAM had higher expression level than the Johnson grass plants inoculated by MDMV. Important genes in maize tolerance like NPR1 and MT-LP, were analyzed by trilinear decomposition analysis and genes clustering. The upregulated expression of genes at one-hour post inoculation showed that the plant response to viruses was activated at the early stage of infection. Keywords: MDMV; BgSMV; gene expression; quantitative real-time PCR; trilinear decomposition analysis.

Beet mosaic virus (BtMV), the only Potyvirus known to infect sugar beet, occurs worldwide in beet crops. The full genome sequencing of a BtMV isolate from Iran (Ir-VRU), enabled us to better understand the evolutionary history of this virus. Selection analysis suggested that BtMV evolution is mainly under negative selection but its strength varies in different proteins with the multifunctional proteins under strongest selection. Recombination has played a major role in the evolution of the BtMVs; only the Ir-VRU and USA isolates show no evidence of recombination. The ML phylogenies of BtMVs from coat protein and full sequences were completely congruent. The primary divergence of the BtMV phylogeny is into USA and Eurasian lineages, and the latter then divides to form a cluster only found in Iran, and a sister cluster that includes all the European and Chinese isolates. A simple patristic dating method estimated that the primary divergence of the BtMV population was only 360 (range 260-490) years ago, suggesting an emergence during the development of sugar beet as a crop over the past three centuries rather than with the use of leaf beet as a vegetable for at least 2000 years.

During the surveys conducted from green space in Shiraz City, Iran, in the summer of 2022, leaf chlorosis and mosaic symptoms were observed on the leaves of black-eyed-susans (Rudbeckia hirta), a Dahlia sp., and Mexican Petunia (Ruellia brittoniana) plants. Total genomic RNA was separately extracted from 10 symptomatic and one symptomless (negative control) leaf samples and subjected to Reverse Transcription-Polymerase Chain Reaction (RT-PCR) using a potyvirus degenerate primer pair (NIb3R, NIb2F). RT-PCR resulted in the amplification of an approximately 350 bp DNA fragment in all symptomatic samples, while no such fragment was amplified from the symptomless plant. The amplified DNA fragment was subjected to Sanger sequencing, and its size was determined to be exactly 350 bp, and confirmed that it belongs to the Nib gene of potato virus Y (PVY). The nucleotide (nt) sequence of the amplicons was compared with the nt sequence of the same region of some other PVY isolates that were available in the GenBank. The sequence analysis revealed that the R. brittoniana isolate exhibited the highest (98.8%) similarity to a PVY isolate from the USA with the Acc. No. of KY_848029.1. Similarly, the R. hirta and the Dahlia isolates showed the highest (98.3%, 98.4 %, respectively ) similarity to a PVY isolate from Kazakhstan with the Acc. No. of ON_583980.1. [ABSTRACT FROM AUTHOR]

The genetic variation and population structure of Soybean mosaic virus (SMV) in Iran was analysed through the characterization of a set of isolates collected in the soybean-growing provinces of Iran. The partial nucleotide sequence of these isolates showed a single, undifferentiated population with low genetic diversity, highly differentiated from other SMV world populations. These traits are compatible with a population bottleneck associated with the recent introduction of SMV in Iran. Phylogenetic analyses suggest that SMV was introduced into Iran from East Asia, with at least three introduction events. The limited genetic diversification of SMV in Iran may be explained by strong negative selection in most viral genes eliminating the majority of mutations, together with recombination purging deleterious mutations. The pathogenicity of Iranian SMV isolates was typified on a set of soybean differential lines either susceptible or carrying different resistance genes or alleles to SMV. Two pathotypes were distinguished according to the ability to overcome Rsv4 resistance in line V94-5152. Amino acid sequence comparisons of virulent and avirulent isolates on V94-5152 (Rsv4), plus site-directed mutagenesis in a biologically active cDNA clone, identified mutation S1053N in the P3 protein as the determinant for virulence on V94-5152. Codon 1053 was shown to be under positive selection, and S1053N-determined Rsv4-virulence occurred in isolates with different genealogies. The V94-5152 (Rsv4)-virulence determinant in Iranian isolates maps into a different amino acid position in the P3 protein than those previously reported, indicating different evolutionary pathways towards resistance breaking that might be conditioned by sequence context.

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.

Onion yellow dwarf virus (OYDV) is one of the most important viral diseases of garlic crops worldwide. This study surveyed the occurrence of OYDV in 26 garlic ecotypes collected from different regions in Iran during 2008-2009. Using an electron microscope, we detected filamentous particles with about 700-800 nm in length and 12 nm in width in five samples. These features are typical of the genus Potyvirus. The coat protein (CP) gene from 26 samples was PCR amplified, cloned, sequenced, and compared with the sequences available in GenBank. Phylogenetic analysis using 235 deduced amino acids of the CP gene showed that virus isolates fell into two groups, group A and group B. Members of group A were divided into two subgroups: A-I and A-II. The subgroup A-I appears to be a new subgroup comprising 17 Iranian isolates. The identity levels among the amino acid of 26 Iranian isolates ranged between 90 and 100%. The results indicated that the genetic diversity found in Iran is due to local OYDV populations rather than introduction from other geographical regions. This study is the first report about the molecular structure and geographically diverse range of OYDV populations in this country.

Potato virus Y (PVY) is the type species in the potyvirus genus of the family potyviridae. This plant pathogenic virus is transmitted through plant sap inoculation by stem and core grafting and by at least 25 aphid species in a non-persistent manner. According to potato specialists in most parts of the world, PVY is currently considered as the most harmful virus in cultivated potatoes. This is also the case for potato production in Iran. In this project we investigated potato leaves that were collected in the Kurdistan province in Iran for the presence of PVY with use of different biochemical/molecular techniques as ELISA, RT-PCR and qPCR. The different PVY strains, including PVY-O, PVY-N, PVYN-TN, PVY-NWi, were determined by using a triplex RT-PCR. In conclusion, the results demonstrated the presence of PVY-NWi strains in the potato leaf samples from Kurdistan (Iran). The data are discussed in relation to prevalence of PVY strains in 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.

Potato Virus Y was known as the main cause of yellowing and vein necrosis of pepper in Tehran Province, using Double Antibody Sandwich Elisa (DAS-ELISA). Biological properties including host range of the isolate was determined after biological purification. Host range studies showed that pepper isolate of PVY caused vein clearing and mosaic symptoms on Datura metel and Capsicum annum, mosaic on Nicotiana tabacum cv. White Barley, N. tabacum cv. Samsun and N. rustica but didn't show any symptoms on Physalis floridana, Chenopodium amaranticolor, C. quinoa and Solanum tuberosum. Also the virus was physically purified from propagative hosts: Datura metel, Nicotiana tabacum cv. White Barley and Capsicum annum using Leiser & Richter (1978) method. The A260/280 absorbance ratio of the isolate was 1.16, 1.50 and 1.04 for purified preparations from D. metel, N. tabacum cv. White Barley and C. annum respectively. SDS-PAGE of the coat protein extracted from purified virus preparations gave bands at position of about 34 KD and Western Blotting (using PVY antiserum with 1/1000 dilution, obtained from DSMZ, Germany) confirmed its as the PVY coat protein. In order to prepare antiserum, five injections were given at 7-10 days intervals to rabbit. A week after the last injection the rabbit was bled and the antiserum collected. The primer pairs NIA/F and NIA/R (Glais et al., 2005) were used in IC-RT-PCR and the length of the amplified fragment was 752 bp. This is the first report of PVY incidence in pepper fields in Iran.

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No abstract Keywords: genetic diversity; Iran and Iraq; water melon; mosaic virus; cucurbits.

Potyviruses are among the most important pathogens of dicotyledonous and monocotyledonous ornamentals and crop plants. In this study, leaf samples were collected from symptomatic narcissus plants and weeds in Fars and Tehran provinces of Iran. Enzyme-linked immunosorbent assay using broad-spectrum potyvirus antibodies gave a positive reaction with 38 out of 61 narcissus samples tested (62.3%); the results were confirmed by reverse-transcription polymerase chain reaction using universal NIb primers, and for thirty samples, by sequencing and phylogenetic studies. The results suggested the infection of almost all positive samples with narcissus yellow stripe virus (NYSV); only one sample seemed to be infected with narcissus late season yellows virus (NLSYV). The 3'-end of the genome of the NLSYV isolate and six NYSV isolates, encompassing the complete coat protein gene, was amplified and sequenced using species-specific and universal potyvirus primers. Sequence analysis indicated the presence of NLSYV and NYSV, not previously identified from Western Asia. No evidence of recombination was found in Iranian isolates. Based on phylogenetic analyses, isolates of NLSYV and NYSV clustered into five and three phylogroups, respectively, where all the Iranian isolates fell into distinct subpopulations in groups NLSYV-I and NYSV-II. Multiple sequence alignments showed some phylogroup-specific amino acid substitutions for both viruses. Phylogroup IV and II populations had higher nucleotide diversities as compared with other populations of NLSYV and NYSV, respectively. Our findings revealed the presence of negative selection in the populations of both viruses. Almost no statistically significant gene flow was found between populations of these viruses. [ABSTRACT FROM AUTHOR]

Several viruses affect iris plants worldwide, and are major constraints in commercial production due to serious economic losses. The first genomic sequences of two potyviruses, namely, Iris Severe Mosaic Virus (ISMV) and Iris Mild Mosaic Virus (IMMV) from naturally infected iris plants (Iris versicolor) in Iran were determined using RNA deep sequencing and RT-PCR followed by sequencing of amplicons. Both viruses (ISMV-Ir and IMMV-Ir) had a typical potyvirus genetic organization, with a large open reading frame translated as a polyprotein, including nine autocatalytic cleavage sites, and a putative smaller protein P3N-PIPO. Phylogenetic analyses and sequence comparisons revealed close relationships between ISMV and members of group Onion Yellow Dwarf Virus (OYDV) of the genus Potyvirus. The ISMV-Ir showed > 92% nucleotide (nt) identity (> 96% amino acid (aa) identity) to the three previously reported ISMV isolates, the highest with the Japanese isolate J (94.10% nt identity, 97.41% aa identity) and the lowest with Chinese isolate BJ (92.73% nt identity, 96.77% aa identity). IMMV-Ir belonged to the Chilli Veinal Mottle Virus (ChVMV) group of potyviruses, had 82.36% nt identity (91.25% aa identity) with the BC32 isolate, and 75.55% nt identity (83.59% aa identity) with the WA-1 isolate from Australia. The genetic distance among IMMV polyprotein-coding genomic sequences or gene-specific sequences indicated a high genetic divergence of these isolates. Our analysis indicated that natural selection has contributed to the evolution of isolates belonging to the two identified potyviruses. The information on genomic sequences presented in this study will improve our understanding of virus function and pathogenicity leading to better control of the disease. [ABSTRACT FROM AUTHOR]

Tobacco (Nicotiana tabacum L.) is one of the important industrial plants in Iran. Viruses as an important group of plant pathogens cause many losses on the quality and quantity of tobacco crop. There was few information on the types of plant viruses infecting the tobacco fields of Guilan and almost no information for Western Azerbaijan province. During 2005-2007, leaf samples were taken from symptomatic plants in the growing areas of these two provinces. The observed symptoms on plants in the fields varied from mild mosaics to severe necrosis. The regions of sampling were including Rasht, Bazar-jomeh, Soumae-Sara, Talesh and Astara in Guilan and Ourmia, Sardasht and Ghara-Ziaeddin in Western Azerbaijan. The tobacco types and varieties from which the samples were taken included air-cured burley variety Burley 21 and to a lesser extent, oriental tobacco variety Basma Serres in W. Azerbaijan and flue-cured varieties Coker 347 and Virginia El in Guilan province. Samples were tested by DAS-ELISA method (Clark and Adams, 1977) using the polyclonal antibodies for a set of tobacco viruses. Some samples with positive reactions in DAS-ELISA were inoculated to indicator test plants such as Chenopodium amaranticolor, Datura metel, D. stramonium, Physalis floridana, Nicotiana rustica, N. glutinosa, and tobacco (varieties White burley and Samsun). The results of greenhouse experiments were consistent with serological tests. The following viruses which are listed in order of their overall abundance within the tested samples were detected: Tobacco streak virus (TSV), Tomato spotted wilt virus (TSWV), Tobacco etch virus (TEV), Tobacco ringspot virus (TRSV), Potato virus Y (PVY), Cucumber mosaic virus (CMV) and Tobacco mosaic virus (TMV). In all samples more than one virus infection was detected. The most severe mosaic type symptoms including the deformation and blistering on leaves were mainly seen in the infections by CMV and TMV. The most severe necrotic type symptoms including necrosis of midribs or veins and in some cases stem necrosis were generally associated with the infections by PVY and TSWV. Except TMV infection which was not detected in the Burley 21 variety in W. Azerbaijan, the above mentioned viruses were present in all sampling regions. The lack of TMV infection on Burley 21 is due to the presence of N gene, conferring resistance in this variety.

During two growing seasons in years of 2003 and 2004 potato and tobacco of virus infected plants were collected from fields in Tehran (Damavand) and Mazandaran (Behshahr) provinces. Serological methods of TAS-ELISA and DIBA were performed by using PVY antiserum (DSMZ - Plant Virus Collection; Germany) but only PVY was detected. The strain of samples was determined by using MAb of potato virus Y (AS-0403/1; DSMZ; Germany). The molecular weight of the virus coat protein was approximately 34 kDa in SDS-PAGE and Western blotting. Total RNA was extracted for RT-PCR. Immunocapture RT-PCR and RT-PCR products were 974 bp by using specific primers of PVY. IC-RT-PCR has given the best results.

As the important resource in human nutrition, vegetables are susceptible to several viruses.Potyvirusas the most important genus in the family Potyviridae causes severe crop yield reduction. We tried to detect a genomic fragment, amplified by RT-PCR by use of thePotyvirusdegenerate primers (NIb2F/NIb3A), from samples of vegetables in East Azerbaijan. A pTZ57R/T vector was prepared by adding thymine nucleotide to the free 5′ end of the linear plasmid, to clone the fragments. Recombinant plasmids were transformed inEscherichia colias a prokaryotic host. To investigate the identity of genomic fragments, sequencing was carried out and finally, some genomic segments were investigated to be SMV and ZYMV that are membranes ofPotyvirusgenus. This is the first report of ZYMV from this region of Iran based on RT-PCR detection and SMV is sequenced for first time from Iran. Finally, phylogenetic comparison with other isolates was carried out for these two isolate ofPotyvirusgenus. [ABSTRACT FROM AUTHOR]

To investigate the infection of carnations (Dianthus caryophillus) to common viruses, a total of 130 samples showing suspected viral disease symptoms were collected from 10 commercial greenhouses located in Mahallat City, Markazi Province. Total DNA and RNA were extracted and amplified by PCR and RT-PCR methods, respectively, using generic primers for the genera Potyvirus and Orthotospovirus and also specific primers of Carnation mottle virus (CarMV), Carnation necrotic fleck virus (CNFV), Carnation etched ring virus (CERV), Carnation latent virus (CLV), Carnation vein mottle virus (CVMV) and Cucumber mosaic virus (CMV). Results revealed that the estimated rates of infection in the collected samples for different viruses in decreasing order were for CarMV, CNFV, CERV, CMV and CVMV, while CLV and species of genus Orthotospovirus were not detected. Mixed viral infections were also investigated and among all of the 130 collected samples, 3.1% showed mixed infections with CarMV, CNFV, CVMV, CERV and CMV, 32% with CarMV, CNFV, and CERV, 20% with CarMV and CNFV, and 9% with CarMV and CERV. For phylogenetical assays, NIb-CP fragment of the CVMV genome was amplified, cloned, and sequenced. Phylogenetic trees of two isolates of this virus revealed that the two Iranian isolates of CVMV (IBR and RCM) were phylogenetically divergent. Mechanical inoculation of CVMV on 16 different indicator plant species showed specific symptoms on six of the indicators that were confirmed by RT-PCR. To the best of our knowledge, this is the first report of CMV and first partial genome sequencing of CVMV from a carnation plant in Iran. [ABSTRACT FROM AUTHOR]

Pepper mottle virus is a member of genus Potyvirus and infects many plants worldwide. Bell pepper (Capsicum annuum) leaves with virus symptoms were collected, and after using RT-PCR amplification using pepper mottle virus-specific primers for the coat protein, amplicons were sequenced. Sequences revealed the presence of pepper mottle virus (PeMV) for the first time in Iran. Phylogenetic analysis of the coat protein sequences showed that Iranian isolates shared greatest pairwise identities (98.6%) with those from Korea, and lowest identities (91.5%) with those from Cuba. [ABSTRACT FROM AUTHOR]

During the surveys conducted from green space in Shiraz City, Iran, in the summer of 2022, leaf chlorosis and mosaic symptoms were observed on the leaves of black-eyed-susans (Rudbeckia hirta), a Dahlia sp., and Mexican Petunia (Ruellia brittoniana) plants. Total genomic RNA was separately extracted from 10 symptomatic and one symptomless (negative control) leaf samples and subjected to Reverse Transcription-Polymerase Chain Reaction (RT-PCR) using a potyvirus degenerate primer pair (NIb3R, NIb2F). RT-PCR resulted in the amplification of an approximately 350 bp DNA fragment in all symptomatic samples, while no such fragment was amplified from the symptomless plant. The amplified DNA fragment was subjected to Sanger sequencing, and its size was determined to be exactly 350 bp, and confirmed that it belongs to the Nib gene of potato virus Y (PVY). The nucleotide (nt) sequence of the amplicons was compared with the nt sequence of the same region of some other PVY isolates that were available in the GenBank. The sequence analysis revealed that the R. brittoniana isolate exhibited the highest (98.8%) similarity to a PVY isolate from the USA with the Acc. No. of KY_848029.1. Similarly, the R. hirta and the Dahlia isolates showed the highest (98.3%, 98.4 %, respectively ) similarity to a PVY isolate from Kazakhstan with the Acc. No. of ON_583980.1. [ABSTRACT FROM AUTHOR]

Crocus sativus L. leaf samples were serologically tested for the presence of beet western yellows virus (BWYV) and 17.6% of samples showed positive reaction. The partial genome sequence of the BWYV isolate-Saf-Th16 from saffron was closely related to that of BWYV isolates from citron in the USA. This is the first report of BWYV on saffron plants from Iran. [ABSTRACT FROM AUTHOR]

Zucchini yellow mosaic v irus (ZYMV; family Potyviridae, genus Potyvirus) causes high yield losses to cucurbits in many parts of the world. The virus was detected for the first time in Iran in 1988, but the isolates have not been characterized. To study the genetic and biological diversity among Iranian ZYMV isolates, a set of twelve isolates, obtained during an extensive survey conducted from 2003 to 2006 in the major cucurbit-growing areas, were characterized. An experimental host range study of these isolates (referred as Iran-1 to Iran-12) revealed some variation in their biological properties. The nucleotide sequences of the genomic portion spanning the C-terminal part of NIb and N-terminal part of coat protein (CP) coding region were determined and compared with other available sequences. The identity among Iranian ZYMV isolates at the amino acid level reached 95.6–100%. The Iranian ZYMV isolates did not form a compact cluster in the phylogenetic tree, and the phylogenetic analyses and the estimation of genetic distance indicate that the Iranian ZYMV group consists of several independent introductions that evolved separately. [ABSTRACT FROM AUTHOR]

One of the destructive potyviruses which cause economic damage and serious yield losses to cucurbit crops around the world is Watermelon mosaic potyvirus. In 2016, 305 leaf samples from different cucurbit cultivars with deformation and reduction in leaf size, blistering, mild and severe mosaic symptoms were collected from different cucurbits-growing regions in Northwest of Iran. Total RNA and their cDNA were tested by RT-PCR assay using two sets of specific primers corresponding to the partial sequences of CP and P1 genomic regions, in which approximately 80 out of 305 samples were found to be infected by WMV. DNA fragments of about 780 bp and 545 bp in length were amplified that belonged to the CP and P1 genes, respectively. Phylogenetic trees of WMV isolates were clustered into three main independent groups with significant FST values (> 0.50 and > 0.55) for CP and P1 genes, respectively. dN/dS ratios obtained less than one (< 1) for CP gene that showed the WMV populations have been under the negative selection, whereas for P1 gene, the dN/dS values were calculated > 1 for EM clade containing; China, France, and Italy populations and < 1 for CL and G2 clades; South Korea and Iran populations. This results demonstrated that the WMV evolutionary selection pressure on the P1 gene is dependent on conditions such as the variety of cultivars and the type of cultivation. [ABSTRACT FROM AUTHOR]

Beet mosaic virus (BtMV), the only potyvirus infecting beets, is distributed worldwide in beet growing areas. Here we report the full-length genome sequence of a BtMV isolate from Iran (Ir-VRU), which has enabled us to better understanding the evolutionary history of the virus. The complete nucleotide sequence of Ir-VRU genome was determined using degenerate and specific primers and 5'-RACE and The complete genomes consisted of 9591 nucleotides, excluding the poly-A tails. The genome has a 165 nt 5´-UTR and a 168 nt 3´-UTR. The RNA of Ir-VRU potentially encodes a single polyprotein of 3086 amino acid residues and has a deduced genome organization typical for members of the genus Potyvirus. Study on five different BtMV isolates showed that Iranian isolate closelly related to German and Chinese isolates, and on the other hand, it showed more differences with American isolate. Phylogenetic analysis, along with other potyviruses, also presents the Ir-VRU as a member of the BCMV supergroup. [ABSTRACT FROM AUTHOR]

Surveys to identify virus diseases affecting garlic ( Allium sativum), onion ( Allium cepa) and Persian leek ( Allium ampeloprasum var. persicum) were conducted from 1999 to 2002. Surveys covered different regions of Iran (Tehran [different vegetable markets, farmer fields and cultivation areas], Noushahr, Chalous, Roudbar, Sari, Hamadan, Touyserkan, Ghazvin and Jiroft). A total of 2045 (1285 garlic, 525 onion and 230 leek) samples showing symptoms of virus infection were collected and tested by ELISA; and in some cases tests were also confirmed by immunoelectron microscopy (IEM) for the presence of Allium viruses. ELISA results showed that the following viruses were detected: Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV) (genus Potyvirus, family Potyviridae), Garlic common latent virus (GarCLV), Shallot latent virus (SLV) (genus Carlavirus), Garlic virus D (GarV-D), Garlic virus B (GarV-B) and Garlic virus C type (GarV-C) (genus Allexivirus). None of the samples reacted with antibodies to Shallot yellow stripe virus (SYSV) genus Potyvirus, family Potyviridae), Shallot virus X (ShVX) and Garlic virus A (GarV-A, genus Allexivirus). GarCLV, SLV, GarV-D, GarV-B and GarV-C are reported for the first time from Allium crops in Iran. [ABSTRACT FROM AUTHOR]

To date, only the complete genome of one malva vein clearing virus (MVCV) has been sequenced worldwide. Here, for the first time, the genomic sequence of an isolate of MVCV affecting Malva sylvestris in Iran was determined, using RNA deep sequencing confirmed by reverse-transcription polymerase chain reaction and Sanger sequencing. The sequence of IR1 was 11,055 nucleotides in length and contained a single open reading frame of 10,527 nucleotides encoding a large polyprotein of 3,508 amino acids with predicted molecular weight of 395,08 KDa. The sequence contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. The P1 of the IR1 was 1236 nucleotides longer than that of the only recently reported sequence from China (MVCV-SX, MN116683). The complete genome sequence obtained from the study showed 81.24% and 91.93% identities to its Chinese counterpart at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The low nt and aa sequence identity with known MVCV isolate seems to indicate that IR1 is a novel strain. Phylogenetic analysis of the coat protein gene also showed that the Iranian isolate was most closely related to the Dutch isolate NAKT-NL (FJ539084), with identities of 94.06 (at nt level) and 96.04% (at aa level). The results of this study will be useful for understanding the global molecular epidemiology of MVCV. [ABSTRACT FROM AUTHOR]

Iris belongs to the Iridaceae family. It is one of the most important pharmaceutical and ornamental plants in the world. To assess the potyvirus incidence in natural resources of iris plants in Iran, Antigen Coated-Plate ELISA (ACP-ELISA) was performed on 490 symptomatic rhizomatous iris leaf samples, which detected the potyvirus in 36.7% of the samples. Genomic 3' end of one mechanically non-transmitted potyvirus isolate, comprising a 3' untranslated region (390 bp) and C-terminus of the coat protein (CP) gene (459 bp), was amplified by reverse transcription polymerase chain reaction (RT-PCR), which was ligated into pTG19-T vector. The nucleotide sequence of amplicons was compared with related sequences, using Blastn software available at NCBI GenBank, and showed the highest similarity with Iris severe mosaic virus (ISMV) isolates. The nucleotide and deduced amino acid sequence of the CP C-terminus region was more than 83% identical with other ISMV isolates, therefore this isolate was designated as ISMV-Ir. This new ISMV isolate is closely related to the Chinese ISMV-PHz in phylogenetic analysis, based on the partial nucleotide and deduced amino acid sequence of the CP region. This is the first report of ISMV occurrence on Iris spp. in Iran. [ABSTRACT FROM AUTHOR]

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 x 10-4 substitutions/site/year (95% credibility interval, 2.828 x 10-4-5.723 x 10-4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517-1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China. [ABSTRACT FROM AUTHOR]

Background: Next-generation Sequencing (NGS) combined with bioinformatic analyses constitutes a powerful approach for identifying and characterizing previously unknown viral genomes. In this study, leaf samples from bitter apple plants (Citrullus colocynthis (L.) Schrad) exhibiting symptoms such as dwarfing, leaf crinkling, and chlorosis were collected from the southern part of Kerman province, Iran. Results: Putative infecting viruses were identified through de novo assembly of sequencing reads using various tools, followed by BLAST analysis. Complete genomes for Squash vein yellowing virus (SqVYV), Citrus-associated rhabdovirus (CiaRV), and a novel polerovirus-related strain termed Bitter apple aphid-borne yellows virus (BaABYV) were assembled and characterized. Additionally, a partial genome for Watermelon mosaic virus (WMV) was assembled. The genomic organization of the BaABYV was determined to be 5'-ORF0-ORF1-ORF1,2-ORF3a-ORF3-ORF3,5-ORF4-3'. Amino acid sequence identities for inferred proteins (P0 and P1, P1,2) with known poleroviruses were found to be the 90% species delineation limit, implying that BaABYV should be considered a new member of the genus Polerovirus. Recombination events were observed in the BaABYV and WMV strains; such events were not found in the CiaRV strain. Conclusions: Molecular evidence from this study suggests that C. colocynthis is a reservoir host of several plant viruses. Among them, BaABYV is proposed as a new member of the genus Polerovirus. Furthermore, the CiaRV strain has been reported for the first time from Iran. [ABSTRACT FROM AUTHOR]

Background and Objectives Chickpea, cultivated in rainfed and irrigated fields across many countries. In terms of chickpea cultivation area, Iran ranks fourth, after India, Australia and Pakistan, and in terms of chickpea production, Iran ranks eighth in the world, but it does not have a good position in terms of average yield. Iran ranks 17th in terms of average yield in irrigated agriculture and 50th in rainfed agriculture in the world. Various factors such as water stress in rainfed cultivation, lack of modern inputs and technologies have been mentioned as reasons for the low yield of chickpeas in Iran. Chickpea also faces biological stresses such as Ascochyta blight caused by the pathogenic fungus Ascochyta rabiei. This disease poses a severe threat to chickpea fields, resulting in substantial annual damage in various countries. Identifying resistance sources through molecular methods, specifically genomic tracking of the resistance trait, holds the potential to expedite and enhance control measures effectively. The use of the Amplification Refractory Mutation System (ARMS) method, involving functional point mutations and resistance-related alleles, proves highly efficient in advancing selection programs targeted at combating Ascochyta blight. Materials and methods Pots containing two chickpea genotypes, sensitive (ILC263) and resistant (MCC133) to Ascochyta blight were cultivated and kept for 45 days under greenhouse conditions. The fragment harboring the SNP18-Pos57723 point mutation within the GSh118 gene sequence underwent amplification and sequencing using PSh118-F/R specific primers. This process utilized DNA extracted from both resistant (MCC113) and susceptible (ILC263) chickpea genotypes. The identification of alleles associated with resistance and sensitivity was established. Distinct differentiating primers were formulated for resistant (PSh118-Fc and PSh118-R) and sensitive (PSh18-Fg and PSh18-R) genotypes. The specific annealing temperature for each reaction was determined through a temperature gradient analysis. The efficacy of the designed primers in distinguishing between resistant and sensitive genotypes was assessed by conducting PCR and comparing their electrophoresis patterns. Results The first symptoms of Ascochyta blight disease was observed on seedlings of resistant and sensitive chickpea genotypes seven days after fungal inoculation under greenhouse conditions. The fragment containing the functional point mutation related to GSh118 gene was tracked using PSh118.2-F/R specific primers in the genomic DNA of susceptible (ILC263) and resistant (MCC133) chickpea genotypes so that after PCR amplification resulted a specific fragment with the expected size of 630 bp. The presence of alleles linked to GSh18-2773C resistance and GSh18-2773g sensitivity was confirmed in resistant and sensitive chickpea genotypes, respectively. The specific primers PSh18-Fc and PSh18-R, designed for detecting the resistance allele, successfully amplified the expected 330 bp fragment in the resistant chickpea genotype MCC133. The study results affirmed the accurate amplification of alleles using these designated primers. Discussion In the present study, the ARMS method, known for its high sensitivity, specificity, rapidity, costeffectiveness, multiplexing capabilities, compatibility with high throughput methods, and nondestructive nature, was employed to differentiate chickpea genotypes resistant to Ascochyta blight. The ARMS method's effectiveness in selecting resistance sources among various plant lines and cultivars has been demonstrated through allele tracking related to the resistance gene in prior studies. The results of this study indicated that the ARMS method accurately distinguishes chickpea genotypes resistant and sensitive to Ascochyta blight based on alleles associated with the GSh18-2773 position's point mutation. Thus, employing specific primers for the resistance allele is recommended in molecular selection studies of chickpea sources resistant to Ascochyta blight. [ABSTRACT FROM AUTHOR]

Saffron is a spice that is obtained by dehydrating the stigmas of the Crocus sativus flower. Iran is the country that produces the largest amount of saffron, exceeding 90% of world production. Currently, there is a growing medicinal use which implies that there is more demand than supply worldwide, in turn, a large amount of labor is required to obtain it; for these two reasons, it reaches a high price in the international market. This demand is due to the high concentration of apocarotenoid metabolites that it biosynthesizes. In this work, the content of these metabolites of saffron from six production areas of Iran and neighbouring countries infected with saffron latent virus (SaLV) and dehydrated at two temperatures is compared. The corms of the six provenances were planted in a homogeneous plot and the stigmas analyzed were those of the second year after planting. The analysis showed that corms do not completely retain the memory of their original origin. In general, the ratio of the sum of mmol/kg of HTCC derivatives to the sum of the mmol of crocins is greater than two. This implies that the biosynthesis of saffron apocarotenoids due to the degradation of β-carotene towards HTCC is more important than that of zeaxanthin formation, which later gives HTCC and crocetin dialdehyde. [ABSTRACT FROM AUTHOR]

Viral symptoms, such as yellowing, leaf deformation, mottling, vein clearing, and reduced yield, were observed in cucurbits in Iran. This study aimed to detect the main suspected causal agent, cucurbit aphid-borne yellows virus (CABYV), in Iran and analyze the genetic diversity among isolates. Two hundred samples were collected from different growing areas between 2019 and 2022. PCR amplification was performed on the P3 and P4 genes. The sequences of 18 Iranian isolates were obtained and deposited in GenBank. Recombination, phylogenetic, and population genetics studies were then carried out for the complete genome and all ORFs sequences, together with other isolates in GenBank. The nucleotide identities of the overlapped ORF3/4 sequences of Iranian isolates were 94.8 to 99.5% among themselves, and with other tested isolates ranging from 94.3 to 99.3%. Phylogenetic trees based on the complete genome and the overlapped ORF3/4 showed two major clades, namely Asian and Mediterranean, and the new isolates from Iran were positioned in both clades. The obtained results also suggest that all the genes and two clades of CABYV populations were under negative selection pressure. Furthermore, rare gene flow between these two clades (FST > 0.33) confirmed the high genetic separation among them. [ABSTRACT FROM AUTHOR]

Oilseed rape ( Brassica napus ssp. oleifera) is an important crop in Iran. Of 581 oilseed rape samples tested by DAS-ELISA and immunoelectron microscopy during a preliminary survey from 1999 to 2001, 14.45% were infected with Beet western yellows virus (BWYV, Luteovirus), 12.9% with Cauliflower mosaic virus (CaMV, Caulimovirus) and 9.3% with Turnip mosaic virus (TuMV, Potyvirus). Cucumber mosaic virus (4.6%) and Tomato spotted wilt virus (0.51%) also occurred, but to a lesser extent. The occurrence of BWYV, TuMV and CaMV in oilseed rape crops could have important consequences for rape seed production in Iran and infected plants could also serve as sources of virus for other susceptible vegetable crops. [ABSTRACT FROM AUTHOR]

Background: In June 2020, severe symptoms of leaf mosaic and fruit malformation were observed on greenhouse-grown cucumber plants in Xizhou Township of Changhua County, Taiwan. An unknown virus, designated CX-2, was isolated from a diseased cucumber sample by single lesion isolation on Chenopodium quinoa leaves. Identification of CX-2 was performed. Moreover, the incidence of cucumber viruses in Taiwan was also investigated. Methods: Transmission electron microscopy was performed to examine virion morphology. The portable MinION sequencer released by Oxford Nanopore Technologies was used to detect viral sequences in dsRNA of CX-2-infected leaf tissue. The whole genome sequence of CX-2 was completed by Sanger sequencing and analyzed. Reverse transcription-polymerase chain reaction (RT-PCR) with species-specific primers and indirect enzyme-linked immunosorbent assay (ELISA) with anti-coat protein antisera were developed for virus detection in the field [see Additional file 1]. Results: Icosahedral particles about 30 nm in diameter were observed in the crud leaf sap of CX-2-infected C. quinoa plant. The complete genome sequence of CX-2 was determined as 4577 nt long and shared 97.0–97.2% of nucleotide identity with that of two cucumber Bulgarian latent virus (CBLV) isolates in Iran and Bulgaria. Therefore, CX-2 was renamed CBLV-TW. In 2020–2022 field surveys, melon yellow spot virus (MYSV) had the highest detection rate of 74.7%, followed by cucurbit chlorotic yellows virus (CCYV) (32.0%), papaya ringspot virus virus watermelon type (PRSV-W) (10.7%), squash leaf curl Philippines virus (SLCuPV) (9.3%), CBLV (8.0%) and watermelon silver mottle virus (WSMoV) (4.0%). Co-infection of CBLV and MYSV could be detected in field cucumbers. Conclusion: The emerging CBLV-TW was identified by nanopore sequencing. Whole genome sequence analysis revealed that CBLV-TW is closely related, but phylogenetically distinct, to two known CBLV isolates in Bulgaria and Iran. Detection methods including RT-PCR and indirect ELISA have been developed to detect CBLV and to investigate cucumber viruses in central Taiwan. The 2020–2022 field survey results showed that MYSV and CCYV were the main threats to cucumbers, with CBLV, SLCuPV and WSMoV were occasionally occurring. [ABSTRACT FROM AUTHOR]

Wheat streak mosaic tritimovirus (WSMV) seriously damages wheat worldwide. We report analyses of new complete ORF (CO) sequences from seven Australian isolates with 56 COs and 128 coat protein (CP) genes sequenced previously. Eleven CO and three CP sequences were recombinants so were removed from our analyses. Patristic distances of maximum‐likelihood phylogenies of nonrecombinant (n‐rec) CO sequences and their CP sequences were closely correlated (R = 0.994, p ≤ 0.00001). The phylogeny of all 188 n‐rec CP genes had four well‐supported phylogroups (I–IV): phylogroup I (one Mexican sequence), phylogroup II (six Iranian sequences), phylogroup III (48 sequences) and phylogroup IV (133 sequences), each with basal Iranian sequences and either mostly European (phylogroup III) or mostly American (phylogroup IV) terminal sequences. Australian and South American sequences formed a phylogroup IV subcluster within a Pacific Northwest USA cluster. Unlike the Iranian, South American and European populations, the North American and Australian populations demonstrated recent population imbalance. Sample collection dates of 40 CO sequences are known, allowing WSMV phylogeny dating by RTDT methodology. The most recent WSMV ancestor was dated at 1456 CE, and the Australian cluster at 1998.7 CE, only 2–3 years before WSMV was first reported. Tritimoviruses originated in central Eurasia, WSMV first entering wheat in its Middle East domestication centre and one basal lineage being taken to Mexico after the Spanish conquest, whereas the other most basal lineage spread throughout Iran, before spreading to other world regions. Probable future spread to other world regions of additional WSMV phylogroups, and of interphylogroup recombinants, constitutes a biosecurity concern. [ABSTRACT FROM AUTHOR]

Grapevine virus A (GVA), the type species of the Vitivirus genus, is one of the causal agents of the Kober stem grooving disease of the rugose wood complex and one of the most frequently detected viruses in grapevine. There is little information on GVA gene(s) marker useful for phylogenetic analysis. To this aim, a total of 403 leaf samples were collected from vineyards of East and West Azarbaijan provinces in the Northwestern provinces of Iran during 2014–2016 and tested by DAS-ELISA and RT-PCR using ORF5-specific primers. GVA was detected in 56 symptomatic samples, corresponding to 14% of infection, while it was not detected in asymptomatic samples. The ORF5 (p10) protein sequence of eight Iranian isolates was compared to other vitiviruses, showing that the most conserved region resides in the N-terminus, carrying an arginine-rich motif followed by a zinc-finger motif. Next, to define a robust phylogenetic marker representative of the whole genome sequence suitable for phylogenetic and evolutionary studies, phylogenetic trees based on the full genome sequences of all the available GVA isolates and on individual genomic regions were constructed and compared. ORF1, which encodes the RNA-dependent RNA polymerase, was found to be the best phylogenetic marker for GVA classification and evolution studies. These results can be used for further research on phylogenetic analyses, evolution history, epidemiology, and etiology of rugose wood complex, and to identify control measures against GVA and other vitiviruses. [ABSTRACT FROM AUTHOR]

Sugar beet is an economically important crop and one of the major sources of sucrose around the world. Beet necrotic yellow vein virus (BNYVV) and Beet severe curly top virus (BSCTV) are two widespread viruses in sugar beet that cause severe damage to its performance. Previously, we have successfully produced resistance to BNYVV based on RNA silencing in sugar beet by introducing constructs carrying the viral coat-protein-encoding DNA sequence, CP21, in sense and anti-sense orientations. Yet, the RNA silencing-mediated resistance to a specific virus could be affected by other ones as a part of synergistic interactions. In this study, we assayed the specificity of the induced resistance against BNYVV in two sets of transgenic events, S3 and S6 carrying 5'-UTR with or without CP21-coding sequences, respectively. These events were subjected to viral challenges with either BNYVV, an Iranian isolate of BSCTV (BSCTV-Ir) or both. All the plants inoculated with just BSCTV-Ir displayed curly-leaf symptoms. However, partial resistance was evident in S3 events as shown by mild symptoms and reduced PCR amplification of the BSCTV-Ir coat protein encoding sequence. Based on the presented data, resistance to BNYVV was stable in almost all the transgenic plants co-infected with BSCTV-Ir, except for one event, S3-229. In general, it seems that the co-infection does not affect the resistance to BNYVV in transgenic plants. These findings demonstrated that the introduced RNA silencing-mediated resistance against BNYVV in transgenic sugar beets is specific and is not suppressed after co-infection with a heterologous virus., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

To date, the complete genome of two wisteria vein mosaic virus (WVMV) has been sequenced worldwide. Here, the genomic sequence of WVMV isolated from Wisteria sinensis in Iran was determined for the first time, using deep RNA sequencing and RT-PCR followed by Sanger sequencing. The sequence was 9694 nucleotides in length; excluding the 3'-poly(A) tail and contained a single open reading frame of 9279 nucleotides encoding a large polyprotein of 3092 amino acids and predicted molecular weight of 35,368 KDa. The genome contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. Sequence analysis suggested that WVMV-Ir sequence shared 76.37–86.01% nucleotide (nt) identity and 82.45–91.91% amino acid (aa) identity with two other isolates (Beijing and JEBU-p) available in the GenBank, the highest with the Chinese isolate Beijing (86.01% nt identity, 91.91% aa identity). Sequence identities over most of the genome were within the range 80–86% and 85–95% at the nt and aa levels, respectively; however, high variability was observed in the 5'-UTR (51.62%), P1 (62.03% nt identity, 50.78% aa identity) and P3 (79.82%nt identity, 78.67% aa identity) regions, suggesting that Ir, Beijing, and JEBU-p are three different strains. These variabilities may be due to different mutation phenomena of a common ancestor virus or mutations caused by different selection pressures in different agro-ecological regions. The results of the phylogenetic analysis indicated that WVMV was most closely related to soybean mosaic virus and watermelon mosaic virus and less closely related to the zantedeschia mild mosaic virus and dasheen mosaic virus. In the greenhouse, WVMV-Ir caused severe symptoms in Phaseolus vulgaris, Vicia faba, W. sinensis, Chenopodium quinoa, C. amaranticolor, and Nicotiana benthamiana. [ABSTRACT FROM AUTHOR]

Bean yellow mosaic virus (BYMV) is an economic potyvirus with worldwide distribution and a broad host range. Recently, phylogenetic studies of BYMV isolates have indicated the importance of comparing the full genome sequences to obtain a reliable classification. However, most available isolates in public databases are partially sequenced, and virologists continue to prefer partial genomes or individual genes for phylogenetic studies. As such, to avoid unbiased classification, phylogenetic studies should be based on either phylogenetic gene markers or a multigene dataset instead of just one random gene. In the present study, we sequenced the full genome of a BYMV isolate collected from an Iranian faba bean field using the Illumina Novaseq 6000 platform. The phylogenetic analysis revealed that the Iranian isolate is closely related to three isolates originating from faba bean fields in Japan, Australia and Germany. To identify the phylogenetic markers of BYMV, the topology distance between reconstructed trees based on individual genes and the whole genome was calculated using topology congruence tests considering only the topology of the compared trees and a character congruence test taking into account the characters, tree topology and estimated bootstrap support value. Accordingly, nuclear inclusion proteins a and b (NIa and NIb) and viral protein genome linked (VPg) were selected as evolutionary markers which can be used as appropriate representations of the full genome in phylogenetic studies. Furthermore, supermatrix approach was used to compare all BYMV isolates that have been fully or partially sequenced. The results demonstrate that all submitted BYMV strains can be divided into 10 main monophyletic clades with high bootstrap values; these are named BYM-1 through BYM-10 to avoid confusion with previously introduced nomenclature. Moreover, the results reveal that clustering based on phylogenetic analysis and their original host is not completely consistent, which supports recent phylogenetic studies based on available whole genome sequences. • Finding the phylogenetic markers of BYMV. • NIb, NIa and VPg have been selected as the evolutionary markers for phylogenetic studies of BYMV isolates. • All publicly available BYMV isolates can be divided into 10 main clades (BYM1-BYM10) with high bootstrap support value. • Clustering of BYMV isolates based on phylogenetic analysis and their original hosts is not completely consistent. [ABSTRACT FROM AUTHOR]

Plant infections to several pathogens at a same time are expected in nature. In most cases, plant mixed infections with viruses and fungi could result in increased susceptibility in plant host. In the present study, the interaction between turnip mosaic virus or cauliflower mosaic virus with Phoma lingam in canola (Brassica napus L.) was investigated. Experiments were carried out using a completely randomized design. Plants were mechanically inoculated with virus-infected turnip leave saps and by medium plug of fungal causal agent. To evaluate the interactions, in addition to recording the type and severity of symptoms, enzymatic (catalase and guaiacol peroxidase) and non-enzymatic (carotenoids and flavonoids) defense responses of treated plants were measured. The results showed that the severity of Phoma symptoms significantly increased in primary infection with turnip mosaic virus and then phoma inoculation, but no significant changes of Phoma symptoms were observed in initial infection with cauliflower mosaic virus. All treatments infected with case studied pathogens compared to the control treatment (no pathogen infection) showed a significant decrease in chlorophyll content, quantity of carotenoids, and flavonoids. While, catalase and guaiacol peroxidase content in the treatments infected with case studied pathogens showed a significant increase compared to the control treatment. Due to the synergistic effect of Phoma lingam and turnip mosaic virus in mixed infection of canola and reporting the incidence of both causal agents in canola cultivated areas in Iran, it is recommended to select canola cultivars that are resistant to both pathogens. [ABSTRACT FROM AUTHOR]

Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years. [ABSTRACT FROM AUTHOR]

During 2016 growing season, samples with leaf yellowing and mosaic like symptoms were collected from main lentil (Lens culinaris Medik L.) fields. Specific ELISA positive PSbMV samples were selected for RT-PCR. Using specific pair of primer towards CP gene region of the virus, PCR product of approx.235 bp was amplified. Based on the nucleotide sequences of the CP gene PSbMV isolates were classified in two major groups. In which, isolates in group I divided into two subgroups of Iranian isolates (B2) and (G1), along with Czech Republic, Australia, China, Greece, Pakistan and Egypt were placed in the subgroup-I. Isolate (V18) from Iran placed independently in group II. In the grouping based on the amino acid sequencing the isolates divided into two phylogenetic groups. Iranian isolates along with an isolate from Australia categorized in group-II, however world isolates were all clustered in group-I. [ABSTRACT FROM AUTHOR]

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Field surveys were conducted to detect the incidence of viruses in major vegetable fruit growing areas in west and northwest of Iran. A total of 100 leaf samples from various vegetable fruit crops were analyzed for Cucumber mosaic virus (CMV), Cucumber green mottle mosaic virus (CGMMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV) by RT-PCR using specific primers for each virus. Among the collected samples, the highest incidence was for CMV (46%), followed by ZYMV (35%), WMV (26%) and CGMMV (8%). Overall, 63.3%, 50%, 40%, 90%, 75% and 80% of green bean, cucumber, eggplant, squash, tomato and watermelon samples, respectively, were positive for at least one virus. CMV, ZYMV and WMV were identified in most regions, whereas CGMMV was found only in East Azerbaijan province. Mixed infections of two and three viruses in various combinations were detected in 30 and 8 samples, respectively. Restriction analysis with MspI (HpaII) on 13 PCR products of CMV coat protein revealed a previously described CMV subgroup I (S-I) specific profile (537 and 335 bp fragments) for the isolates. To the best of our knowledge, this is the first report of WMV and ZYMV from watermelon, tomato, eggplant and green bean in the West and Northwest regions of Iran and first report of ZYMV infecting green bean (Phaseolus vulgaris L.) in Iran. [ABSTRACT FROM AUTHOR]

Brassicaceae crops in eight provinces of the North-west Iran were surveyed for Turnip mosaic virus (Tu MV) infection during 2011 and 2012. Many symptomatic plants (38%; 226 of 598) were found to be infected with Tu MV. The highest frequency was in turnip (61%), followed by radish (55%), oilseed rape (38%), and brassica weeds including annual bastard cabbage (42%), small tumbleweed-mustard (50%) and wild radish (45%), but not Brassica oleracea and Lepidium sativum. Using biological assays, Iranian Tu MV isolates grouped in three [B], [B(R)] and [ BR] host-infecting types. Phylogenetic analysis using complete coat protein ( CP) gene nucleotide sequences showed that the Iranian isolates belonged to the Basal-B and Asian- BR populations. No evidence of recombination was found in these isolates using different recombination-detecting programmes. To our knowledge, our study shows for the first time the occurrence of Tu MV Asian- BR subpopulation in the mid Eurasian region of Iran. The data suggest that the Asian- BR subtype population is found across southern Eurasia and might be a continuous population in East Asia (mostly Japan and China) and Minor Asia (Turkey), the places considered to be one of the origins of Tu MV populations. [ABSTRACT FROM AUTHOR]

Forty-eight fig orchards were surveyed to determine the presence and incidence of Fig cryptic virus ( FCV), Fig fleck-associated virus ( FFkaV), Fig leaf mottle-associated virus 1 ( FLMaV-1), Fig leaf mottle-associated virus 2 ( FLMaV-2) and Fig mosaic virus ( FMV) in four provinces of northeast, northwest and central regions of Iran. A total of 197 leaf samples from commercial and outdoor fig gardens were collected in April and September 2012 and tested by reverse-transcription polymerase chain reaction ( RT- PCR). Approximately 14.7% of the tested fig trees were infected by FCV, FFkaV and FMV with a peak of 18% in Tehran province. None of samples was found to be infected with FLMaV-1 or FLMaV-2. FFkaV was found in fig trees collected in all the four provinces, but no FCV infection was found in Semnan province, and FMV was just occurred in Markai and Tehran. Mixed infections of FCV with FFkaV and FMV were detected in 2.5% of the samples. The sequence of the CP fragment of six Iranian FCV isolates showed 97-99% nucleotide (nt) identity with the reference FCV isolate, while that of a RdRp and Gp fragments of nine FFkaV and two FMV Iranian isolates showed 87-91% nt and 89-90% identity with the reference isolates, respectively. Phylogenetic analysis grouped the FCV and FFkaV isolates in two distinct clusters, with the Iranian isolates included in both clusters. Results showed genetic diversity among Iranian viruses. Structure and diversity of FCV and FFkaV populations are discussed. [ABSTRACT FROM AUTHOR]

Beet yellows virus ( BYV), a member of the Closteroviridae family, is one of the most important sugar beet yellowing viruses. The nine ORFs of BYV genome encode different proteins required for BYV life cycle. We sequenced a part of the genome of BYV Iranian isolate consisting of ORF6, ORF7 and ORF8. The primer pair BYVA/Z was used for amplification of this region in RT-PCR. The amplicon (1615 bp) was cloned and sequenced. Comparisons showed the amplified segment is corresponding to ORF6, ORF7 and ORF8 of BYV genome encoding coat protein, p20 and p21 proteins, respectively. The ORF7 of BYV Iranian isolate overlaps with ORF6 and ORF8 in four and 26 nucleotides at 5′ and 3′ ends, respectively. The ORF7 of Iranian isolate of BYV was sequenced completely. However, approximately 24 nt. from the beginning of ORF6 and 23 nt. from end of ORF8, including the stop codon, were not determined. ORF6, ORF7 and ORF8 showed the highest similarity at nucleotide (98.3, 99.4 and 99.2%) and amino acid (97.4, 98.9 and 100%) sequence levels, with BYV Ukrainian isolate. Phylogenetic analysis of the deduced amino acid sequences of ORF6, ORF7 and ORF8 revealed closer relationship of Iranian isolate of BYV with BYV Ukrainian isolate than other BYV isolates available at Gen Bank. [ABSTRACT FROM AUTHOR]