Japanese flowering cherry (Prunus serrulata Lindl.) is a deciduous tree with great decorative value due to its splendid spring bloom. Flowering cherry is native to East Asia and is cultivated in many other parts of the world. Two trees with virus-like symptoms on leaves, denoted by S14 and S27, were found in the town of Sochi, Russia. Virome analysis of these trees using high-throughput sequencing revealed the presence of several viruses, including little cherry virus 2 (LChV-2), American plum line pattern virus (APLPV), and cherry virus A (CVA) in the S14 tree, as well as CVA, prune dwarf virus (PDV), and alfalfa mosaic virus (AMV) in the S27 tree. Nearly complete genomes of the detected viruses have been recovered and characterized. In the S14 tree, CVA was represented by three diverse genotypes sharing 80.8-83.5% nt identity. The complete APLPV genome from flowering cherry has been first sequenced. AMV was detected on Prunus species for the first time. This is the first report of LChV-2 from Russia. Thus, PDV, APLPV, AMV, LChV-2, and CVA were first found on P. serrulata from Russia, adding to the information on their genetic diversity, host range, and global geographical distribution.

A novel idaeovirus was discovered in stinging nettles (Urtica dioica) with yellow mosaics on the leaves. The virus was initially detected in the Main Botanical Garden, Moscow, Russia, using high-throughput sequencing and was tentatively named “nettle idaeovirus” (NIdV). The complete NIdV genomes from two symptomatic plants (designated as YM and VB) consisted of two RNAs of 5424 and 2195 nucleotides (nt) that were predicted to encode typical idaeovirus proteins. NIdV-YM and NIdV-VB isolates shared 98.6

Phlox are ornamentals of great decorative value, grown throughout the world for their attractive flowers. Phlox cultivar collections at the Tsitsin Main Botanical Garden and the Botanical Garden of Lomonosov Moscow State University (both Moscow, Russia) were surveyed for virus diseases. Tobacco streak ilarvirus (TSV), beet ringspot nepovirus (BRSV), and BRSV satellite RNA (satRNA) were first detected in phlox when viromes of symptomatic Phlox paniculata plants were studied using high-throughput sequencing. The nearly complete genomes of three TSV and BRSV isolates and two BRSV satRNAs were assembled and characterized. TSV isolates shared 96.9–99.7% nucleotide sequence identity and were 82.2–89.1% identical to their closest relatives from broad bean, dahlia, and echinacea. BRSV isolates were distantly related to each other (83.7–89.3% identity) and were closest to those from oxalis and potato. BRSV satRNAs shared 90.6% identity and were 87.8–94.1% identical to satRNAs associated with tomato black ring virus L and S serotypes. Thus, TSV, BRSV, and BRSV satRNA were for the first time detected in a new natural host P. paniculata in Russia, adding to the list of known phlox viruses and expanding information on the host range, geographic distribution, and genetic diversity of these viruses.

The disease “sharka”, caused by Potyvirus plumpoxi (plum pox virus), is the most harmful viral disease affecting stone fruits. The virus spreads over long distances through illegal and insufficiently controlled exchange of infected propagative plant material. Once established in an area, the virus spreads locally through vegetative propagation of infected plant material, and naturally through aphid-vectors. Previously considered a European problem, sharka has now been reported in 54 Prunus-growing countries in all continents except Oceania, although the disease has been eradicated from the United States of America. The economic cost of the disease in the 28 years from 1995 to 2023 is estimated to be €2.4 × 109, equivalent to approx. 0.17% of the stone fruit industry’s value. This includes more than over €2 × 109 in direct fruit losses, €1.4 million from international rejection of symptomatic fruit, and over €100 million in eradication and disease limitation costs. Indirect costs include €137 million, mainly associated with ELISA analyses, and approx. €130 million in costs related to research and science networks. Cumulative global losses from the sharka pandemic since the decade 1910/20 probably surpass €13 × 109. These outlays exclude indirect trade costs, economic losses, genetic erosion of traditional cultivars, and the costs of developing new cultivars tolerant or resistant to plum pox virus. The decline in these costs compared to the previously evaluated €10 billion from the 1970s to 2006 is analyzed. Four case studies (for Spain, Turkey, Chile, and Greece) illustrate different sharka scenarios and management strategies.

The first complete genome of spiranthes mosaic virus 3 (SpiMV3, genus Potyvirus, Potyviridae) was determined using high-throughput sequencing (GenBank PQ374234). The virus was detected from a Phlox paniculata plant, displaying severe foliar mosaic, in the Botanical Garden of Lomonosov Moscow State University, Moscow, Russia. The complete SpiMV3 genome comprised 9544 nucleotides (nt), excluding the 3'-terminal poly(A) tail. The large open-reading frame 9258 nt long encoded a polyprotein of 3085 amino acid residues, in which nine putative cleavage sites were identified. BLASTn showed that the complete SpiMV3 genome had the highest identity (66.4%) to Colombian datura potyvirus. Eight more SpiMV3 isolates were found on different phlox cultivars in the Tsitsin Main Botanical Garden, Moscow, by RT-PCR using primers designed based on the complete genome of the Russian SpiMV3 isolate. The coat protein (CP) gene phylogeny showed that known SpiMV3 isolates formed two distinct clusters and were grouped irrespective of their host plant species or geographical origin. The Russian isolates were assigned to one of the clusters. The CP genes of the Russian SpiMV3 isolates shared 94.4-98.1% nucleotide identity to each other, 92.2-96.9% to the rest of the isolates from this group, and 72.7-75.6% to the isolates from another cluster. This is the first report of SpiMV3 from Russia expanding the information on the geographical distribution and genetic diversity of the virus. The complete genome of this virus was sequenced and characterized for the first time.

Virus diseases of stone fruit crops (Prunus spp.) reduce both fruit yield and quality and shorten the productive life of fruit trees. Cherry virus A (CVA, genus Capillovirus, family Betaflexiviridae) is one of the most common among more than 50 known viruses affecting these crops. A sweet cherry (P. avium) tree of the cultivar Iput with virus-like rugosity symptoms on the leaves was found during a survey of stone fruit collections of the Tsitsin Main Botanical Garden of the Russian Academy of Sciences (Moscow). When studying the virome of this plant using high-throughput sequencing, reads related to CVA were generated, and the complete genome of a new isolate of this virus, named SwC14, was assembled. Typical of capilloviruses, the SwC14 genome contained two open reading frames encoding a viral replicase, a coat protein, and a movement protein. The SwC14 genome sequence was shown to be closest to the genomes of some Canadian sweet cherry CVA isolates (99.4

A new badnavirus was discovered in nettle plants (Urtica dioica L., family Urticaceae) with vein banding symptoms using high-throughput sequencing. This virus was provisionally named "nettle badnavirus 1" (NBV 1). The complete NBV 1 genome consists of 7598 bp and contains three overlapping open reading frames. NBV 1 found to be was most closely related to green Sichuan pepper vein clearing-associated badnavirus, sharing 73.9% nucleotide sequence identity in the whole genome. These two viruses showed 76.3% nucleotide sequence identity in the region of the genome encoding RT-RNase H. This is lower than the species demarcation cutoff (80%) for the genus Badnavirus of the family Caulimoviridae, suggesting that NBV 1 is a new member of this genus. Phylogenetic analysis based on full-length badnavirus genome sequences showed that NBV 1 belongs to the same clade as a badnavirus whose genome was found to be integrated into chromosome 6 of the nettle genome, sharing 78% identity. Using PCR, NBV 1 was detected in a symptomless nettle plant growing next to symptomatic ones. It is therefore likely that the observed vein banding was due to an idaeovirus or a partitivirus, which were shown to be coinfecting the symptomatic plant. These findings expand the list of viruses infecting nettle.

Fig mosaic is the most serious viral disease affecting figs. A fig germplasm collection from the Nikita Botanical Garden on the Crimean Peninsula was surveyed for viruses using high-throughput sequencing and RT-PCR with primers specific to known fig viruses. Reads related to fig umbra-like virus (FULV) were generated in samples from Ficus carica caprifig (pollinator) trees of the cultivar Belle dure. F. carica trees of other cultivars, as well as F. afghanistanica, F. palmata, and F. virgata trees, tested negative for FULV. Near-complete genomes of five Crimean fig umbra-like virus (FULV-CR) isolates shared 99.4% to 99.9% identity and were most closely related (85.2% identity) to the Hawaiian FULV isolate Oahu1 (MW480892). Based on their genome structure and a phylogenetic analysis, the FULV-CR isolates were determined to be dicot-infecting Class 2 umbra-like viruses and seem to be highly divergent forms of the same virus found recently in Hawaii, USA. This is the first report of an umbra-like virus found on figs in Crimea and outside of Hawaii, expanding information on the geographical distribution and genetic diversity of FULV. All of the Crimean FULV-positive plants were also co-infected with fig mosaic virus, fig badnavirus 1, and grapevine badna FI virus.

Tomato aspermy virus (TAV, genus Cucumovirus from the family Bromoviridae) is one of the most common and harmful chrysanthemum viruses, causing severe flower distortion, size reduction, and color breaking. Metatranscriptome sequencing of chrysanthemum plants of the Ribonette and Golden Standard cultivars from the collection of the Nikita Botanical Garden (Yalta, Republic of Crimea) generated TAV-related RNA reads. The complete genomes of two Russian isolates of the virus were assembled from the reads. This is the first report of full-length TAV genomes from Russia. Typically of cucumoviruses, the segmented TAV genome is represented by three single-stranded positive-sense linear RNA molecules of 3412 (RNA1), 3097 (RNA2) and 2219 (RNA3) nucleotides. Five open reading frames (ORF) have been identified that encode replicase (ORF1), RNA-dependent RNA polymerase (ORF2a), silencing suppressor protein (OFR2b), movement protein (OFR3a) and the coat protein (ORF3b). The identity of TAV genomes from the two chrysanthemum cultivars was 99.8% for all three viral RNAs; with other TAV isolates from GenBank it was 97.5-99.7% (RNA1), 93.8-99.8% (RNA2), and 89.3-99.3% (RNA3). Phylogenetic analysis showed that RNA1 and RNA3 of the Russian isolates were assigned to heterogeneous groups of TAV isolates found on various plant species in different regions of the world. At the same time, RNA2 clearly clustered with tomato isolates SKO20ST2 from Slovenia and PV-0220 from Bulgaria and, to a lesser extent, with the Iranian isolate Ker.Mah.P from petunia and the Chinese isolate Henan from chrysanthemum. The incongruence of phylogenetic trees reconstructed from different genome segments suggests pseudo-recombination (reassortment) in the Russian TAV isolates.

We conducted a survey of the phytosanitary status of the Prunus germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. The virome of plants displaying virus-like symptoms was studied using Illumina MiSeq high-throughput sequencing. Reads related to prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and ourmia-like virus 1 (OuLV1) were generated in a number of samples. Near complete genomes of two divergent PNRSV isolates, PDV isolate, and a contig partly covered OuLV1 genome were assembled de novo using the metaSPAdes program. The structure of the genomic RNA1, RNA2, and RNA3 of the new ilarvirus isolates was shown to be typical of PNRSV and PDV. This is the first report and characterization of the PNRSV and PDV full-length genomes from Russia, expanding the information on their geographical distribution and genetic diversity. An open reading frames (ORF)-based phylogeny of all full-length PNRSV and PDV genomes available in GenBank divided each ORF into two or three main clusters. A number of isolates migrated from one cluster to another cluster, depending on the analyzed genome segment. The different branching order may indicate reassortment in the evolutionary history of some PDV and PNRSV isolates.

Virus diseases affect the yield and fruit quality and shorten the productive life of stone fruits (Prunus spp. in the family Rosaceae). Of over fifty known viruses infecting these crops, cherry virus A (CVA) is among the most common, and little cherry virus 1 (LChV1) is one of the most economically important. Using high-throughput sequencing, full-length genomes of CVA and LChV1 isolates, found on interspecies hybrids in the Prunus collection of the Nikita Botanical Gardens, Russia, were sequenced, assembled, and characterized. CVA was found in the P. cerasifera × P. armeniaca hybrid and in phylogenetic analysis clustered with non-cherry virus isolates. The LChV1 isolate Stepnoe was detected in ((P. cerasifera Ehrh. × P. armeniaca L.) × P. brigantiaca Vill.) trihybrid suggesting that both P. cerasifera and P. brigantiaca potentially can be the LChV1 hosts. The isolate Stepnoe was most closely related to the Greece isolate G15_3 from sweet cherry, sharing 77.3% identity at the nucleotide level. Possibly, the highly divergent Russian isolate represents one more phylogroup of this virus. This is the first report of CVA and LChV1 from Russia, expanding the information on their geographical distribution and genetic diversity.

Fig mosaic disease is spread worldwide and is believed to have a viral etiology. Divergent isolates of grapevine badnavirus 1 (GBV1), named fGBV1, were discovered on Ficus carica, F. palmata, F. virgata, and F. afghanistanica in the fig germplasm collection of the Nikita Botanical Gardens, Russia, expanding the list of viruses infecting this crop. The complete genomes of five fGBV1 isolates from F. carica and F. palmata trees were determined using high-throughput and Sanger sequencing. The genomes comprised 7283 base pairs, contained four overlapping open reading frames, were 99.7 to 99.9% identical to each other, and related to GBV1 (83.2% identity). The reverse transcriptase RNase H genome regions of fGBV1 and GBV1 share 84.6% identity, indicating that fGBV1 is a divergent isolate of GBV1, which was found on the new natural hosts from a different family (Moraceae). Further, fGBV1-specific primers were developed to detect the virus using RT-PCR. Survey of 47 trees, belonging to four fig species and 14 local and introduced F. carica cultivars, showed the high fGBV1 prevalence in the collection (93.6%), including trees with no obvious symptoms of fig mosaic disease.

Plum pox virus (PPV) is the most pathogenic virus of stone fruit crops worldwide. Unusual PPV isolates were discovered on sour cherry (Prunus cerasus L.) and steppe cherry (P. fruticosa Pall.) in the Republic of Tatarstan and the Middle Ural region, Russia. They induced typical sharka symptoms and tested positive for PPV by ELISA and RT-PCR, but were not detected by PCR using known strain-specific primers. Their complete genomes were determined using high-throughput sequencing. Phylogenetic analysis allocated new isolates to four clearly distinguished lineages (SC, TAT, Y, Tat-26) within a cluster of PPV cherry-adapted strains. The phylogroups SC and TAT had 84.5 to 86.9% average nucleotide identity to each other and strain CR, with which they comprised a common subcluster. Isolates from the Middle Ural region (group Y) were closer to strain C, sharing 96.9% identity. The fourth lineage is represented by the isolate Tat-26, which was a recombinant of strain CR and C isolates as major and minor parents, respectively. These results show that the genetic diversity of PPV is higher than thought and may contribute to a better understanding of the origin and evolution of cherry-adapted strains of the virus. P. fruticosa was reported as a new natural PPV host for the first time.

Tomato bushy stunt virus (TBSV), prunus virus I (PrVI), and cucumber mosaic virus (CMV) were found using RT-PCR in the clematis ( Clematis spp.) cultivar collection of the Nikita Botanical Gardens, Yalta, Russia. PrVI was detected in clematis for the first time that extends both the list of viruses infecting this crop and the information on the geographical distribution and host range of PrVI. Using high-throughput sequencing, the nearly complete genomes of TBSV, PrVI, CMV, and clematis chlorotic mottle virus, which was previously found in the collection, were assembled and characterized. The genome of TBSV was most closely related to the cherry strain of this virus sharing 95.9% identity. Five open reading frames of the PrVI isolate from clematis were 95.8 to 97.7% and 95.6 to 98.6% identical to PrVI from sweet cherry at the nucleotide and amino acid levels, respectively. CMV was revealed in a single plant of the introduced cultivar Valge Daam. Based on phylogeny of complete genomes, RNA1, RNA2, and RNA3 identities, and the size of the proteins 2a and 2b (840 and 100 amino acid residues, respectively), the CMV isolate was shown to belong to subgroup II. TBSV, CMV, and PrVI did not induce visible symptoms on leaves or flowers of at least some clematis cultivars. This is the first report about clematis viruses in Russia and the first molecular characterization of TBSV, PrVI, and CMV isolates from clematis.

The impact of plum pox virus (PPV) on sour cherry (Prunus cerasus L.) productivity has been studied by comparing the yield of PPV-infected and PPV-free fruit-bearing trees. A total of 152 16- to 17-year-old trees of nine cultivars and hybrids were surveyed in the production orchards (cultivar collection and hybrid testing plots) in the Republic of Tatarstan, Russia. Sixty trees tested positive for PPV using ELISA and RT-PCR. Among them, 58 PPV isolates belonged to the strain C and the other 2 isolates to the strain CV. For the cultivars Sevastyanovskaya, Shakirovskaya, hybrids 88-2 and 80-8, the average (2012 to 2019) productivity of infected trees was 38% to 45% lower than for PPV-free trees of the same cultivar or hybrid. No ilarviruses (prunus necrotic ringspot virus, prune dwarf virus, apple mosaic virus, American plum line pattern virus) were detected in PPV-infected trees, suggesting that reduced cherry productivity was attributed to the PPV infection. Thus, it was shown for the first time that PPV can reduce the productivity of at least some sour cherry cultivars and hybrids, and strain C isolates are responsible for crop losses.

Ficus carica L. (family Moraceae) is valuable highly productive early subtropical plant, with the fruit of high calorie and diet value. At the same time, in many fig cultivation areas infection with Fig mosaic virus, Fig leaf mottle-associated virus(-1), Fig leaf mottle-associated virus-2, Fig latent virus(-1), Fig badnavirus(-1) and others was noticed. Monitoring studies in collection plots on the south of Russia allowed us to identify a number of cultivars affected with viral diseases, and presented studies give the analysis for four of them: 'Pomoriyskiy', 'Medovyiy', 'Sabrutsiya Rozovaya' and 'Smena'. The percentage of leaves with clear symptoms was 10-30% of the whole tree crown. At the same time, mosaic chlorosis and leaf folding were localized along the veins and at the base of the leaf. Morphometric analysis of the leaves from visually asymptomatic trees and ones with clear symptoms let us to consider the tendency of dwarfism and more frequent cases of heterophilicity in the damaged plants (in the damaged plants in 'Medovyiy', a significant decrease in the linear parameters of both leaves and plants was noted; in 'Smena'- atypical round shape of leaf blades appeared). In the structural parameters under viral infection damage following significant differences were noted: a decrease in leaf thickness by 5-16%; a decrease in the palisade index to 0.50-0.61; large intercellular spaces appeared in the spongy tissue; chloroplast destruction started in the middle mesophyll layers and then it spread throughout the mesophyll, necrosis initiated in the spongy chlorenchyma; the number of lithocyst with cytolites and crystalline inclusions significantly increased, a decrease in the adaxial epidermis thickness was observed, the distribution density of stomatal apparatus changed. These structural features reduced the drought resistance of plants; degradation of chlorenchyma provoked the inhibition of production processes.

Prunus armeniaca L. (genus Prunus L., family Rosaceae) is one of the most important fruit crops in the world. In the Nikita Botanical Gardens in the south of Russia, the collection of apricot is represented by 479 apricot cultivars and 227 breeding forms. One of the most harmful viral diseases of stone fruit crops is Sharka caused by the Plum pox virus (PPV, genus Potyvirus, family Potyviridae). Due to its virulence and ability to spread rapidly in the orchards, it causes significant economic damage to the industrial production of apricot fruits. In countries that grow this crop, breeding programs aimed at increasing the resistance of industrial apricot cultivars against PPV and the search for donors of resistance to Sharka disease are being developed. To identify PPV and select tolerant cultivars the collection and breeding orchards of apricot were monitored for viruses. Such virus diagnostic methods as biological method (indicator-plants), ELISA-test and RT-PCR were used. The studied apricot samples were assessed for PPV infection and ones with low, medium and high content of viral particles in the cell sap were determined. Breeding combinations of apricot cultivars and forms were selected according to their economically valuable features and tolerance to PPV. Apricot cultivars were crossed: 'Krymskiy Amur' x 'Harcot', 'Krymskiy Amur' x 'Henderson', 'Krymskiy Amur' x 'Stark Early Orange', 'Krymskiy Medunets' x 'Harcot', 'Krymskiy Medunets' x 'Stark Early Orange', 'Henderson' x 'Harlayne', 'Zorkiy' x 'Stark Early Orange'. To obtain new breeding plant material in vitro embryo culture method was used. Regeneration methods of in vitro cleaning up apricot cultivars and hybrid forms are being developed.