First report of Tobacco ringspot virus on Sophora microphylla, a native tree of New Zealand

Hostas (Hosta spp.) are one of the most widely grown and economically important landscape perennials in the nursery industry in North America. Several viruses including Hosta virus X (HVX), Tobacco rattle virus (TRV), Tobacco ringspot virus (ToRSV), Tomato ringspot virus (TomRSV), Impatiens necrotic spot virus (INSV), and Tomato spotted wilt virus (TSWV) are known to occur in hostas (4). This report confirms the occurrence of an additional virus, Arabis mosaic virus (ArMV), in hostas in North America. This virus was first identified during the summer of 2004 in Hosta fortunei 'Sharmon' in several garden centers in Minneapolis and St. Paul, MN. Entire lots of this variety, numbering several dozen plants, showed symptoms consisting of blanching of the foliage similar to those caused by ToRSV and TomRSV infection (4). Symptoms persisted throughout the growing season. Virus-like particles, 28 to 30 nm in diameter, were observed by electron microscopy in partially purified extracts of symptomatic leaf tissue following fixation with 5% glutaraldehyde and negative staining with 2% sodium phosphotungstate, pH 7.0. Particles had an angular outline and some were penetrated by stain. No other virus-like particles were observed in these extracts. The particles were identified as those of ArMV. Identification was made using double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and immunosorbent electron microscopy (ISEM) with antiserum to ArMV (PVAS-587) obtained from the American Type Culture Collection, Manassas, VA. In the spring and summer of 2005, ArMV was again identified as described above in 'Sharmon', H. undulata 'Albomarginata' samples from Minnesota, Michigan, and Nebraska, and H. 'Marion Bachman' and H. 'Touch of Class' from two wholesale nurseries in Minnesota. Symptoms in these hosta cultivars were similar to those observed in 'Sharmon' and were accompanied by stunting and leaf deformation. A portion of the coat protein (CP) gene of the ArMV isolate from 'Sharmon', designated ArMV-H, was amplified using reverse transcription-polymerase chain reaction (RT-PCR) with ArMV-specific CP primers (3) and total RNA extracted with a RNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). Amplicons of the expected size (220 bp) were cloned and five clones were sequenced. Nucleotide sequence identities of the ArMV-H CP sequence to corresponding ArMV databank entries varied from 94 to 88% (Genbank Accession Nos. AY017339 and D10086 and X55460 and X81815, respectively). Interestingly, the hosta ArMV isolate was not transmitted by mechanical inoculation to diagnostically susceptible indicator plants (cucumber, tobacco, and petunia) (2) or to hosta (H. undulata 'Albormarginata', H. 'Honeybells', and H. 'Royal Standard'). Testing by using ELISA and ISEM showed that 'Sharmon' source plants contained high levels of ArMV antigen and virions, and a high percentage of virions were not penetrated by negative stain, indicating that they were not empty (i.e., devoid of RNA). It appears that ArMV-H may be transmitted only vertically, (i.e., clonal propagation) and this raises some interesting questions about the molecular basis of this anomaly. An isolate of ArMV from hops was similarly reported to have a very restricted host range (1) suggesting a possibility of a common mechanism of host range restriction.

Tobacco ringspot virus (TRSV) is a quarantine pathogen in Europe. During an official inspection in November 2011, Impatiens walleriana plants showing symptoms were found in a nursery in the Czech Republic. The causal agent of the disease was detected as Nepovirus group A by RT-PCR using specific primers of the Nepovirus group. Sequence analysis of PCR fragments confirms that the detected virus is TRSV. TRSV detection in these plants was further confirmed by ELISA and one-step RT-PCR using specific primers. The coat protein (CP) gene of the Czech TRSV isolate was sequenced, and the sequence analysis showed high identity of both nucleotide (99.28%) and amino acid (99.96%) levels compared with other known TRSV isolates from GenBank. Two amino acid motifs characteristic of nepoviruses, FDDY (FDAY) and FWGR (FYGR), were found equally at positions 80 and 497 of the TRSV CP genes, respectively, including the sequences described in this study.

In order to understand the occurrence of sorghum mosaic virus (SrMV), one of pathogenic virus causing sugarcane mosaic disease in south China, sugarcane leaf samples with mosaic symptom were collected from commercial growing fields in Guangzhou, Wengyuan, Boluo of Guangdong province and Nanning of Guangxi province. The virus was detected by one-step RT-PCR with SrMV specific primers P1 (5′-ACAGCAGAWGCAACRGCACAAGC-3′) and P2 (5′-CTCWCCGACATTCCCAT CCAAGCC-3′, Y=C/T, W=T/A, K=G/T, R=A/G) based on the viral coat protein (CP) gene. The results showed that 48% samples were infected with SrMV. Ten amplified cDNA products were chosen based on host and geographic origin for direct sequencing. BLAST analysis revealed that they were all homologous to reported SrMV CP gene. To investigate the genetic diversity within the species SrMV, multiple alignment analysis of CP gene nucleotide sequences of the 10 SrMV isolates, together with all 18 SrMV isolates documented in GenBank up to date, was perfermed using Clustal W algorithm. It was showed that 28 SrMV isolates were clustered into two groups, namely hybrid sugarcane (HS) group and noble sugarcane (NS) group. The average CP gene nucleotide identities were 80% between groups, and 87% and 90% between isolates within HS and NS groups, respectively. Coincidently, most isolates in HS group were from hybrid sugarcane, whereas most isolates in NS group from noble sugarcane. This implies that SrMV has evolved under host selection. Hence, not only different pathogens and host types, but also the virus genetic diversity should be taken into consideration in sugarcane mosaic disease controlling and virus-resistance breeding.

Zamia furfuracea (Zamiaceae) is native of coastal Mexico. It is a popular houseplant and easy to grow outdoors in warm climates. In November 2005, a plant of Z. furfuracea, originally from Texas, was received at the Division of Plant Industry in Gainesville, FL. The plant had numerous chlorotic spots on the leaves that eventually became necrotic. Leaves were ground in phosphate buffer (pH 7.2) with Carborundum and used to inoculate a host range that included Chenopodium amaranticolor, C. quinoa, Gomphrena globosa, Datura stramonium, and Nicotiana benthamiana. Systemic symptoms were seen in C. quinoa (necrotic lesions), G. globosa (stunting), D. stramonium (chlorotic ringspots), and N. benthamiana (wavy line patterns) 1 to 2 weeks after inoculation. C. amaranticolor showed only small necrotic local lesions. In further host range studies, systemic infections of Beta vulgaris, D. metaloides, Lactuca sativa, N. clevelandii, Pisum sativus, Petunia hybrida, Zinnia elegans (symptomless), and Cucumis sativa were observed. However, no infection of Zea mays, Verbena hybrida, Glycine max, Phaseolus vulgaris, Catharanthus roseus, Arachis hypogaea, Trifolium spp., Vigna unguiculata, Vicia faba or Digitalis spp. was detected. Inclusions observed in leaf strips of N. benthamiana and D. stramonium indicated a possible infection of this plant with a nepovirus (1). A 337-bp fragment was amplified from total RNA isolated from an inoculated D. stramonium using reverse transcription-PCR with nepovirus group primers provided by Agdia Inc. (Elkhart, IN). Sequence analysis indicated that the nucleotide (nt) and deduced amino acid (aa) sequences of the fragment were 89 to 91% and 91 to 95% identical, respectively, to sequences of the RNA-dependent RNA polymerase gene for Tobacco ringspot virus (TRSV) contained in GenBank (Accession Nos. U50869 and AJ698718). This region was only 50% (nt) and 38% (aa) identical to Cycas necrotic stunt virus (GenBank Accession No. NC_003791), a nepovirus previously reported to infect cycads (2). The original plant, symptomatic inoculated hosts, and the symptomless zinnia tested positive by double-antibody sandwich-ELISA using commercially available antiserum for TRSV (Agdia, Inc.), further confirming the presence of TRSV. Although the virus infecting Z. furfuracea has a more restricted host range than that reported for TRSV, the serology and gene sequence indicates that this virus is a unique isolate of TRSV.

Leaves displaying bright yellow or light green line pattern symptoms were collected from individual, large, mature buddleias in a home garden in Clemson, SC, a botanical garden in Knoxville, TN, and a container-grown plant on sale in a retail home and garden store in Seneca, SC. Buddleias grown in the southeastern United States frequently display virus-like symptoms, but the line pattern symptom displayed by these plants was atypical of the mosaic, mottling, and leaf deformation seen when buddleias are infected with Alfalfa mosaic virus (AMV) or Cucumber mosaic virus (CMV) (2,4). Line pattern symptoms are frequently seen in woody species infected by ilarviruses or nepoviruses (2). No ilarviruses are reported to infect buddleia and only the nepovirus, Strawberry latent ringspot virus, which is restricted mainly to Europe, is reported to infect this species (1,2). The nepoviruses Tomato ringspot virus (ToRSV) and Tobacco ringspot virus (TRSV) are frequently found infecting plants of many species in the southeastern United States (3). Total RNA was extracted from the three symptomatic plants and used in reverse transcription-polymerase chain reactions (RT-PCR) to detect ToRSV and TRSV using primer pairs developed in this laboratory, which amplify regions around the amino terminus of the coat protein of the respective viruses. The expected amplification product for ToRSV of 327 base pairs was obtained from samples tested from each plant, and the nucleotide sequence of the product showed 96% identity with the corresponding fragment of GenBank Accession No. NC_003839 that the primers were designed to amplify. Repeated attempts to isolate a virus from symptomatic leaves using sap inoculation to Chenopodium amaranticolor Coste & Reyne, C. quinoa Willd, Nicotiana clevelandii Gray, and N. tabacum L. have failed. Repeated testing by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) of leaves from the plant growing in Clemson consistently produced absorbance values at 405 nm in the range of 0.47 to 0.55 (mean of 8 separate samples per test) for symptomatic and asymptomatic leaves. The range of values for the positive control (ToRSV-G growing in N. clevelandii) was 1.3 to 1.5. The ranges of values for the noninfected controls (noninfected N. clevelandii and leaf tissue from a buddleia known to be infected with AMV and CMV but in which ToRSV or TRSV had never been detected by RT-PCR) were 0.102 to 0.104 and 0.102 to 0.106, respectively. The extraction buffer produced absorbance readings in the range of 0.098 to 0.102. RT-PCR of RNA extracted from other portions of the leaves used in the ELISA consistently amplified the 327-bp product from symptomatic leaves and from the positive control but not from noninfected control tissues. RNA from asymptomatic leaves on the infected plant also produced the 327-bp product in RT-PCR. Isolation of viruses from woody hosts is frequently difficult, and although, we have yet to succeed to confirm the association between the observed symptom and ToRSV, the evidence from PCR and ELISA would indicate ToRSV is present in these plants. To our knowledge, this is the first report of ToRSV, a member of the genus Nepovirus, in buddleia.

We investigated the phylogenetic relationships of the endemic New Zealand (NZ) species of Festuca (Poaceae, Pooideae) by assessing sequence variation from the nuclear internal transcribed spacers (ITS) and a chloroplast intergenic spacer (trnL-trnF) and by measuring DNA content using flow cytometry. The ITS and trnL-trnF data sets were congruent in showing that the NZ species of Festuca have two origins. One group, containing F. coxii, F. luciarum, F. multinodis, and F. ultramafica, is closely related to Festuca sect. Aulaxyper. The other group includes a clade of five endemic species (F. actae, F. deflexa, F. madida, F. matthewsii, F. novae-zelandiae) and one species (F. contracta) with a circumAntarctic distribution. The North American species F. californica is sister to the latter group in the trnL-trnF phylogeny but not so in the ITS phylogeny. The differentiation of endemic NZ species into two groups is supported by differences in chromosome number and genome size, the latter showing an inverse relationship to ploidy level. We discuss the ecology and biogeography of NZ's endemic species of Festuca. Origin from Northern Hemisphere ancestors via dispersal to NZ through the American continents is a plausible hypothesis based on current information.

A virus with filamentous particles ca. 700 nm long, denoted Fig latent virus 1 (FLV-1) is widespread in Apulian (southern Italy) fig orchards, in trees showing or not mosaic symptoms and in symptomless seedlings. This virus was transmitted by sap inoculation to a very restricted range of herbaceous hosts without inducing apparent symptoms. It was successfully purified from root tissues of infected figs. A virus-specific antiserum raised in rabbits, proved useful for its detection in fig leaf dips by immunosorbent electron microscopy. The cytology of infected cells was little affected. Bundles of filamentous particles were observed in the cytoplasma of parenchyma cells of infected fig trees and seedlings. The viral genome is a single-stranded positive-sense RNA with an estimated size of ca. 8,000 nt, 6,620 of which have been sequenced, starting from the polyadenylated 3’ terminus. Genomic RNA consists of four open reading frames encoding, in the 5’?3’ direction, the replication-associated proteins (ORF 1), a 43 kDa putative movement protein (ORF 2), the 46 kDa coat protein (ORF 3), and a 12 kDa protein with nucleic acid binding properties. The viral genome structure and organization resembles that of members of the genus Trichovirus, family Flexiviridae and, indeed, FLV- 1 clusters with trichoviruses in phylogenetic trees constructed with coat protein sequences. However, a distinct difference with all members of the genus rests with the size of the coat protein subunits (46 versus 22-27 kDa) and the presence of ORF 4, which is present only in three tentative species of this genus.

In 2006, primocane stunted growth and crumbly berry development were observed on 4-year-old Kiowa and Apache blackberry cultivars grown at the Chilton Research and Extension Center, Clanton, AL. Samples from affected plants were tested for virus infection by ELISA kits (Agdia, Inc., Elkhart, IN) specific to each of 14 different viruses. Most samples tested positive for Tobacco ringspot virus (TRSV). TRSV was detected in blackberry samples from North Carolina and South Carolina (2). Bray et al. (1) studied the incidence of viruses in blackberry nursery stock in the United States and reported that 9% of the tested samples contained TRSV. Thus, a survey was conducted for TRSV incidence among commercial blackberry stands in eight counties in Alabama during July 2007. Blackberry plants were observed to express virus-like symptoms including chlorotic spots on leaves, leaf veinal chlorosis, stunting, and combinations thereof. Fruit-bearing plants sometimes had crumbly fruit symptoms characteristic of virus infection. Leaf samples that were collected from symptomatic and nonsymptomatic plants representing 14 cultivars were tested by TRSV ELISA (Agdia, Inc.). Of 180 blackberry samples, 68 tested positive for TRSV. Positive ELISA reactions for TRSV were on average 28 times greater than the reactions of known negative control samples considered negative for TRSV. Blackberry plants shown to be infected with TRSV during the 2007 survey were tested in July 2008 in an effort to confirm the presence of TRSV. Fifty-four percent of the samples tested positive by ELISA with the average positive ELISA value being 21 times higher than the average negative ELISA value for known negative control samples. To further confirm the occurrence of TRSV in Alabama-grown blackberry plants, leaf samples were tested by reverse transcription (RT)-PCR to amplify a 329-bp fragment of the viral coat protein gene (TRSV RNA 2 sequence accession no. NC_005096; primers TRSCP-F (5'-TCTGGCACTATAAGCGGAAG-3') and TRSCP-R (5'-GAAAACATGGGAGGATGCAC-3'). A single band of the anticipated size was amplified (analyzed by agarose gel electorphoresis and visualized by ethidium bromide staining) from RNA samples extracted with a RNeasy Mini kit (Qiagen, Valencia, CA) from blackberry samples that tested positive for TRSV by ELISA and a known positive control. No amplified product resulted from a blackberry sample that tested negative for TRSV by ELISA. These results illustrate and confirm the presence of TRSV in blackberry leaf tissues grown in Alabama. To our knowledge, this is the first report of TRSV infection of blackberry plants in Alabama.

Molecular and morphological techniques were used to examine New Zealand ascomycetous truffle (Tuber spp.) samples deposited in the Plant & Food Research and Landcare Research Fungi Herbarium collections. Truffles have been found on the roots of many Northern Hemisphere tree species growing in New Zealand, but not on indigenous plant species. Comparisons of ribosomal DNA sequences proved to be a simple and rapid method to identify the Tuber species. Tuber maculatum was by far the predominant species in New Zealand, and was distributed throughout the country. A single truffle sample from Christchurch was identified as T. rufum. Two other groups of truffle samples from Pinus spp. were closely related to anonymous Northern Hemisphere Tuber sequences. Ascocarps with these sequences have not previously been described. Specific primers for the PCR detection of these Pinus isolates were developed. None of these Tuber species accidentally introduced to New Zealand is of economic value.

Four o'clock (Mirabilis jalapa) and M. himalaica var. chinensis are members of the family Nyctaginaceae and are widely distributed weeds in Yunnan Province, China. In 2009, mosaic and malformation symptoms were observed on leaves of the four o'clock on the campus of Yunnan Agricultural University and in the Black Dragon Pool Park in Kunming City, China. More than 30% of the four o'clock plants showed symptoms of the disease. Sap from leaves of symptomatic four o'clock plants caused local chlorotic and necrotic lesions in inoculated Chenopodium amaranticolor after 7 to 10 days and systemic mosaic symptoms in C. quinoa and Nicotiana benthamiana after 10 to 12 days. No symptoms were observed following inoculation of sap from asymptomatic plants. A pure virus isolate (MJ) was obtained after three successive single-lesion transfers from C. amaranticolor. Following mechanical inoculation of the MJ isolate, seedlings of indicator plants, N. benthamiana, displayed mosaic symptoms. Moreover, back transmission to healthy four o'clock seedlings by leaf extracts from systemically infected N. benthamiana plants caused similar mosaic and malformation symptoms. Flexuous, filamentous particles (650 to 700 nm long and 13 nm wide) and cytoplasmic laminar aggregates and pinwheel inclusions typical of members of the genus Potyvirus were observed in infected four o'clock leaves by electron microscopy. No other virus particles were observed. Serological testing of 10 symptomatic and healthy plants using a monoclonal antibody specific for Potyvirus group members in an indirect ELISA (Agdia Inc., Elkhart, IN) also resulted in positive reactions in infected leaves, however, all healthy seedlings tested were negative. Total RNAs were extracted from infected four o'clock leaves with the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) and the 3'-terminal portion of the viral genome (including part of the NIb polymerase, the entire coat protein (CP), and 3'-UTR) was then amplified by reverse transcription-PCR with a universal Potyviridae primer Sprimer/M4 and an M4T as the initial primer (2). A fragment of 1,720 nucleotides long were separated, purified, and cloned and three independent clones were sequenced (GenBank Accession No. JN250997). Nucleotide and amino acid sequence analysis of the putative CP gene, respectively, revealed 75.1 to 76.3% and 80.3 to 82.1% identity with the Basella rugose mosaic virus (BaRMV) (GenBank Accession Nos. DQ821938, DQ394891, and DQ821939), 77.4 and 81.0% identity with Peace lily mosaic virus (GenBank Accession No. DQ851494), and 76.0 and 81.7% identity with the Phalaenopsis chlorotic spot virus (GenBank Accession No. HM021142). However, on the basis of the CP gene sequence analyses, these three viruses shared high (>88.5 and >94.3%) CP nucleotide and amino acid identity and should be classified as the same Potyvirus species. According to the species demarcation criteria for the Potyviridae (1), the pathogen causing mosaic and malformation symptoms on four o'clock was BaRMV (3). To our knowledge, this is the first report of BaRMV in four o'clock.

Pawpaw (Asimina triloba (L.) Dunal, Annonaceae) is a fruit tree native to eastern North America, increasingly grown for commercial production in the United States (Callaway, 1992; Layne, 1996), Europe, and Western Asia (Brannan and Coyle, 2021; Lolletti et al., 2021). In 2012, virus-like symptoms were noticed in a 0.3 ha pawpaw orchard at Michigan State University Plant Pathology Research Station; ~30% of the trees presented symptoms which included foliar mosaic, vein yellowing, and necrosis, and were first mistaken for nutrient (magnesium/zinc) deficiency. Trees were treated for magnesium/zinc deficiency but continued to decline in fruit yield and overall vigor, and typically died within 3─4years after symptoms were first observed (Fig. S1). Preliminary testing using Agdia ImmunoStrips for cucumber mosaic virus, impatiens necrotic spot virus, tobacco mosaic virus, tomato spotted wilt virus and the genus Potyvirus were negative. However, icosahedral virus particles were observed by TEM (Fig. S2). To establish virus identity, we deep-sequenced tissue from a symptomatic pawpaw obtained from same site in summer 2021. Virus particles were purified , and virion-associated nucleic acids (VANA) were extracted using the Purelink viral RNA/DNA kit (Invitrogen) (Maclot et al., 2021). Both viral RNA and DNA were subjected to high-throughput sequencing (HTS) on the Illumina NextSeq 500 platform (GIGA, University of Liege, Belgium). A total of 574,274 trimmed reads (150 nt read length) were de novo assembled using Geneious Prime 2022.2.2 software (https://www.geneious.com) and subjected to BLASTn analysis. Two contigs of 7511 bp (average coverage: 1048) and 3924 bp (average coverage: 3012) showed 94% and 95% nt identities with tobacco ringspot virus (TRSV) RNA1 isolate YW (MT042825) and RNA2 isolate OH19 (MT561435) respectively. These two contigs (Accession no. OP589177 and OP589178) covered the complete TRSV genome for each segment. HTS found no other plant-associated viral / virus-like sequences in this symptomatic pawpaw sample. To further confirm TRSV infection, leaf extract from this sample was tested with RT-PCR using primers specific to the RdRp gene of TRSV RNA1 (Forward, 5'-TAACCTCATTGCAGTTGATCCTT-3'; Reverse, 5'-TAATTCAAGCTCAGGTCTCTTCT-3'; 739 bp amplicon) and the coat protein of TRSV RNA2 (Forward, 5'-TCATGCTTAAAGATGCAGATGTG-3'; Reverse, 5'-TATAAAGCTCCGCACTAGAAAACA-3'; 753 bp amplicon). Sanger sequence analysis showed 99.5% and 99.8% nt identity between the amplicons and the HTS contigs (RNA1 and RNA2 respectively) assembled from the pawpaw sample, and the amplicons likewise matched GenBank TRSV sequences (91.7% and 95.6% nt identities respectively with TRSV RNA1 isolate CmTX-H (MN504766) and TRSV RNA2 isolate IA-1-2017 (MT563079)). We further screened for TRSV infection in leaves from four symptomatic and three non-symptomatic pawpaw trees collected from the same site in 2022. RT-PCR revealed positive infection in all four symptomatic samples and one of the three (33%) non-symptomatic samples. Our results confirm the presence of TRSV infection in symptomatic pawpaw trees and emphasize the importance of also monitoring non-symptomatic trees. We confirmed graft transmission with 100% transmission rate observed in 200 trees grafted from a TRSV-infected pawpaw (Shenandoah cultivar), and investigation of other transmission vectors is on going. Because of TRSV's wide host range (Tolin, 2008), its broad transmission profile in other crops (via nematodes, thrips, seeds, sap inoculation, and grafting) (Hill and Whitham, 2014), and the notable decline observed in infected pawpaws from different cultivars (10-35, NC-1, Overleese, Pennsylvania-Golden, Shenandoah, Sunflower, Wabash), TRSV appears to pose a new threat to pawpaw orchards. To the best of our knowledge, this is the first report of TRSV infecting pawpaw in North America and the world.

Previous work has shown that the presence of excess coat protein (CP) of cucumber mosaic virus (CMV) in the chloroplasts was related with mosaic symptoms. However, whether these mosaic symptoms are directly induced by the interaction between CP and chloroplasts is unknown. To directly demonstrate the interaction between CP and the chloroplast, Synechocystis sp. PCC 6803 was used as the chloroplast model. The cDNA encoding the CMV‐CP was cloned in a cyanobacterial shuttle vector (pKT‐CP) and transferred to Synechocystis sp. PCC 6803. The CP was expressed in the cyanobacterium with the psbA promoter. The expression of CMV‐CP hindered the growth of transgenic cyanobacterium cells and decreased its photosynthetic rate and the PS II activity. The transgenic cells showed increased fluorescence (F) from the phycobilisome terminal emitters and increased fluorescence (F) from PS II. The absorption spectra at room temperature showed the Chl and the phycocyanin absorption peak of the mutant strain significantly decreased. These results showed that CP may directly affect the cyanobacterium cells and decreased its photosynthesis, especially the PS II activity. These data might provide new evidence for mosaic symptoms being directly induced by the interaction between CP and chloroplasts.

Cotton (Gossypium hirsutum L.) is one of the major cash crops grown in the United States (U.S.) with a total acreage of over 11.5 million acres in 2021 (NASS, 2021). In Oklahoma, cotton represents an important economic crop and was grown on 490,000 acres during the 2021 growing season (NASS, 2021). In 2021, during a survey of a cotton field in Beckham County of Oklahoma, cotton plants showed typical virus-like symptoms including mosaic, yellow ring spots, discoloration and short internodes (Supplementary Fig. 1). Thirteen symptomatic and five asymptomatic samples were collected from cotton plants and brought to the University of Tulsa for further processing. Total RNA was extracted from all samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich). Total RNA from two symptomatic samples (named EC3 and EC4) were subjected to high-throughput sequencing (HTS) on the NextSeq 500/550 High-Output kit v2.5 (Illumina, USA) at the genomic facility, Oklahoma State University (Stillwater, OK, USA). A total of 17,542,322 and 22,572,118 trimmed pair-ends reads for both samples were assembled using CLC Genomics Workbench (v12.0.3) (Qiagen, Inc) and subjected to BLASTn analysis. Two contigs of 556 bp and 1062 bp (average coverage 2,799X) for sample EC3 showed 99% and 91% nucleotide (nt) identities with 3'-UTR, 5'-UTR and P1A gene respectively of the Tobacco ringspot virus (TRSV) RNA1 of isolates WA-AM1 (MW495243.1), and IA-1-2017 (MT563078.1) respectively. The other two contigs, 221 bp and 561 bp (average coverage 23,070X) for sample EC4 showed, 100% and 96% nt identities with 3'-UTR, protease, and RdRp genes of TRSV RNA1, isolates WA-AM1 and YW (MT042825.1) respectively. The HTS data did not reveal any other viral sequence in these two cotton samples. To further confirm the presence of TRSV in these samples, previously designed specific primers to TRSV (Forward: 5'-GGAAATTAACTGGGATGATTT-3' and Reverse: 5'-GAGCTCCAACCTTAAAACCA-3') for RNA1, targeting the P1A and helicase genes, and another primer pair (Forward: 5'-GCATCCTCCCATGTTTTCT-3' and Reverse: 5'-GGGACAAACACGACACTA-3') for RNA2, targeting the coat protein and 3'-untranslated region, of TRSV were tested by RT-PCR assay. The sizes of amplified PCR products obtained from both isolates (EC3 and EC4) on 1% agarose gel were approximately 1,000 bp for RNA1 and 1,100 bp for RNA2. The amplified PCR products were cloned and three independent recombinant clones for each primer set were analyzed by Sanger sequencing. The resulting consensus sequences were used in a BLASTn search against the Genbank and matched with TRSV sequences. Consensus nt sequences analysis specific to RNA1 of EC3 isolate (Accession no. OM563300) and EC4 isolate (Accession no OM563301) showed 97% nt identities with TRSV isolate IA-1-2017. Consensus nt sequences specific to RNA 2 of EC3 isolate (Accession no. OM630605) and EC4 isolate (Accession no OM5630606) showed 92% and 90% nt identities with the corresponding sequences of WA-AM1 and IA-1-2017 isolates respectively. Further screening of the remaining 11 symptomatic samples resulted in two more positive TRSV samples that were co-infected with Cotton leafroll dwarf virus (CLRDV), six were positive to only CLRDV, and three were negative to both viruses by RT-PCR assay using the above TRSV specific primers and CLRDV specific primers AL674F/1407R (Avelar et al. 2019). None of the asymptomatic cotton samples were positive by RT-PCR to TRSV or CLRDV. Our results confirmed the presence of TRSV infection in these symptomatic cotton plants. The presence of TRSV could pose a new threat to cotton crops in Oklahoma and the U.S. due to its wide host range (Adam and Antoniw, 2005), and transmission through many vectors including nematodes, (Keinath et al. 2017), and seed (Hill and Whitman, 2014). To the best of our knowledge, this is the first report of TRSV infecting cotton naturally in the U.S. and in the world.

Carnation (Dianthus caryophyllus) is a popular ornamental plant widely used as a cut flower and in landscaping. In New Zealand, several viruses are known to infect plants of the genus Dianthus: arabis mosaic virus, carnation etched ring virus (CERV), carnation latent virus, carnation mottle virus, carnation necrotic fleck virus, carnation ringspot virus, carnation vein mottle virus and cucumber mosaic virus (Veerakone et al. 2015). In October 2020, a carnation sample with leaf chlorotic spots and distortion from a home garden in Auckland, New Zealand was submitted to the Plant Health and Environment Laboratory (PHEL) for virus testing. Leaf tissue of the sample was mechanically inoculated onto a range of herbaceous species using the method described in Tang et al. (2013). Chenopodium amaranticolor and C. quinoa plants developed local necrotic pinpoint spots while Nicotiana benthamiana, N. clevelandii, and N. occidentalis plants exhibited systemic leaf mosaic symptoms 7 days post-inoculation. The carnation plant and all five symptomatic indicator species tested positive for tombusviruses using an in-house designed generic RT-qPCR (available on request). Direct sequencing of the ~140 bp PCR product revealed the presence of grapevine Algerian latent virus (GALV). To further characterise the detected sequence, forward (5'-GTAGCGATGTATTGGGATAAGGA-3') and reverse (5'-TGCCGACACCCCGAAAGGT-3') primers were designed based on an alignment of the conserved region in the coat protein (CP) of 19 GALV isolates deposited in GenBank. Products of the expected size of 406 bp were amplified from all infected plants and their sequences found to be identical (GenBank accession No. OM891837). BLAST searches showed that the CP region of the sequence shared 97.0% (nucleotide) and 97.8% (amino acid) identity to the type isolate of GALV (GenBank accession no. NC_011535). GALV was first reported in Italy from a symptomless Algerian grapevine (Vitis vinifera) (Gallitelli et al., 1989), and is the only report of GALV in Vitis in the world. Since then, GALV has been reported in Germany, the Netherlands and Japan in several ornamental plant species including Alstroemeria sp. (Tomitaka et al., 2016), Gypsophila paniculata, Limonium sinuatum (Koenig et al., 2004, Fujinaga et al., 2009) and Solanum mammosum (Ohki et al., 2006). These infected ornamental host plants were reported to show various types of foliar symptoms, including chlorotic leaf spots. The GALV-infected carnation plant in this study was tested by PCR for all viruses that are known to infect D. caryophyllus in New Zealand, and CERV was identified. It is therefore unclear if the observed symptoms were induced by either GALV or CERV, or if they were the results of a synergistic interaction between GALV and CERV. Samples from a further 11 plants, comprised of nine symptomatic Dianthus spp. and two asymptomatic Alstroemeria spp. were collected from the same address and tested individually using the GALV-specific RT-PCR. GALV (along with CERV) was detected from all Dianthus plants while the Alstroemeria samples were negative. To our knowledge, this is the first report of GALV in New Zealand, and the first report in the host Dianthus in the world. Given the GALV-infected carnation plants were purchased from a local garden centre between 2007-2020, and plants from this garden centre have been widely distributed over this period of time to various customers, the virus is very likely to have spread throughout the country.

Grapevine leafroll-associated virus-3 (GLRaV-3) is considered the most predominant cause of grapevine leafroll disease (GLD), one of the most destructive viral diseases affecting grapevines and wine production worldwide (Maree et al. 2013). GLRaV-3 is a positive-sense, single-stranded RNA (+ssRNA) virus in the family Closteroviridae, genus Ampelovirus, species tritis (Martelli et al., 2012; Maree et al., 2013). Grape plants (cultivar ‘Errante Noir’) were planted at the Chilton Research and Extension Center (CREC), Chilton County, Alabama, in the spring of 2024. In November 2024, a plant exhibited symptoms of dark-purplish red veins with cupping of the leaf margins, and in July 2025, symptoms of reddish-brown blotches randomly distributed on the foliage appeared (Supplemental Figure 1: A: I-II). To investigate if a pathogen caused this, a sample was sent to Agdia, Inc. (Elkhart, IN, USA), where tissues were subjected to a pathogen screen, including alfalfa mosaic virus (AMV), arabis mosaic virus (ArMV), grapevine fanleaf virus (GFLV), Phytophthora (Phyt), peach rosette mosaic virus (PRMV), strawberry latent ringspot virus (SLRSV), tomato ringspot virus (ToRSV), tobacco ringspot virus (TRSV), GLRaV-3, grapevine pinot gris virus (GPGV), grapevine red blotch-associated virus (GRBaV), and Xylella fastidiosa (Xf). The sample tested negative for all except for GLRaV-3. To confirm GLRaV-3, RT-PCR was used. Total RNA was extracted from 0.1 g petiole tissue from three subsamples using the RNeasy Plant Mini Kit (Qiagen), producing three separate RNA samples. The cDNA was synthesized using SuperScript IV Reverse Transcriptase (Invitrogen), and Platinum Taq DNA Polymerase (Invitrogen) was used to amplify the heat shock protein (HSP70) and the coat protein (CP) using specific primers (Thompson et al. 2019). PCR products were checked on the TapeStation using the D1000 ScreenTape kit (Agilent), and amplicons corresponding to 600 bp (HSP70) and 280 bp (CP) were detected (Supplemental Figure 1: B). Sanger sequencing was conducted at Azenta Life Sciences in both directions. The manufacturer’s instructions were followed in all used kits. Sequences were analyzed using BLASTn (Altschul et al. 1990) to confirm that all three sequences from each gene match GLRaV-3. Sequences were submitted to GenBank (accessions: PX123059-64), and an isolate name was given (GLRaV-3_Chilton-AL.1.1-3). The closest BLAST hit is GLRav3-8415B (KY073324.1) with 100% (HSP70), 98.24% (CP) nucleotide similarities (Supplemental Table 1). The CP sequences of GLRaV-3_Chilton-AL.1.1-3 were compared to 139 isolates of GLRaV-3 from GenBank (Supplemental Table 1) to construct a maximum likelihood tree using methods described by Shehata et al. (2025), with a modification where IQ-TREE was used to construct the tree with 1000 replicates (Nguyen et al. 2015). This tree indicated that GLRaV-3_Chilton-AL.1.1-3 is within group XII, with two isolates from Canada (Supplemental Figure 1: C). Other grape plants planted along with the infected plant at the Chilton Co. site (n=15) were also tested for GLRaV-3 as described above, and all tested negative. This constitutes the first report of GLRaV-3 in Alabama, highlighting the importance of purchasing clean material to prevent introduction of the disease in vineyards, a crop with a total impact of $1.5 billion in Alabama (Good, T. 2023).