Comparing RT-PCR of individual samples with high throughput sequencing of pooled plant samples for field-level surveillance of viruses in blackberry and wild Rubus

Blackberry production is increasing in the southeastern U.S. with the availability of new cultivars. In addition to high production costs, growers are challenged by virus diseases. Blackberry yellow vein disease (BVYD) significantly limits blackberry production. BYVD is associated with the crinivirus blackberry yellow vein-associated virus (BYVaV) in mixed infections with other viruses. The specific disease etiology and ecological factors underlying BYVD are not well understood and rely on the effective diagnosis of several viruses involved in the complex. In 2021, we collected samples from blackberry plants showing BYVD symptoms, asymptomatic blackberry plants, and wild Rosaceae spp. from nine farms across South Carolina, for a total of 372 individual plant samples. RNA from individual samples was isolated and pooled into sample groups (i.e., symptomatic, asymptomatic, and wild) from each farm for a total of 24 pooled samples. We sequenced the pooled RNA using Illumina and analyzed sequence profiles using the Virtool bioinformatics application. We also tested each plant for six viruses by RT-PCR or RT-qPCR and compared plant (PCR)-level and field (high throughput sequencing (HTS))-level data. Virtool detected 17 known viruses in the pooled samples, including 11 blackberry viruses. PCR testing was mostly consistent with HTS, with some notable disagreements for specific viruses. Our study demonstrates that HTS could be used as an efficient tool to detect viruses in bulked samples in blackberry fields, though limitations to using HTS for field-level surveillance are also discussed here.

Detection and characterization of Xylella fastidiosa subsp. fastidiosa in rabbiteye blueberry in South Carolina

Xylella fastidiosa causes bacterial leaf scorch in southern highbush (Vaccinium corymbosum interspecific hybrids) and is also associated with a distinct disease phenotype in rabbiteye blueberry (V. virgatum) cultivars in the southeastern U.S. Both subspecies X.f. fastidiosa and X.f. multiplex have been reported to cause problems in southern highbush blueberry, but so far only X.f. multiplex has been reported in rabbiteye cultivars in Louisiana. In this study, we report detection of X. fastidiosa in rabbiteye blueberry plants in association with symptoms of foliar reddening and shoot dieback. High throughput sequencing of a X. fastidiosa-positive plant sample and comparative analyses identified the strain in one of these plants as being X. fastidiosa subspecies fastidiosa. We briefly discuss the implications of these findings, which may spur research into blueberry as a potential inoculum source that could enable spread to other susceptible fruit crops in South Carolina.

Analysis of Cotton Leafroll Dwarf Virus P0 Gene Sequences from South Carolina Reveals Low Variability Among Isolates

Cotton leafroll dwarf virus (CLRDV) is emerging across the major cotton-producing states of the southern United States. Because it was detected in nearly all cotton-producing states within a few years of its initial detection in the United States, the spread of the virus has apparently occurred rapidly. In this study spanning three growing seasons in South Carolina, we collected CLRDV isolates from symptomatic and asymptomatic cotton plants in 10 counties. The genomic region encoding P0, the viral suppressor of RNA silencing, was sequenced and compared among CLRDV isolates. Low variability among CLRDV P0 sequences from South Carolina isolates with similarities to other United States isolates was revealed by amino acid sequence alignment and phylogenetic analysis. Low variability among South Carolina isolates was also confirmed by sequencing a subset of eight near-complete genomes of CLRDV isolates. Although sequence variability was low among South Carolina isolates, this data should be taken in the context of all United States isolates, for which diversity may be higher than initially expected. Sequences gathered in this study add to the body of knowledge on CLRDV diversity in the United States.

Bees and thrips carry virus-positive pollen in peach orchards in South Carolina, United States

Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV) are pollen-borne viruses of important stone fruit crops, including peaches, which can cause substantial yield loss. Although both horizontal and vertical (i.e., seed) transmission of both viruses occurs through pollen, the role of flower-visiting insects in their transmission is not well understood. Bees and thrips reportedly spread PNRSV and PDV in orchards and greenhouse studies; however, the field spread of PNRSV and PDV in peach orchards in the southeastern United States is not explored. We hypothesized that bees and thrips may facilitate virus spread by carrying virus-positive pollen. Our 2-yr survey results show that 75% of captured bees are carrying virus-positive pollen and moving across the orchard while a subsample of thrips were also found virus positive. Based on morphology, Bombus, Apis, Andrena, Eucera, and Habropoda are the predominant bee genera that were captured in peach orchards. Understanding the role of bees and thrips in the spread of PNRSV and PDV will enhance our understanding of pollen-borne virus ecology.

Prevalence and Genetic Diversity of Grabloviruses in Free-Living Vitis spp

The distribution and diversity of grapevine red blotch virus (GRBV) and wild Vitis virus 1 (WVV1) (genus Grablovirus; family Geminiviridae) were determined in free-living Vitis spp. in northern California and New York from 2013 to 2017. Grabloviruses were detected by polymerase chain reaction in 28% (57 of 203) of samples from California but in none of the 163 samples from New York. The incidence of GRBV in free-living vines was significantly higher in samples from California counties with high compared with low grape production (χ² = 83.09; P < 0.001), and in samples near (<5 km) to compared with far (>5 km) from vineyards (χ² = 57.58; P < 0.001). These results suggested a directional spread of GRBV inoculum predominantly from vineyards to free-living Vitis spp. WVV1 incidence was also significantly higher in areas with higher grape production acreage (χ² = 16.02; P < 0.001). However, in contrast to GRBV, no differential distribution of WVV1 incidence was observed with regard to distance from vineyards (χ² = 0.88; P = 0.3513). Two distinct phylogenetic clades were identified for both GRBV and WVV1 isolates from free-living Vitis spp., although the nucleotide sequence variability of the genomic diversity fragment was higher for WWV1 (94.3 to 99.8% sequence identity within clade 1 isolates and 90.1 to 100% within clade 2 isolates) than GRBV (98.3% between clade 1 isolates and 96.9 to 100% within clade 2 isolates). Additionally, evidence for intraspecific recombination events was found in WVV1 isolates and confirmed in GRBV isolates. The prevalence of grabloviruses in California free-living vines highlights the need for vigilance regarding potential grablovirus inoculum sources in order to protect new vineyard plantings and foundation stock vineyards in California.

Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease

Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch's postulates and revealed the causative role of GRBV in red blotch disease.