First report of tobacco rattle virus infecting Weigela florida in the USA

Authors: SALDAGO SERRANO, JOANA - UNIVERSITY OF MINNESOTA; ALVAREZ-QUINTO, ROBERT - OREGON STATE UNIVERSITY; BAUMAN, MATTIE - UNIVERSITY OF MINNESOTA; ARENZ, BRETT - UNIVERSITY OF MINNESOTA; LOCKHART, BENHAM - UNIVERSITY OF MINNESOTA; MOLLOV, DIMITRE

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/19/2023
Publication Date: 6/19/2023
Citation: Saldago Serrano, J., Alvarez-Quinto, R., Bauman, M., Arenz, B., Lockhart, B., Mollov, D.S. 2023. First report of tobacco rattle virus infecting Weigela florida in the USA. Plant Disease. https://doi.org/10.1094/PDIS-02-23-0351-PDN.
DOI: https://doi.org/10.1094/PDIS-02-23-0351-PDN

Interpretive Summary: Weigela is a deciduous shrub used for ornamental purposes in landscape. Ten weigela plants obtained from a commercial nursery were identified with virus-like symptoms. Upon electron microscopy evaluation virus particles were identified from these symptomatic plants. Nucleic acid extraction from the virus particles and consequent analysis confirmed that these plants are infected with tobacco rattle virus (TRV). TRV is a nematode transmitted virus and a pathogen of significant economic importance for crops like potatoes. This finding is useful to help understand the role of additional hosts as reservoirs of pathogens that affect cultivated crops.

Technical Abstract: Weigela (Weigela florida (Bunge) A. DC., Family: Caprifoliaceae) are woody shrubs native to North China, Korea, and Japan. They are commonly used as landscape ornamental plants (McNamara et al. 2010). Two viruses have been reported in weigela, tomato spotted wilt orthotospovirus and impatiens necrotic spot orthotospovirus (Sastry et al. 2019). Ten weigela plants, originating from commercial nurseries in Minnesota, exhibiting chlorosis, chlorotic line patterns, and necrosis were submitted for virus diagnostics at the University of Minnesota Plant Disease Clinic and the Virology Lab during 2019 and 2020 (5 plants each year). Under greenhouse conditions symptoms progressed from chlorosis to necrosis and plant death in some plants. Electron microscopy revealed rod-shaped particles of ˜20 nm in diameter and length between 40-200 nm with similar morphology to members of the genus Tobravirus. Virus-like particles were enriched by ultracentrifugation and total nucleic acids were then extracted from partial purifications by phenol:chloroform extraction (Lockhart et al. 1997). Tobacco rattle virus (TRV) was identified by cloning and sequencing of RT-PCR amplicons (463bp) obtained with TRV detection primers (Robinson 1992). High throughput sequencing (HTS) was implemented to complement TRV detection associated with the weigela symptoms. A cDNA library was prepared using the TruSeq Stranded mRNA kit and sequenced on Illumina NovaSeq 6000 platform as 150 bp-paired end reads. The obtained 44,316,446 raw data reads were preprocessed using the BBDuk plugin and de novo assembled using SPAdes assembler, then viral contigs were identified by BLASTX searches. The assembly of TRV RNA1 was 6,842 nt with 20,627,348 reads (47% of total reads) mapped to it and average coverage per nucleotide at 323,639X. The assembly of TRV RNA2 was 3,033 nt with 22,769,253 reads (52% of total reads) mapped to it and average coverage per nucleotide at 798,660X. NCBI GenBank accession numbers for the assemblies representing RNA1 and RNA2 are OQ408335 and OQ408336, respectively. The weigela TRV genomic RNA segments showed the highest level of nucleotide sequence identity 97% and 99% to RNA1 (GQ903771) and RNA2 (GQ903772) of TRV isolate MI-1 originated in potatoes from Michigan. No other viral contigs were detected from the virion nucleic acid extraction by HTS. In addition to using the detection primers by Robinson 1992, we designed primers based on our HTS data: TRV-WG-DetF3 5’-GACGAAGGAGGCTGTCATTGC-3’ and TRV-WG-DetR3 5’-CGGACTATCGTGATGCCCATGC-3’. RT-PCR amplicons were cloned, sequenced, and confirmed TRV infection in all 10 symptomatic plants. To the best of our knowledge, this is the first report of TRV infecting the ornamental host W. florida worldwide. TRV is a nematode-transmitted viral pathogen of economic importance worldwide (Sastry et al. 2019). In the USA, TRV have been reported on several landscape ornamentals, horticultural crops, and native habitats. Further research is needed to investigate the impact of TRV on the ornamental industry and the role of ornamentals as reservoirs for cultivated crops like potatoes.