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Shushan A, Luria N, Lachman O, Sela N, Laskar O, Belausov E, Smith E, Dombrovsky A. Characterization of a novel psyllid-transmitted waikavirus in carrots. Virus Res 2023; 335:199192. [PMID: 37558054 PMCID: PMC10448213 DOI: 10.1016/j.virusres.2023.199192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/19/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
Carrots collected from the Western Negev region in Israel during the winter of 2019 showed disease symptoms of chlorosis, leaf curling, a loss of apical dominance, and multiple lateral roots that were not associated with known pathogens of the carrot yellows disease. Symptomatic carrots were studied for a possible involvement of plant viruses in disease manifestations using high throughput sequencing analyses. The results revealed the presence of a waikavirus, sharing a ∼70% nucleotide sequence identity with Waikavirus genus members. Virions purified from waikavirus-positive carrots were visualized by transmission electron microscopy, showing icosahedral particle diameter of ∼28 nm. The genome sequence was validated by overlapping amplicons by designed 12 primer sets. A complete genome sequence was achieved by rapid amplification of cDNA ends (RACE) for sequencing the 5' end, and RT-PCR with oligo dT for sequencing the 3' end. The genome encodes a single large ORF, characteristic of waikaviruses. Aligning the waikavirus-deduced amino-acid sequence with other waikavirus species at the Pro-Pol region, a conserved sequence between the putative proteinase and the RNA-dependent RNA polymerase, showed a ∼40% identity, indicating the identification of a new waikavirus species. The amino-acid sequence of the three coat proteins and cleavage sites were experimentally determined by liquid chromatography-mass spectrometry. A phylogenetic analysis based on the Pro-Pol region revealed that the new waikavirus clusters with persimmon waikavirus and actinidia yellowing virus 1. The new waikavirus genome was localized in the phloem of waikavirus-infected carrots. The virus was transmitted to carrot and coriander plants by the psyllid Bactericera trigonica Hodkinson (Hemiptera: Triozidae).
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Affiliation(s)
- Ariel Shushan
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel; The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of University of Jerusalem, Rehovot 761001, Israel
| | - Neta Luria
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
| | - Oded Lachman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
| | - Noa Sela
- Bioinformatics Unit, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, P.O.B 19, Ness Ziona 74100, Israel
| | - Eduard Belausov
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Elisheva Smith
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel.
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Barnard TR, Wang AB, Sagan SM. A highly sensitive strand-specific multiplex RT-qPCR assay for quantitation of Zika virus replication. J Virol Methods 2022; 307:114556. [PMID: 35654259 DOI: 10.1016/j.jviromet.2022.114556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro. Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B Wang
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
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Uddin F, Srivastava M. Strand-specific detection of overlapping transcripts via purification involving denaturation of biotinylated cDNA. Biotechniques 2020; 69:141-7. [PMID: 32372698 DOI: 10.2144/btn-2020-0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Reverse transcription-PCR (RT-PCR) is the most widely employed technique for gene expression analysis owing to its high sensitivity, easy reproducibility and fast output. It has been conceived that priming RT reactions with gene-specific primers generates cDNA only from the specific RNA. However, several reports have revealed that cDNA is synthesized even without addition of exogenous primers in RT reactions. Owing to such self-priming activity, the signals from specific strands cannot be accurately detected and can confound the expression analysis, especially in context of overlapping bidirectional transcripts. Here, we demonstrate that purification of biotin-tagged cDNA in conjunction with alkaline denaturation can obviate the problem of background priming and enable accurate strand-specific detection of overlapping transcripts.
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