Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context

dc.contributor.authorCandresse, T
dc.contributor.authorFilloux, D
dc.contributor.authorMuhire, B
dc.contributor.authorJulian, C
dc.contributor.authorGalzi, S
dc.contributor.authorFort, G
dc.contributor.authorBernardo, P
dc.contributor.authorDaugrois, J-H
dc.contributor.authorFernandez, E
dc.contributor.authorMartin, D P
dc.contributor.authorVarsani, A
dc.contributor.authorRoumagnac, P
dc.date.accessioned2016-08-11T14:48:02Z
dc.date.available2016-08-11T14:48:02Z
dc.date.issued25
dc.date.updated2016-08-11T11:55:04Z
dc.description.abstractComprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share .91% genomewide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.en_ZA
dc.identifierhttp://dx.doi.org/10.1371/journal.pone.0102945
dc.identifier.apacitationCandresse, T., Filloux, D., Muhire, B., Julian, C., Galzi, S., Fort, G., ... Roumagnac, P. (25). Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. <i>PLoS ONE</i>, http://hdl.handle.net/11427/21205en_ZA
dc.identifier.chicagocitationCandresse, T, D Filloux, B Muhire, C Julian, S Galzi, G Fort, P Bernardo, et al "Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context." <i>PLoS ONE</i> (25) http://hdl.handle.net/11427/21205en_ZA
dc.identifier.citationCandresse, T., Filloux, D., Muhire, B., Julian, C., Galzi, S., Fort, G., ... & Varsani, A. (2014). Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PloS one, 9(7), e102945.en_ZA
dc.identifier.issn1932-6203en_ZA
dc.identifier.ris TY - Journal Article AU - Candresse, T AU - Filloux, D AU - Muhire, B AU - Julian, C AU - Galzi, S AU - Fort, G AU - Bernardo, P AU - Daugrois, J-H AU - Fernandez, E AU - Martin, D P AU - Varsani, A AU - Roumagnac, P AB - Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share .91% genomewide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations. DA - 25 DB - OpenUCT DP - University of Cape Town J1 - PLoS ONE LK - https://open.uct.ac.za PB - University of Cape Town PY - 25 SM - 1932-6203 T1 - Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context TI - Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context UR - http://hdl.handle.net/11427/21205 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21205
dc.identifier.vancouvercitationCandresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, et al. Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS ONE. 25; http://hdl.handle.net/11427/21205.en_ZA
dc.languageengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsCreative Commons Attribution 4.0 International (CC BY 4.0)*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_ZA
dc.sourcePLoS ONEen_ZA
dc.source.urihttp://journals.plos.org/plosone/s/journal-information
dc.titleAppearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine contexten_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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