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

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dc.contributor.authorCandresse, Thierryen_ZA
dc.contributor.authorFilloux, Denisen_ZA
dc.contributor.authorMuhire, Brejneven_ZA
dc.contributor.authorJulian, Charlotteen_ZA
dc.contributor.authorGalzi, Sergeen_ZA
dc.contributor.authorFort, Guillaumeen_ZA
dc.contributor.authorBernardo, Paulineen_ZA
dc.contributor.authorDaugrois, Jean-Heindrichen_ZA
dc.contributor.authorFernandez, Emmanuelen_ZA
dc.contributor.authorMartin, Darren Pen_ZA
dc.date.accessioned2015-12-28T06:47:33Z
dc.date.available2015-12-28T06:47:33Z
dc.date.issued2014en_ZA
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% genome-wide 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.identifier.apacitationCandresse, T., Filloux, D., Muhire, B., Julian, C., Galzi, S., Fort, G., ... Martin, D. P. (2014). 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/11427/16034en_ZA
dc.identifier.chicagocitationCandresse, Thierry, Denis Filloux, Brejnev Muhire, Charlotte Julian, Serge Galzi, Guillaume Fort, Pauline Bernardo, Jean-Heindrich Daugrois, Emmanuel Fernandez, and Darren P Martin "Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context." <i>PLoS One</i> (2014) http://hdl.handle.net/11427/16034en_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. doi:10.1371/journal.pone.0102945en_ZA
dc.identifier.ris TY - Journal Article AU - Candresse, Thierry AU - Filloux, Denis AU - Muhire, Brejnev AU - Julian, Charlotte AU - Galzi, Serge AU - Fort, Guillaume AU - Bernardo, Pauline AU - Daugrois, Jean-Heindrich AU - Fernandez, Emmanuel AU - Martin, Darren 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% genome-wide 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 - 2014 DB - OpenUCT DO - 10.1371/journal.pone.0102945 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2014 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/11427/16034 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16034
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0102945
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. 2014; http://hdl.handle.net/11427/16034.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2014 Candresse et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherSmall interfering RNAsen_ZA
dc.subject.otherPlant genomicsen_ZA
dc.subject.otherQuarantinesen_ZA
dc.subject.otherPlant viral pathogensen_ZA
dc.subject.otherRNA sequencingen_ZA
dc.subject.otherViral structureen_ZA
dc.subject.otherNucleic acidsen_ZA
dc.subject.otherStructural genomicsen_ZA
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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