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

 

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dc.contributor.author Candresse, Thierry en_ZA
dc.contributor.author Filloux, Denis en_ZA
dc.contributor.author Muhire, Brejnev en_ZA
dc.contributor.author Julian, Charlotte en_ZA
dc.contributor.author Galzi, Serge en_ZA
dc.contributor.author Fort, Guillaume en_ZA
dc.contributor.author Bernardo, Pauline en_ZA
dc.contributor.author Daugrois, Jean-Heindrich en_ZA
dc.contributor.author Fernandez, Emmanuel en_ZA
dc.contributor.author Martin, Darren P en_ZA
dc.date.accessioned 2015-12-28T06:47:33Z
dc.date.available 2015-12-28T06:47:33Z
dc.date.issued 2014 en_ZA
dc.identifier.citation Candresse, 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.0102945 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16034
dc.identifier.uri http://dx.doi.org/10.1371/journal.pone.0102945
dc.description.abstract 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. en_ZA
dc.language.iso eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights This 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.uri http://creativecommons.org/licenses/by/4.0 en_ZA
dc.source PLoS One en_ZA
dc.source.uri http://journals.plos.org/plosone en_ZA
dc.subject.other Small interfering RNAs en_ZA
dc.subject.other Plant genomics en_ZA
dc.subject.other Quarantines en_ZA
dc.subject.other Plant viral pathogens en_ZA
dc.subject.other RNA sequencing en_ZA
dc.subject.other Viral structure en_ZA
dc.subject.other Nucleic acids en_ZA
dc.subject.other Structural genomics en_ZA
dc.title Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2014 Candresse et al en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image


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This 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. Except where otherwise noted, this item's license is described as This 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.