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

Thierry Candresse, Denis Filloux, Brejnev Muhire, Charlotte Julian, Serge Galzi, Guillaume Fort, Pauline Bernardo, Jean Heindrich Daugrois, Emmanuel Fernandez, Darren P. Martin, Arvind Varsani, Philippe Roumagnac

Research output: Contribution to journalArticle

43 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere102945
JournalPLoS One
Volume9
Issue number7
DOIs
StatePublished - Jul 25 2014
Externally publishedYes

Fingerprint

Quarantine
High-Throughput Nucleotide Sequencing
Virus Diseases
quarantine
Viruses
Saccharum
viruses
Geminiviridae
Mastrevirus
sugarcane
infection
small interfering RNA
Genes
Small Interfering RNA
Egypt
Genome
Pathogens
genome
Nucleic Acids
high-throughput nucleotide sequencing

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Candresse, T., Filloux, D., Muhire, B., Julian, C., Galzi, S., Fort, G., ... Roumagnac, P. (2014). Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One, 9(7), [e102945]. https://doi.org/10.1371/journal.pone.0102945

Appearances can be deceptive : Revealing a hidden viral infection with deep sequencing in a plant quarantine context. / Candresse, Thierry; Filloux, Denis; Muhire, Brejnev; Julian, Charlotte; Galzi, Serge; Fort, Guillaume; Bernardo, Pauline; Daugrois, Jean Heindrich; Fernandez, Emmanuel; Martin, Darren P.; Varsani, Arvind; Roumagnac, Philippe.

In: PLoS One, Vol. 9, No. 7, e102945, 25.07.2014.

Research output: Contribution to journalArticle

Candresse, T, Filloux, D, Muhire, B, Julian, C, Galzi, S, Fort, G, Bernardo, P, Daugrois, JH, Fernandez, E, Martin, DP, Varsani, A & Roumagnac, P 2014, 'Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine context', PLoS One, vol. 9, no. 7, e102945. https://doi.org/10.1371/journal.pone.0102945
Candresse, Thierry ; Filloux, Denis ; Muhire, Brejnev ; Julian, Charlotte ; Galzi, Serge ; Fort, Guillaume ; Bernardo, Pauline ; Daugrois, Jean Heindrich ; Fernandez, Emmanuel ; Martin, Darren P. ; Varsani, Arvind ; Roumagnac, Philippe. / Appearances can be deceptive : Revealing a hidden viral infection with deep sequencing in a plant quarantine context. In: PLoS One. 2014 ; Vol. 9, No. 7.
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