Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection

Hanafi, Marwa; Tahzima, Rachid; BEN KAAB, Sofiene; Tamisier, lucie; Roux, Nicolas; Massart, Sébastien

doi:10.3390/pathogens9121045

Article (Scientific journals)

Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection

Hanafi, Marwa; Tahzima, Rachid; BEN KAAB, Sofiene et al.

2020 • In Pathogens

Peer Reviewed verified by ORBi

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https://hdl.handle.net/2268/255167

DOI
10.3390/pathogens9121045

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Keywords :

high throughput sequencing (HTS); diagnostic; BanMMV; Betaflexiviridae; primers; novel isolates; plant virus; total RNA

Abstract :

[en] Banana mild mosaic virus (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects Musa spp. with a very wide geographic distribution. The genome variability of plant viruses, including the members of the Betaflexiviridae family, makes their molecular detection by specific primers particularly challenging. During routine indexing of the Musa germplasm accessions, a discrepancy was observed between electron microscopy and immunocapture (IC) reverse transcription (RT) polymerase chain reaction (PCR) test results for one asymptomatic accession. Filamentous viral particles were observed while molecular tests failed to amplify any fragment. The accession underwent high-throughput sequencing and two complete genomes of BanMMV with 75.3% of identity were assembled. Based on these sequences and on the 54 coat protein sequences available from GenBank, a new forward primer, named BanMMV CP9, compatible with Poty1, an oligodT reverse primer already used in diagnostics, was designed. A retrospective analysis of 110 different germplasm accessions from diverse origins was conducted, comparing BanMMCP2 and BanMMV CP9 primers. Of these 110 accessions, 16 tested positive with both BanMMCP2 and BanMMV CP9, 3 were positive with only BanMMCP2 and 2 tested positive with only BanMMV CP9. Otherwise, 89 were negative with the two primers and free of flexuous virions. Sanger sequencing was performed from purified PCR products in order to confirm the amplification of the BanMMV sequence for the five accessions with contrasting results. It is highly recommended to use the two primers successively to improve the inclusiveness of the protocol.

Disciplines :

Biotechnology

Author, co-author :

Hanafi, Marwa ; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs

Tahzima, Rachid ; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs

BEN KAAB, Sofiene; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs

Tamisier, lucie ; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs

Roux, Nicolas; Consultative Group on International Agricultural Research, 34090 Montpellier, France

Massart, Sébastien ; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs

Language :

English

Title :

Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection

Publication date :

12 December 2020

Journal title :

Pathogens

eISSN :

2076-0817

Publisher :

Molecular Diversity Preservation International (MDPI), Basel, Switzerland

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 15 January 2021

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