Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection
<i>Banana mild mosaic virus</i> (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects <i>Musa</i> spp. with a very wide geographic distribution. The genome variability of plant viruses, includi...
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| Format: | Article |
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MDPI AG
2020-12-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/9/12/1045 |
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| author | Marwa Hanafi Rachid Tahzima Sofiene Ben Kaab Lucie Tamisier Nicolas Roux Sébastien Massart |
| author_facet | Marwa Hanafi Rachid Tahzima Sofiene Ben Kaab Lucie Tamisier Nicolas Roux Sébastien Massart |
| author_sort | Marwa Hanafi |
| collection | DOAJ |
| description | <i>Banana mild mosaic virus</i> (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects <i>Musa</i> 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 <i>Musa</i> 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. |
| first_indexed | 2024-03-10T14:06:42Z |
| format | Article |
| id | doaj.art-3bad0843019a42bfab26807f9a23c065 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T14:06:42Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-3bad0843019a42bfab26807f9a23c0652023-11-21T00:33:42ZengMDPI AGPathogens2076-08172020-12-01912104510.3390/pathogens9121045Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve DetectionMarwa Hanafi0Rachid Tahzima1Sofiene Ben Kaab2Lucie Tamisier3Nicolas Roux4Sébastien Massart5Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, BelgiumIntegrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, BelgiumIntegrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, BelgiumIntegrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, BelgiumConsultative Group on International Agricultural Research, 34090 Montpellier, FranceIntegrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium<i>Banana mild mosaic virus</i> (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects <i>Musa</i> 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 <i>Musa</i> 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.https://www.mdpi.com/2076-0817/9/12/1045high throughput sequencing (HTS)diagnosticBanMMVBetaflexiviridaeprimersnovel isolates |
| spellingShingle | Marwa Hanafi Rachid Tahzima Sofiene Ben Kaab Lucie Tamisier Nicolas Roux Sébastien Massart Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection Pathogens high throughput sequencing (HTS) diagnostic BanMMV Betaflexiviridae primers novel isolates |
| title | Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection |
| title_full | Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection |
| title_fullStr | Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection |
| title_full_unstemmed | Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection |
| title_short | Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection |
| title_sort | identification of divergent isolates of banana mild mosaic virus and development of a new diagnostic primer to improve detection |
| topic | high throughput sequencing (HTS) diagnostic BanMMV Betaflexiviridae primers novel isolates |
| url | https://www.mdpi.com/2076-0817/9/12/1045 |
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