Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus
<i>Dichorhavirus</i> is a recently accepted plant virus genus within the family <i>Rhabdoviridae</i>. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by <i>Brevipalpus</i> spp. Currently, there...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-03-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/17/3/441 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849340416695992320 |
|---|---|
| author | Avijit Roy Jonathan Shao Andres S. Espindola Daniel Ramos Lopez Gabriel Otero-Colina Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla William L. Schneider Kitty Cardwell |
| author_facet | Avijit Roy Jonathan Shao Andres S. Espindola Daniel Ramos Lopez Gabriel Otero-Colina Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla William L. Schneider Kitty Cardwell |
| author_sort | Avijit Roy |
| collection | DOAJ |
| description | <i>Dichorhavirus</i> is a recently accepted plant virus genus within the family <i>Rhabdoviridae</i>. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by <i>Brevipalpus</i> spp. Currently, there are five recognized species and two unclassified members in the genus <i>Dichorhavirus.</i> Four out of seven-orchid fleck virus (OFV), citrus leprosis virus N, citrus chlorotic spot virus, and citrus bright spot virus-can infect citrus and produce leprosis disease-like symptoms. The E-probe Diagnostic for Nucleic Acid Analysis (EDNA) was developed to reduce computational effort and then integrated within Microbe-Finder (MiFi<sup>®</sup>) online platform to design and evaluate e-probes in raw High Throughput Sequencing (HTS) data. During this study, <i>Dichorhavirus</i> genomes were downloaded from public databases and e-probes were designed using the MiProbe incorporated into the MiFi<sup>®</sup> platform. Three different sizes of e-probes, 40, 60, and 80 nucleotides, were developed and selected based on whole genome comparisons with near-neighbor genomes. For curation, each e-probe was searched in the NCBI nucleotide sequence database using BLASTn. All the e-probes that had hits with non-target species with ≥90% identities were removed. The sensitivity and specificity of <i>Dichorhavirus</i> genus, species, strain, and variant-specific e-probes were validated in vivo using HTS meta-transcriptomic libraries generated from <i>Dichorhavirus</i>-suspected citrus, orchid, and ornamentals. Through downstream analysis of HTS data, EDNA not only detected the known hosts of OFV but also discovered an unknown host leopard plant (<i>Farfugium japonicum</i>), and the possible existence of a new ornamental strain of OFV in nature. |
| format | Article |
| id | doaj-art-c20d9ce9a9064b8ca56d4ac7eb2bd90b |
| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-c20d9ce9a9064b8ca56d4ac7eb2bd90b2025-08-20T03:43:55ZengMDPI AGViruses1999-49152025-03-0117344110.3390/v17030441Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck VirusAvijit Roy0Jonathan Shao1Andres S. Espindola2Daniel Ramos Lopez3Gabriel Otero-Colina4Yazmín Rivera5Vessela A. Mavrodieva6Mark K. Nakhla7William L. Schneider8Kitty Cardwell9Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center (BARC), United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Beltsville, MD 20705, USAAnimal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center (BARC), United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Beltsville, MD 20705, USAInstitute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, USAInstitute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, USAColegio de Postgraduados, Campus Montecillo, Texcoco 56264, MexicoPlant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Animal Plant Health Inspection Service, United States Department of Agriculture (USDA), Laurel, MD 20708, USAPlant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Animal Plant Health Inspection Service, United States Department of Agriculture (USDA), Laurel, MD 20708, USAPlant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Animal Plant Health Inspection Service, United States Department of Agriculture (USDA), Laurel, MD 20708, USAF1/K9 LLC, Palm Coast, FL 32164, USAInstitute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, USA<i>Dichorhavirus</i> is a recently accepted plant virus genus within the family <i>Rhabdoviridae</i>. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by <i>Brevipalpus</i> spp. Currently, there are five recognized species and two unclassified members in the genus <i>Dichorhavirus.</i> Four out of seven-orchid fleck virus (OFV), citrus leprosis virus N, citrus chlorotic spot virus, and citrus bright spot virus-can infect citrus and produce leprosis disease-like symptoms. The E-probe Diagnostic for Nucleic Acid Analysis (EDNA) was developed to reduce computational effort and then integrated within Microbe-Finder (MiFi<sup>®</sup>) online platform to design and evaluate e-probes in raw High Throughput Sequencing (HTS) data. During this study, <i>Dichorhavirus</i> genomes were downloaded from public databases and e-probes were designed using the MiProbe incorporated into the MiFi<sup>®</sup> platform. Three different sizes of e-probes, 40, 60, and 80 nucleotides, were developed and selected based on whole genome comparisons with near-neighbor genomes. For curation, each e-probe was searched in the NCBI nucleotide sequence database using BLASTn. All the e-probes that had hits with non-target species with ≥90% identities were removed. The sensitivity and specificity of <i>Dichorhavirus</i> genus, species, strain, and variant-specific e-probes were validated in vivo using HTS meta-transcriptomic libraries generated from <i>Dichorhavirus</i>-suspected citrus, orchid, and ornamentals. Through downstream analysis of HTS data, EDNA not only detected the known hosts of OFV but also discovered an unknown host leopard plant (<i>Farfugium japonicum</i>), and the possible existence of a new ornamental strain of OFV in nature.https://www.mdpi.com/1999-4915/17/3/441<i>Brevipalpus</i> transmitted virus (BTV)EDNAMiFie-probehigh-throughput sequencingorchid fleck virus |
| spellingShingle | Avijit Roy Jonathan Shao Andres S. Espindola Daniel Ramos Lopez Gabriel Otero-Colina Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla William L. Schneider Kitty Cardwell Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus Viruses <i>Brevipalpus</i> transmitted virus (BTV) EDNA MiFi e-probe high-throughput sequencing orchid fleck virus |
| title | Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus |
| title_full | Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus |
| title_fullStr | Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus |
| title_full_unstemmed | Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus |
| title_short | Detection and In Vivo Validation of <i>Dichorhavirus</i> e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi<sup>®</sup>) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus |
| title_sort | detection and in vivo validation of i dichorhavirus i e probes in meta transcriptomic data via microbe finder mifi sup r sup discovers a novel host and a possible new strain of orchid fleck virus |
| topic | <i>Brevipalpus</i> transmitted virus (BTV) EDNA MiFi e-probe high-throughput sequencing orchid fleck virus |
| url | https://www.mdpi.com/1999-4915/17/3/441 |
| work_keys_str_mv | AT avijitroy detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT jonathanshao detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT andressespindola detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT danielramoslopez detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT gabrieloterocolina detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT yazminrivera detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT vesselaamavrodieva detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT markknakhla detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT williamlschneider detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus AT kittycardwell detectionandinvivovalidationofidichorhavirusieprobesinmetatranscriptomicdataviamicrobefindermifisupsupdiscoversanovelhostandapossiblenewstrainoforchidfleckvirus |