High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex
Citrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus....
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1058847/full |
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| author | Chellappan Padmanabhan Schyler Nunziata Guillermo Leon M. Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla Avijit Roy Avijit Roy |
| author_facet | Chellappan Padmanabhan Schyler Nunziata Guillermo Leon M. Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla Avijit Roy Avijit Roy |
| author_sort | Chellappan Padmanabhan |
| collection | DOAJ |
| description | Citrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus. The localized CiL symptoms observed in multiple citrus species and other alternate hosts indicates that these viruses might have originated from the mites and eventually adopted citrus as a secondary host. Genetic diversity in the genomes of viruses associated with the CiL disease complex have complicated current detection and diagnostic measures that prompted the application of High-Throughput Sequencing (HTS) protocols for improved detection and diagnosis. Two cileviruses are known to infect citrus, and among them only citrus leprosis virus C2 (CiLV-C2) hibiscus strain (CiLV-C2H) has been reported in hibiscus and passion fruit in the US. Based on our current CiL disease complex hypothesis, there is a high probability that CiL disease is associated with more viruses/strains that have not yet been identified but exist in nature. To protect the citrus industry, a Ribo-Zero HTS protocol was utilized for detection of cileviruses infecting three different hosts: Citrus spp., Swinglea glutinosa, and Hibiscus rosa-sinensis. Real-time RT-PCR assays were used to identify plants infected with CiLV-C2 or CiLV-C2H or both in mixed infection in all the above-mentioned plant genera. These results were further confirmed by bioinformatic analysis using HTS generated data. In this study, we utilized HTS assay in confirmatory diagnostics to screen BTVs infecting Dieffenbachia sp. (family: Araceae), Passiflora edulis (Passifloraceae), and Smilax auriculata (Smilacaceae). Through the implementation of HTS and downstream data analysis, we detected not only the known cileviruses in the studied hosts but also discovered a new strain of CiLV-C2 in hibiscus from Colombia. Phylogenetically, the new hibiscus strain is more closely related to CiLV-C2 than the known hibiscus strain, CiLV-C2H. We propose this strain to be named as CiLV-C2 hibiscus strain 2 (CiLV-C2H2). The findings from the study are critical for citrus growers, industry, regulators, and researchers. The possible movement of CiLV-C2H2 from hibiscus to citrus by the Brevipalpus spp. warrants further investigation. |
| first_indexed | 2024-04-10T20:22:23Z |
| format | Article |
| id | doaj.art-b3daaf680c0e4b7ca949b3b58e36a23f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T20:22:23Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-b3daaf680c0e4b7ca949b3b58e36a23f2023-01-25T14:44:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011310.3389/fpls.2022.10588471058847High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complexChellappan Padmanabhan0Schyler Nunziata1Guillermo Leon M.2Yazmín Rivera3Vessela A. Mavrodieva4Mark K. Nakhla5Avijit Roy6Avijit Roy7United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesUnited States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesAGROSAVIA, Centro de Investigación La Libertad, Meta, ColombiaUnited States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesUnited States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesUnited States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesUnited States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United StatesUnited States Department of Agriculture (USDA), Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, United StatesCitrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus. The localized CiL symptoms observed in multiple citrus species and other alternate hosts indicates that these viruses might have originated from the mites and eventually adopted citrus as a secondary host. Genetic diversity in the genomes of viruses associated with the CiL disease complex have complicated current detection and diagnostic measures that prompted the application of High-Throughput Sequencing (HTS) protocols for improved detection and diagnosis. Two cileviruses are known to infect citrus, and among them only citrus leprosis virus C2 (CiLV-C2) hibiscus strain (CiLV-C2H) has been reported in hibiscus and passion fruit in the US. Based on our current CiL disease complex hypothesis, there is a high probability that CiL disease is associated with more viruses/strains that have not yet been identified but exist in nature. To protect the citrus industry, a Ribo-Zero HTS protocol was utilized for detection of cileviruses infecting three different hosts: Citrus spp., Swinglea glutinosa, and Hibiscus rosa-sinensis. Real-time RT-PCR assays were used to identify plants infected with CiLV-C2 or CiLV-C2H or both in mixed infection in all the above-mentioned plant genera. These results were further confirmed by bioinformatic analysis using HTS generated data. In this study, we utilized HTS assay in confirmatory diagnostics to screen BTVs infecting Dieffenbachia sp. (family: Araceae), Passiflora edulis (Passifloraceae), and Smilax auriculata (Smilacaceae). Through the implementation of HTS and downstream data analysis, we detected not only the known cileviruses in the studied hosts but also discovered a new strain of CiLV-C2 in hibiscus from Colombia. Phylogenetically, the new hibiscus strain is more closely related to CiLV-C2 than the known hibiscus strain, CiLV-C2H. We propose this strain to be named as CiLV-C2 hibiscus strain 2 (CiLV-C2H2). The findings from the study are critical for citrus growers, industry, regulators, and researchers. The possible movement of CiLV-C2H2 from hibiscus to citrus by the Brevipalpus spp. warrants further investigation.https://www.frontiersin.org/articles/10.3389/fpls.2022.1058847/fullBrevipalpus transmitted virusesCitrus leprosis virusCilevirusDichorhavirusHigh-throughput sequencingKitaviridae |
| spellingShingle | Chellappan Padmanabhan Schyler Nunziata Guillermo Leon M. Yazmín Rivera Vessela A. Mavrodieva Mark K. Nakhla Avijit Roy Avijit Roy High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex Frontiers in Plant Science Brevipalpus transmitted viruses Citrus leprosis virus Cilevirus Dichorhavirus High-throughput sequencing Kitaviridae |
| title | High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| title_full | High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| title_fullStr | High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| title_full_unstemmed | High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| title_short | High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| title_sort | high throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex |
| topic | Brevipalpus transmitted viruses Citrus leprosis virus Cilevirus Dichorhavirus High-throughput sequencing Kitaviridae |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1058847/full |
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