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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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Autores principales: Padmanabhan, Chellappan, Nunziata, Schyler, Leon M., Guillermo, Rivera, Yazmín, Mavrodieva, Vessela A., Nakhla, Mark K., Roy, Avijit
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9907091/
https://www.ncbi.nlm.nih.gov/pubmed/36762187
http://dx.doi.org/10.3389/fpls.2022.1058847
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author Padmanabhan, Chellappan
Nunziata, Schyler
Leon M., Guillermo
Rivera, Yazmín
Mavrodieva, Vessela A.
Nakhla, Mark K.
Roy, Avijit
author_facet Padmanabhan, Chellappan
Nunziata, Schyler
Leon M., Guillermo
Rivera, Yazmín
Mavrodieva, Vessela A.
Nakhla, Mark K.
Roy, Avijit
author_sort Padmanabhan, Chellappan
collection PubMed
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.
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spelling pubmed-99070912023-02-08 High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex Padmanabhan, Chellappan Nunziata, Schyler Leon M., Guillermo Rivera, Yazmín Mavrodieva, Vessela A. Nakhla, Mark K. Roy, Avijit Front Plant Sci Plant Science 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. Frontiers Media S.A. 2023-01-24 /pmc/articles/PMC9907091/ /pubmed/36762187 http://dx.doi.org/10.3389/fpls.2022.1058847 Text en Copyright © 2023 Padmanabhan, Nunziata, León, Rivera, Mavrodieva, Nakhla and Roy https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Padmanabhan, Chellappan
Nunziata, Schyler
Leon M., Guillermo
Rivera, Yazmín
Mavrodieva, Vessela A.
Nakhla, Mark K.
Roy, Avijit
High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex
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 Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9907091/
https://www.ncbi.nlm.nih.gov/pubmed/36762187
http://dx.doi.org/10.3389/fpls.2022.1058847
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