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Padmanabhan C, Nunziata S, Leon M. G, Rivera Y, Mavrodieva VA, Nakhla MK, Roy A. High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1058847. [PMID: 36762187 PMCID: PMC9907091 DOI: 10.3389/fpls.2022.1058847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
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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Affiliation(s)
- Chellappan Padmanabhan
- United 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 States
| | - Schyler Nunziata
- United 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 States
| | | | - Yazmín Rivera
- United 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 States
| | - Vessela A. Mavrodieva
- United 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 States
| | - Mark K. Nakhla
- United 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 States
| | - Avijit Roy
- United 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 States
- United States Department of Agriculture (USDA), Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, United States
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Chabi-Jesus C, Ramos-González PL, Postclam-Barro M, Fontenele RS, Harakava R, Bassanezi RB, Moreira AS, Kitajima EW, Varsani A, Freitas-Astúa J. Molecular Epidemiology of Citrus Leprosis Virus C: A New Viral Lineage and Phylodynamic of the Main Viral Subpopulations in the Americas. Front Microbiol 2021; 12:641252. [PMID: 33995302 PMCID: PMC8116597 DOI: 10.3389/fmicb.2021.641252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of viral strains/variants as agents of emerging diseases, genetic and evolutionary processes affecting their ecology are not fully understood. To get insight into this topic, we assessed the population and spatial dynamic parameters of citrus leprosis virus C (CiLV-C, genus Cilevirus, family Kitaviridae). CiLV-C is the etiological agent of citrus leprosis disease, a non-systemic infection considered the main viral disorder affecting citrus orchards in Brazil. Overall, we obtained 18 complete or near-complete viral genomes, 123 complete nucleotide sequences of the open reading frame (ORF) encoding the putative coat protein, and 204 partial nucleotide sequences of the ORF encoding the movement protein, from 430 infected Citrus spp. samples collected between 1932 and 2020. A thorough examination of the collected dataset suggested that the CiLV-C population consists of the major lineages CRD and SJP, unevenly distributed, plus a third one called ASU identified in this work, which is represented by a single isolate found in an herbarium sample collected in Asuncion, Paraguay, in 1937. Viruses from the three lineages share about 85% nucleotide sequence identity and show signs of inter-clade recombination events. Members of the lineage CRD were identified both in commercial and non-commercial citrus orchards. However, those of the lineages SJP were exclusively detected in samples collected in the citrus belt of São Paulo and Minas Gerais, the leading Brazilian citrus production region, after 2015. The most recent common ancestor of viruses of the three lineages dates back to, at least, ∼1500 years ago. Since citrus plants were introduced in the Americas by the Portuguese around the 1520s, the Bayesian phylodynamic analysis suggested that the ancestors of the main CiLV-C lineages likely originated in contact with native vegetation of South America. The intensive expansion of CRD and SJP lineages in Brazil started probably linked to the beginning of the local citrus industry. The high prevalence of CiLV-C in the citrus belt of Brazil likely ensues from the intensive connectivity between orchards, which represents a potential risk toward pathogen saturation across the region.
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Affiliation(s)
- Camila Chabi-Jesus
- Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, São Paulo, Brazil.,Instituto Biológico/IB, São Paulo, Brazil
| | | | | | - Rafaela Salgado Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | | | | | - Alecio S Moreira
- Fundo de Defesa da Citricultura, Araraquara, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Juliana Freitas-Astúa
- Instituto Biológico/IB, São Paulo, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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Freitas-Astúa J, Ramos-González PL, Arena GD, Tassi AD, Kitajima EW. Brevipalpus-transmitted viruses: parallelism beyond a common vector or convergent evolution of distantly related pathogens? Curr Opin Virol 2018; 33:66-73. [PMID: 30081359 DOI: 10.1016/j.coviro.2018.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Although diseases caused by Brevipalpus-transmitted viruses (BTV) became relevant for agriculture a century ago, their causal agents have been only recently characterized and classified in two new genera of plant-infecting viruses: Cilevirus and Dichorhavirus. In this review, we highlight both similarities and differences between these viruses emphasizing their current taxonomy and historical classification, phylogeny, genomic organization, gene expression, and the latest research developments on BTVs. Additionally, we stress particular features of interactions with their mite vectors and plant hosts that support, from an evolutionary perspective, the potential convergence of both viral groups.
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Affiliation(s)
- Juliana Freitas-Astúa
- Embrapa Cassava and Fruits, 44380-000 Cruz das Almas, BA, Brazil; Instituto Biológico, 04014-900 São Paulo, SP, Brazil.
| | | | - Gabriella Dias Arena
- Centro Apta Citros Sylvio Moreira, IAC, 13490-000 Cordeirópolis, SP, Brazil; Instituto de Biologia, Unicamp, 13083-862 Campinas, SP, Brazil
| | - Aline Daniele Tassi
- Departmento de Fitopatologia e Nematologia, ESALQ/USP, 13418-900 Piracicaba, SP, Brazil
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