High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex

Authors: PADMANABHAN, CHELLAPPAN - Animal And Plant Health Inspection Service (APHIS); NUNZIATA, SCHYLER - Animal And Plant Health Inspection Service (APHIS); GUILLERMO, LEON - Colombian Corporation Of Agriculture And Livestock- Agrosavia; RIVERA, YAZMIN - Animal And Plant Health Inspection Service (APHIS); MAVRODIEVA, VESSELA - Animal And Plant Health Inspection Service (APHIS); NAKHLA, MARK - Animal And Plant Health Inspection Service (APHIS); Roy, Avijit

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2022
Publication Date: 1/24/2023
Citation: Padmanabhan, C., Nunziata, S., Guillermo, L.M., Rivera, Y., Mavrodieva, V.A., Nakhla, M.K., Roy, A. 2023. High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex. Frontiers in Plant Science. 13. Article e1058847. https://doi.org/10.3389/fpls.2022.1058847.
DOI: https://doi.org/10.3389/fpls.2022.1058847

Interpretive Summary: Citrus leprosis (CiL) is associated with multiple Brevipalpus transmitted viruses (BTVs) belongs to the genus Cilevirus and Dichorhavirus and is considered one of the destructive emerging viral diseases of citrus in Americas. So, far hibiscus strain of Citrus leprosis cilevirus C2 (CiLV-C2H) has been reported in hibiscus and passionfruit in US and has potential to cause citrus leprosis disease. To protect the multibillion dollar citrus industry, a high throughput sequencing (HTS) method was optimized to detect regulatory citrus viruses. The optimized protocol was successfully utilized to detect citrus leprosis associated viruses infecting different hosts, such as citrus, hibiscus, swinglea, dieffenbachia, passionfruit, orchids, smilax, monkey grass, lilyturf, and Cast-iron plant. The newly developed HTS protocol not only detected the known viruses but also discovered a new hibiscus strain CiLV-C2H2 from a RT-qPCR negative hibiscus sample. Overall, the optimized HTS method will enhance the surveillance of regulatory viruses associated with the CiLD complex in multiple hosts by detecting known viruses and identifying novel virus/strain if any, in the samples.

Technical 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.