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Abrahamian P, Tian T, Posis K, Guo Y, Yu D, Blomquist CL, Wei G, Adducci B, Vidalakis G, Bodaghi S, Osman F, Roy A, Nunziata SO, Nakhla M, Mavrodieva V, Rivera Y. Genetic Analysis of the Emerging Citrus Yellow Vein Clearing Virus Reveals a Divergent Virus Population in American Isolates. PLANT DISEASE 2024; 108:1544-1554. [PMID: 38127632 DOI: 10.1094/pdis-09-23-1963-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Citrus yellow vein clearing virus is a previously reported citrus virus from Asia with widespread distribution in China. In 2022, the California Department of Food and Agriculture conducted a multipest citrus survey targeting multiple citrus pathogens including citrus yellow vein clearing virus (CYVCV). In March 2022, a lemon tree with symptoms of vein clearing, chlorosis, and mottling in a private garden in the city of Tulare, California, tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and noncitrus species, were collected and tested for CYVCV using conventional reverse transcription polymerase chain reaction, reverse transcription quantitative polymerase chain reaction, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using 17 complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study made up the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, the CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area.
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Affiliation(s)
- Peter Abrahamian
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Tongyan Tian
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Katie Posis
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Ying Guo
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Doris Yu
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Cheryl L Blomquist
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Gang Wei
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Benjamin Adducci
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD 20705
| | - Schyler O Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Mark Nakhla
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Vessela Mavrodieva
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Yazmín Rivera
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
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Jin T, Kim JK, Byun HS, Choi HS, Cha B, Kwak HR, Kim M. Occurrence and Multiplex PCR Detection of Citrus Yellow Vein Clearing Virus in Korea. THE PLANT PATHOLOGY JOURNAL 2024; 40:125-138. [PMID: 38606443 PMCID: PMC11016552 DOI: 10.5423/ppj.oa.09.2023.0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 04/13/2024]
Abstract
Citrus yellow vein clearing virus (CYVCV) is a member of the Alphaflexiviridae family that causes yellow vein clearing symptoms on citrus leaves. A total of 118 leaf samples from nine regions of six provinces in Korea were collected from various citrus species in 2020 and 2021. Viral diagnosis using next-generation sequencing and reverse transcription polymerase chain reaction (RT-PCR) identified four viruses: citrus tristeza virus, citrus leaf blotch virus, citrus vein enation virus, and CYVCV. A CYVCV incidence of 9.3% was observed in six host plants, including calamansi, kumquat, Persian lime, and Eureka lemon. Among the citrus infected by CYVCV, only three samples showed a single infection; the other showed a mixed infection with other viruses. Eureka lemon and Persian lime exhibited yellow vein clearing, leaf distortion, and water-soak symptom underside of the leaves, while the other hosts showed only yellowing symptoms on the leaves. The complete genome sequences were obtained from five CYVCV isolates. Comparison of the isolates reported from the different geographical regions and hosts revealed the high sequence identity (95.2% to 98.8%). Phylogenetic analysis indicated that all the five isolates from Korea were clustered into same clade but were not distinctly apart from isolates from China, Pakistan, India, and Türkiye. To develop an efficient diagnosis system for the four viruses, a simultaneous detection method was constructed using multiplex RT-PCR. Sensitivity evaluation, simplex RT-PCR, and stability testing were conducted to verify the multiplex RT-PCR system developed in this study. This information will be useful for developing effective disease management strategies for citrus growers in Korea.
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Affiliation(s)
- Taemin Jin
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Ji-Kwang Kim
- Chungcheongnam-do Agricultural Research and Extension Services, Buyeo 33168, Korea
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Byeongjin Cha
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Mikyeong Kim
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
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Kong W, Lv X, Ran X, Mukangango M, Eric Derrick B, Qiu B, Guo C. Comprehensive Assessment of Reference Gene Expression within the Whitefly Dialeurodes citri Using RT-qPCR. Genes (Basel) 2024; 15:318. [PMID: 38540377 PMCID: PMC10970672 DOI: 10.3390/genes15030318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 06/14/2024] Open
Abstract
The citrus whitefly, Dialeurodes citri, is a destructive pest that infests citrus plants. It is a major vector in transmitting plant viruses such as citrus yellow vein clearing virus (CYVCV), which has caused severe economic losses worldwide, and therefore efficient control of this pest is economically important. However, the scope of genetic studies primarily focused on D. citri is restricted, something that has potentially limited further study of efficient control options. To explore the functionalities of D. citri target genes, screening for specific reference genes using RT-qPCR under different experimental conditions is essential for the furtherance of biological studies concerning D. citri. The eight candidate reference genes were evaluated by dedicated algorithms (geNorm, Normfinder, BestKeeper and ΔCt method) under five specific experimental conditions (developmental stage, sex, tissue, population and temperature). In addition, the RefFinder software, a comprehensive evaluation platform integrating all of the above algorithms, ranked the expression stability of eight candidate reference genes. The results showed that the best reference genes under different experimental settings were V-ATP-A and RPS18 at different developmental stages; α-tubulin, 18S and V-ATP-A in both sexes; EF1A and α-tubulin in different tissues; Actin and Argk under different populations; and RPS18 and RPL13 in different temperatures. The validation of selected reference genes was further identified using heat shock protein (Hsp) 70 as a reporter gene. Our study, for the first time, provides a detailed compilation of internal reference genes for D. citri that are suitable for RT-qPCR analysis, which is robust groundwork for comprehensive investigation of the functional target genes of D. citri.
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Affiliation(s)
- Weizhen Kong
- Engineering Research Center of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510640, China; (W.K.); (X.L.); (X.R.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Xiaolu Lv
- Engineering Research Center of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510640, China; (W.K.); (X.L.); (X.R.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Xiaotong Ran
- Engineering Research Center of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510640, China; (W.K.); (X.L.); (X.R.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Marguerite Mukangango
- College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze P.O. Box 210, Rwanda; (M.M.); (B.E.D.)
| | - Bugenimana Eric Derrick
- College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze P.O. Box 210, Rwanda; (M.M.); (B.E.D.)
| | - Baoli Qiu
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Changfei Guo
- Engineering Research Center of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510640, China; (W.K.); (X.L.); (X.R.)
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Sun YD, Yokomi R. Genotype Sequencing and Phylogenetic Analysis Revealed the Origins of Citrus Yellow Vein Clearing Virus California Isolates. Viruses 2024; 16:188. [PMID: 38399964 PMCID: PMC10891506 DOI: 10.3390/v16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The Citrus yellow vein clearing virus (CYVCV) causes a viral disease that has been reported in some citrus-growing regions in countries in Eurasia including Pakistan, India, Türkiye, Iran, China, and South Korea. Recently, CYVCV was detected in a localized urban area in a town in the middle of California's citrus-growing region and marks the first occurrence of the virus in North America. CYVCV has been reported to be spread by aphid and whitefly vectors and is graft and mechanically transmitted. Hence, it is an invasive pathogen that presents a significant threat to the California citrus industry, especially lemons, which are highly symptomatic to CYVCV. To elucidate the origin of the CYVCV California strain, we used long-read sequencing technology and obtained the complete genomes of three California CYVCV isolates, CA1, CA2, and CA3. The sequences of these isolates exhibited intergenomic similarities ranging from 95.4% to 97.4% to 54 publicly available CYVCV genome sequences, which indicated a relatively low level of heterogeneity. However, CYVCV CA isolates formed a distinct clade from the other isolates when aligned against other CYVCV genomes and coat protein gene sequences as shown by the neighbor network analysis. Based on the rooted Maximum Likelihood phylogenetic trees, CYVCV CA isolates shared the most recent common ancestor with isolates from India/South Asia. Bayesian evolutionary inferences resulted in a spatiotemporal reconstruction, suggesting that the CYVCV CA lineage diverged from the Indian lineage possibly around 1995. This analysis placed the origin of all CYVCV to around 1990, with South Asia and/or Middle East as the most plausible geographic source, which matches to the first discovery of CYVCV in Pakistan in 1988. Moreover, the spatiotemporal phylogenetic analysis indicated an additional virus diffusion pathway: one from South Asia to China and South Korea. Collectively, our phylogenetic inferences offer insights into the probable dynamics of global CYVCV dissemination, emphasizing the need for citrus industries and regulatory agencies to closely monitor citrus commodities crossing state and international borders.
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Affiliation(s)
- Yong-Duo Sun
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Raymond Yokomi
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
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Zeng T, Liao P, Zheng C, Gao H, Ye X, Zhou C, Zhou Y. The interaction between the lemon ribosomal protein ClRPS9-2 and citrus yellow vein clearing virus coat protein affects viral infection and gene silencing suppressor activity. MOLECULAR PLANT PATHOLOGY 2023; 24:1047-1062. [PMID: 37148475 PMCID: PMC10423326 DOI: 10.1111/mpp.13347] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/08/2023]
Abstract
Citrus yellow vein clearing virus (CYVCV) is an emerging virus that causes serious economic damage to the lemon industry worldwide. The coat protein (CP) of CYVCV is a strong RNA silencing suppressor and is associated with the severity of symptoms in citrus, yet the interaction between CP and host factors remains unknown. In this study, the 40S ribosomal subunit protein S9-2 (ClRPS9-2) was identified as a CP-binding partner using the yeast two-hybrid system from a lemon (cv. Eureka) cDNA library, and the interaction between CP and ClRPS9-2 was demonstrated by in vivo methods. The results suggest that the N-terminal 8-108 amino acid sequence of ClRPS9-2 is crucial for its interaction with CP and may be associated with the nuclear localization of ClRPS9-2. The accumulation and silencing suppressor activity of CP were reduced by transient expression of ClRPS9-2 in Nicotiana benthamiana. Reverse transcription-quantitative PCR analysis showed that the content of CYVCV in ClRPS9-2 transgenic Eureka lemon plants was approximately 50% of that in CYVCV-infected wild-type plants 1 month after inoculation, and mild yellowing and vein clearing symptoms were observed in the transgenic plants. These findings demonstrate that ClRPS9-2 plays a role in host defensive reactions, and the enhanced resistance of transgenic plants to CYVCV may be associated with the up-regulation of salicylic acid-related and R genes.
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Affiliation(s)
- Ting Zeng
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Ping Liao
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Cairong Zheng
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Haixing Gao
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Xiao Ye
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Yan Zhou
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
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Bin Y, Zhang Q, Su Y, Wang C, Jiang Q, Song Z, Zhou C. Transcriptome analysis of Citrus limon infected with Citrus yellow vein clearing virus. BMC Genomics 2023; 24:65. [PMID: 36750773 PMCID: PMC9903606 DOI: 10.1186/s12864-023-09151-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Citrus yellow vein clearing virus (CYVCV) is the causative agent of citrus yellow vein clearing disease, and poses a serious threat to the lemon industry in Asia. The common symptoms of CYVCV-infected lemon plants are leaf crinkling, leaf chlorotic mottling, and yellow vein clearing. However, the molecular mechanisms underlying CYVCV-citrus interaction that responsible for symptom occurrence is still unclarified. In this study, RNA-seq was performed to analyze the gene expression patterns of 'Eureka' lemon (Citrus limon Burm. f.) plants in response to CYVCV infection. RESULTS There were 3691 differentially expressed genes (DEGs) identified by comparison between mock and CYVCV-infected lemon plants through RNA-seq. Bioinformatics analyses revealed that these DEGs were components of different pathways involved in phenylpropanoid biosynthesis, brassinosteroid biosynthesis, flavonoid biosynthesis and photosynthesis. Among these, the DEGs related to phytohormone metabolism and photosynthesis pathways were further enriched and analyzed. This study showed that different phytohormone-related genes had different responses toward CYVCV infection, however almost all of the photosynthesis-related DEGs were down-regulated in the CYVCV-infected lemon plants. The obtained RNA-seq data were validated by RT-qPCR using 12 randomly chosen genes, and the results of mRNA expression analysis were consistent with those of RNA-seq. CONCLUSIONS The phytohormone biosynthesis, signaling and photosynthesis-related genes of lemon plants were probably involved in systemic infection and symptom occurrence of CYVCV. Notably, CYVCV infection had regulatory effects on the biosynthesis and signaling of phytohormone, which likely improve systemic infection of CYVCV. Additionally, CYVCV infection could cause structural changes in chloroplast and inhibition of photosynthesis pathway, which probably contribute to the appearance of leaf chlorotic mottling and yellow vein clearing in CYVCV-infected lemon plants. This study illustrates the dynamic nature of the citrus-CYVCV interaction at the transcriptome level and provides new insights into the molecular mechanism underlying the pathogenesis of CYVCV in lemon plants.
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Affiliation(s)
- Yu Bin
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Qi Zhang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Yue Su
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Chunqing Wang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Qiqi Jiang
- grid.263906.80000 0001 0362 4044Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Zhen Song
- Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
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Bin Y, Xu J, Duan Y, Ma Z, Zhang Q, Wang C, Su Y, Jiang Q, Song Z, Zhou C. The Titer of Citrus Yellow Vein Clearing Virus Is Positively Associated with the Severity of Symptoms in Infected Citrus Seedlings. PLANT DISEASE 2022; 106:828-834. [PMID: 34645307 DOI: 10.1094/pdis-02-21-0232-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Citrus yellow vein clearing virus (CYVCV), a new member of the genus Mandarivirus in the family Alphaflexiviridae, is the causal agent of citrus yellow vein clearing disease. CYVCV is transmitted to citrus by Dialeurodes citri, grafting, and contaminated knife blades, threatening citrus production. In this study, four infectious full-length complementary DNA clones of CYVCV (namely AY112, AY132, AY212, and AY221) derived from CYVCV isolate AY were obtained through yeast homologous recombination and inoculated to 'Eureka' lemon (Citrus limon Burm. f.) by Agrobacterium-mediated vacuum infiltration. Pathogenicity analysis indicated that the clones AY212 and AY221 caused more severe symptoms than AY112 and AY132. Northern blot and quantitative reverse transcription PCR analyses showed that the titers of virulent clones (AY212 and AY221) were significantly higher than those of attenuated clones (AY112 and AY132) in the infected 'Eureka' lemon seedlings. Subsequent comparative studies of viral infectivity, accumulation, and symptoms induced by AY221 in nine citrus cultivars indicated that the infectivity of AY221 varied from 25 to 100% between cultivars; 'Oota' ponkan (C. reticulata L.) showed the lowest infection rate, with mild symptoms, which might be a useful resource for CYVCY-resistance genes; and CYVCV titer was positively associated with the symptom development in infected citrus seedlings. In general, this report revealed the biological properties of CYVCV, thus laying a foundation for further investigation of pathogenic mechanisms in this virus.
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Affiliation(s)
- Yu Bin
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Jianjian Xu
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Yu Duan
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Zhimin Ma
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Qi Zhang
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Chunqing Wang
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Yue Su
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Qiqi Jiang
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Zhen Song
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Chongqing, 400712, P.R. China
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Song S, Ma L, Xu X, Shi H, Li X, Liu Y, Hao P. Rapid screening and identification of viral pathogens in metagenomic data. BMC Med Genomics 2021; 14:289. [PMID: 34903237 PMCID: PMC8668262 DOI: 10.1186/s12920-021-01138-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified. RESULTS In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references). CONCLUSIONS Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).
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Affiliation(s)
- Shiyang Song
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Liangxiao Ma
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Xintian Xu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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Hou W, Li S, Massart S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. Front Microbiol 2020; 11:592816. [PMID: 33329473 PMCID: PMC7710903 DOI: 10.3389/fmicb.2020.592816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.
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Affiliation(s)
- Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Wu J, Zhang S, Atta S, Yang C, Zhou Y, Di Serio F, Zhou C, Cao M. Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan. PLANT DISEASE 2020; 104:1593-1600. [PMID: 32357118 DOI: 10.1094/pdis-08-19-1744-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.
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Affiliation(s)
- Jiaxing Wu
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Sagheer Atta
- Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering Shenyang University, Shenyang 110044, China
| | - Yan Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
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Development of a sensitive and reliable reverse transcription droplet digital PCR assay for the detection of citrus yellow vein clearing virus. Arch Virol 2018; 164:691-697. [DOI: 10.1007/s00705-018-04123-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
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