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Yang Z, Chen Z, Bakht F, Li S, Zi S, Li X, Zhao X, Wen G, Zhao M. Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China. Arch Virol 2024; 169:97. [PMID: 38619640 DOI: 10.1007/s00705-024-06023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/11/2024] [Indexed: 04/16/2024]
Abstract
The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.
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Affiliation(s)
- Zefen Yang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- Quality Standard and Testing Technology Research Institute, Yunnan Academy of Agricultural Sciences, No. 2238, Beijing Road, Kunming, 650205, Yunnan, China
| | - Faryal Bakht
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Shaomei Zi
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xin Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xiyan Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.
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Lim S, Park JM, Kwon SY, Cho HS, Kim HS, Lee SH, Moon JS. Complete genome sequence of a tentative new member of the genus Badnavirus identified in Codonopsis lanceolata. Arch Virol 2019; 164:1733-1737. [PMID: 30953204 DOI: 10.1007/s00705-019-04238-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/22/2019] [Indexed: 10/27/2022]
Abstract
High-throughput sequencing revealed a tentative new badnavirus infecting Codonopsis lanceolata, provisionally named Codonopsis vein clearing virus (CoVCV). The complete 8,112-nt CoVCV genomic DNA sequence (GenBank accession: MK044821) comprises three open reading frames (ORFs) encoding conserved domains, with typical features of badnaviruses. Additionally, BLASTn searches indicated the CoVCV genome sequence is most similar to the grapevine vein clearing virus (GVCV) genome (72% identity and 46% query coverage). Moreover, the polyprotein encoded in CoVCV ORF3 is most similar to the corresponding protein of GVCV, with 60% amino acid sequence identity (89% query coverage). These results suggest that CoVCV is a new member of the genus Badnavirus in the family Caulimoviridae.
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Affiliation(s)
- Seungmo Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
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Li YC, Shen JG, Zhao GH, Yao Q, Li WM. A novel endogenous badnavirus exists in Alhagi sparsifolia. J Zhejiang Univ Sci B 2018; 19:274-284. [PMID: 29616503 DOI: 10.1631/jzus.b1700171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report the recovery of a 7068-nt viral sequence from the "viral fossils" embedded in the genome of Alhagi sparsifolia, a typical desert plant. Although the full viral genome remains to be completed, the putative genome structure, the deduced amino acids and phylogenetic analysis unambiguously demonstrate that this viral sequence represents a novel species of the genus Badnavirus. The putative virus is tentatively termed Alhagi bacilliform virus (ABV). Southern blotting and inverse polymerase chain reaction (PCR) data indicate that the ABV-related sequence is integrated into the A. sparsifolia genome, and probably does not give rise to functional episomal virus. Molecular evidence that the ABV sequence exists widely in A. sparsifolia is also presented. To our knowledge, this is the first endogenous badnavirus identified from plants in the Gobi desert, and may provide new clues on the evolution, geographical distribution as well as the host range of the badnaviruses.
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Affiliation(s)
- Yong-Chao Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jian-Guo Shen
- Inspection & Quarantine Technology Center, Fujian Entry-Exit Inspection and Quarantine Bureau, Fuzhou 350003, China
| | - Guo-Huan Zhao
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming 650201, China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Wei-Min Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Bhat AI, Hohn T, Selvarajan R. Badnaviruses: The Current Global Scenario. Viruses 2016; 8:E177. [PMID: 27338451 PMCID: PMC4926197 DOI: 10.3390/v8060177] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.
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Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
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Kazmi SA, Yang Z, Hong N, Wang G, Wang Y. Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus. PLoS One 2015. [PMID: 26207896 PMCID: PMC4514669 DOI: 10.1371/journal.pone.0134147] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.
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Affiliation(s)
- Syeda Amber Kazmi
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ni Hong
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
| | - Guoping Wang
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanfen Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Kalischuk ML, Fusaro AF, Waterhouse PM, Pappu HR, Kawchuk LM. Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs. Virus Res 2013; 178:306-13. [PMID: 24076299 DOI: 10.1016/j.virusres.2013.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Abstract
Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants.
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Affiliation(s)
- Melanie L Kalischuk
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-106, United States; Agriculture and Agri-Food Canada, P.O. Box 3000, Lethbridge, Alberta T1J 4B1, Canada
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Karuppaiah R, Viswanathan R, Kumar VG. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes 2013; 46:505-16. [PMID: 23430710 DOI: 10.1007/s11262-013-0890-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/05/2013] [Indexed: 02/05/2023]
Abstract
Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively.
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Affiliation(s)
- R Karuppaiah
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007, India
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Molecular analysis of the complete genomic sequences of four isolates of Gooseberry vein banding associated virus. Virus Genes 2011; 43:130-7. [PMID: 21533750 DOI: 10.1007/s11262-011-0614-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
The presence of Gooseberry vein banding associated virus (GVBaV), a badnavirus in the family Caulimoviridae, is strongly correlated with gooseberry vein banding disease in Ribes spp. In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649-7663 nucleotides. These isolates share identities of 96.4-97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1-3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNA(met)-binding site is also present in the 935-bp intergenic region of GVBaV. The identities of the genomic sequences of GVBaV and other badnaviruses range from 49.1% (Sugarcane bacilliform Mor virus) to 51.7% (Pelargonium vein banding virus, PVBV). Phylogenetic analysis using the amino acid sequence of the ORF 3 putative protein shows that GVBaV groups most closely to Dioscorea bacilliform virus, PVBV, and Taro bacilliform virus. These results confirm that GVBaV is a pararetrovirus of the genus Badnavirus in the family Caulimoviridae.
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Herzog E, Guerra-Peraza O, Hohn T. The rice tungro bacilliform virus gene II product interacts with the coat protein domain of the viral gene III polyprotein. J Virol 2000; 74:2073-83. [PMID: 10666237 PMCID: PMC111688 DOI: 10.1128/jvi.74.5.2073-2083.2000] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus whose DNA genome contains four genes encoding three proteins and a large polyprotein. The function of most of the viral proteins is still unknown. To investigate the role of the gene II product (P2), we searched for interactions between this protein and other RTBV proteins. P2 was shown to interact with the coat protein (CP) domain of the viral gene III polyprotein (P3) both in the yeast two-hybrid system and in vitro. Domains involved in the P2-CP association have been identified and mapped on both proteins. To determine the importance of this interaction for viral multiplication, the infectivity of RTBV gene II mutants was investigated by agroinoculation of rice plants. The results showed that virus viability correlates with the ability of P2 to interact with the CP domain of P3. This study suggests that P2 could participate in RTBV capsid assembly.
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Affiliation(s)
- E Herzog
- Friedrich Miescher Institute, CH-4002 Basel, Switzerland
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Briddon RW, Phillips S, Brunt A, Hull R. Analysis of the sequence of dioscorea Alata bacilliform virus: comparison to others members of the badnavirus group. Virus Genes 1999; 18:277-83. [PMID: 10456795 DOI: 10.1023/a:1008076420783] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complete nucleotide sequence of the genome of Dioscorea alata bacilliform virus (DaBV) has been determined from cloned fragments. Features of the genome confirm DaBV to be a pararetrovirus of the genus Badnavirus which is more similar to other mealy-bug transmitted badnaviruses, in particular to cacao swollen shoot virus, than to rice tungro bacilliform virus. Sequence variability between cloned fragments suggests that the genetic variability of the virus may be quite high (up to 11% nucleotide sequence variation for some small regions of the genome) although the overall variability detected was 4.2% at the nucleotide level.
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Affiliation(s)
- R W Briddon
- Department of Virus Research, John Innes Centre, Norwich, UK.
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