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Identification of a novel polerovirus in cocoa (Theobroma cacao) germplasm and development of molecular methods for use in diagnostics

Ullah, I. ORCID:, Kamran, M. and Dunwell, J. M. ORCID: (2023) Identification of a novel polerovirus in cocoa (Theobroma cacao) germplasm and development of molecular methods for use in diagnostics. Pathogens, 12 (11). 1284. ISSN 2076-0817

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To link to this item DOI: 10.3390/pathogens12111284


The cocoa crop (Theobroma cacao L.) is known to be a host for several badnaviruses, some of which cause severe disease, while others are asymptomatic. Recently, the first preliminary evidence has been published concerning the occurrence of a polerovirus in cacao. We report here the first near-complete genome sequence of cacao polerovirus (CaPV) by combining bioinformatic searches of cacao transcript databases, with cloning from the infected germplasm. The reported novel genome has all the genome features known for poleroviruses from other species. Pairwise identity analyses of RNA-dependent RNA polymerase and coat protein indicates < 60% similarity of CaPV with any reported poleroviruses; hence, we propose that the polerovirus isolate reported in this study is a novel polerovirus. The genome sequence information was also used to develop a multiplex RT-PCR assay, which was applied to screen a selected range of germplasms and to identify several infected clones. Although there is no evidence that this virus causes any severe disease, this new information, together with a robust diagnostic assay, are of strategic importance in developing protocols for the safe international transfer of cacao germplasms.

Item Type:Article
Divisions:Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
ID Code:113813
Uncontrolled Keywords:cacao; polerovirus; genome; RT-PCR; NGS; ORF


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