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Title: Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World.

item CHINGANDU, NOMA - University Of Arizona
item ZIA-UR-REHMAN, MUHAMMED - Pakistan University Of Agriculture
item REEVNIVANSAN, T.N. - Cocoa Research Unit - Trinidad
item SURUJDEO-MAHARAJ, SURENDRA - Cocoa Research Unit - Trinidad
item UMAHARAN, PATH - Cocoa Research Unit - Trinidad
item Gutierrez, Osman
item BROWN, JUDITH - University Of Arizona

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2017
Publication Date: 1/25/2017
Citation: Chingandu, N., Zia-Ur-Rehman, M., Reevnivansan, T., Surujdeo-Maharaj, S., Umaharan, P., Gutierrez, O.A., Brown, J. 2017. "Molecular cahracterization of previously elusive badnaviruses associated with symptomatic cacao in the New World". Archives of Virology.

Interpretive Summary: Cacao is a perennial crop cultivated in the tropical regions of the world and the source of beans used to make chocolate. Cacao viruses, especially Badnavirus, which are transmitted by mealybugs, causes severe damage since plants do not recover after the initial infection and die within 2 or 3 years. Because plants can be infected and do not show any symptoms, the detection of Badnavirus in cacao is currently done by grafting a scion of the introduced variety into a susceptible Amelonado rootstock and waiting for the development of the viral symptoms. A new virus detection assay is urgently needed, however, sequence information for Cacao Trinidad virus is not available. The main goal of this research was to sequence the Cacao Trinidad virus (CTV) strains A and B genomes. Results of the genome sequence analysis of the CTV strains A and B indicated that they both belong to the Badnaviruses genus. In addition, based on the sequence results, they can be classified as Cacao mild mosaic virus and Cacao yellow vein-clearing virus respectively. Finally, the sequence information of these two new Badnaviruses can be used in the development of diagnostic tools for the detection of both viruses

Technical Abstract: ABSTRACT Cacao (Theobroma cacao L.) is a tropical tree cultivated for beans used to make chocolate. Distinct virus-like symptoms, referred to as the putative Cacao Trinidad virus (CTV) strains A and B, have been observed in Trinidad and Tobago since 1944, however, viral etiology had not been demonstrated. Total DNA was isolated from symptomatic cacao leaves and subjected to Illumina HiSeq DNA sequencing. Based on the de novo assemblies two apparently full-length Badnavirus genomes of 7,533 and 7,491 nucleotides (nt) were associated with strain A and B symptoms, respectively. Sequence accuracy was verified by Sanger sequencing. Both genomes contained four predicted open reading frames (ORFs), three being characteristic of all known badnaviruses, and a fourth found only in some. The badnaviral genomes contained the hallmark Caulimovirus-like sequences, a tRNAmet priming sequence, CAAT and TATA boxes, and polyadenylation signals. Pairwise distance analysis of the viral RT-RNase H (taxonomic) region using the Sequence Demarcation Tool indicated they shared 57-71% nt identity with other known badnaviruses. Based on the ICTV species demarcation cut-off at <80% nt identity, they represent two previously unidentified badnaviral species, herein, Cacao mild mosaic virus and Cacao yellow vein-clearing virus, and are the first cacao-infecting badnaviruses identified in the Western Hemisphere.