Metagenomic analysis of plant viruses associated with papaya ringspot disease in Carica papaya L. in Kenya

Affiliation
Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology
Mumo, Naomi Nzilani;
Affiliation
Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology
Mamati, George Edward;
Affiliation
Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology
Ateka, Elijah Miinda;
Affiliation
Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology
Rimberia, Fredah K.;
Affiliation
Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University
Asudi, George Ochieng;
Affiliation
ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia
Boykin, Laura M.;
Affiliation
Biosciences Eastern and Central Africa-International Livestock Research Institute Hub
Machuka, Eunice M.;
Affiliation
Biosciences Eastern and Central Africa-International Livestock Research Institute Hub
Njuguna, Joyce Njoki;
Affiliation
Biosciences Eastern and Central Africa-International Livestock Research Institute Hub
Pelle, Roger;
Affiliation
Biosciences Eastern and Central Africa-International Livestock Research Institute Hub
Stomeo, Francesca

Carica papaya L. is an important fruit crop grown by small- and large-scale farmers in Kenya for local and export markets. However, its production is constrained by papaya ringspot disease (PRSD). The disease is believed to be caused by papaya ringspot virus (PRSV). Previous attempts to detect PRSV in papaya plants showing PRSD symptoms, using enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with primers specific to PRSV, have not yielded conclusive results. Therefore, the nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing. Viruses were detected in 38 out of the 48 leaf samples sequenced. Sequence analysis revealed the presence of four viruses: a Potyvirus named Moroccan watermelon mosaic virus (MWMV) and three viruses belonging to the genus Carlavirus. The Carlaviruses include cowpea mild mottle virus (CpMMV) and two putative Carlaviruses —closely related but distinct from cucumber vein-clearing virus (CuVCV) with amino acid and nucleotide sequence identities of 75.7–78.1 and 63.6–67.6%, respectively, in the coat protein genes. In reference to typical symptoms observed in the infected plants, the two putative Carlaviruses were named papaya mottle-associated virus (PaMV) and papaya mild mottle-associated virus (PaMMV). Surprisingly, and in contrast to previous studies conducted in other parts of world, PRSV was not detected. The majority of the viruses were detected as single viral infections, while a few were found to be infecting alongside another virus (for example, MWMV and PaMV). Furthermore, the NGS and RT-PCR analysis identified MWMV as being strongly associated with ringspot symptoms in infected papaya fruits. This study has provided the first complete genome sequences of these viruses isolated from papaya in Kenya, together with primers for their detection—thus proving to be an important step towards the design of long-term, sustainable disease management strategies.

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License Holder: Copyright © 2020 Mumo, Mamati, Ateka, Rimberia, Asudi, Boykin, Machuka, Njuguna, Pelle and Stomeo.

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This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.

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