Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya

Naomi Nzilani Mumo; George Edward Mamati; Elijah Miinda Ateka; Fredah K Rimberia; George Ochieng' Asudi; Laura M Boykin; Eunice M Machuka; Joyce Njoki Njuguna; Roger Pelle; Francesca Stomeo

doi:10.3389/fmicb.2020.00205

Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya

Front Microbiol. 2020 Mar 4:11:205. doi: 10.3389/fmicb.2020.00205. eCollection 2020.

Authors

Affiliations

¹ Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
² Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya.
³ Department of Plant Physiology, Faculty of Bioscience, Matthias-Schleiden-Institute, Friedrich Schiller University Jena, Jena, Germany.
⁴ ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
⁵ Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya.

Abstract

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.

Keywords: Carlavirus; Potyvirus; diagnostic primers; next-generation sequencing; papaya; ringspot disease.