Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya
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Date
2020-03
Authors
Mumo, Naomi Nzilani
Mamati, George Edward
Ateka, Elijah Miinda
Rimberia, Fredah K.
Asudi, George Ochieng’
Boykin, Laura M.
Machuka, Eunice M.
Njuguna, Joyce Njoki
Pelle, Roger
Stomeo, Francesca
Journal Title
Journal ISSN
Volume Title
Publisher
Frontiers in Microbiology
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.
Description
article
Keywords
papaya, next-generation sequencing, Carlavirus, Potyvirus, ringspot disease, diagnostic primers
Citation
Mumo NN, Mamati GE, Ateka EM, Rimberia FK, Asudi GO, Boykin LM, Machuka EM, Njuguna JN, Pelle R and Stomeo F (2020) Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya. Front. Microbiol. 11:205. doi: 10.3389/fmicb.2020.00205