Potato virus Y (PVY) exists as a complex of strains differing in their host range and geographical distribution (Quenoille et al. 2013). In January 2013, a small-scale virus survey of six farmers’ fields planted with local tomato cultivars was conducted in Thika District, Central Province, Kenya. In one field, nearly 10% plants showed leaf necrosis and leaf curling. Leaf samples from two plants showing necrosis and two showing leaf curling were pressed separately onto FTA PlantSaver Cards (Whatman International Ltd., Maidstone, UK) (Ndunguru et al. 2005), air dried in the fields, and transported to the Plant Virology Laboratories in the United States for further characterization. Total nucleic acids eluted from each FTA card tested positive in PCR with degenerate primers specific to a portion of the cylindrical inclusion body protein of potyviruses and negative with primers specific to the common region of geminiviruses, the replicase gene of tospoviruses, and the capsid protein (CP) of Cucumber mosaic virus (data not shown). Subsequently, nucleic acids from the sample showing necrosis (#138) and with leaf curling (#139) were tested by RT-PCR using PVY-specific universal primers (PVY-F: ATGCCAACTGYGATGAATGG and PVY-R: CTCTGTGTTYTCCTCTTGTGTAC) to amplify a segment of 420 bp of the central conserved part of CP coding region. The two samples produced amplicons of the expected size, indicating PVY infections. To identify the PVY strain, a degenerate primer PVY8499F (RCYTTCACTGARATGATGG) was designed targeting a conserved part of the NIb region in all PVY strains, including PVYC, and used with an oligo-dT primer to test the #138 and #139 samples. A band of ca. 1,200 bp was amplified from both samples spanning the partial NIb, CP, and 3′NCR. These bands were gel-purified using Wizard SV Gel and PCR Clean-Up System (Promega, USA), cloned in a pGEM-T vector (pGEM-T Vector System, Promega, USA), and a total of 22 clones were sequenced for each PCR product. All clones of the sample #139 were identical and shared 97% nucleotide sequence identity with a PVYO isolate from China (AJ488834). However, the 22-clones for the sample #138 revealed two consensus sequences: 17 clones showed 97% nucleotide sequence identity with the same PVYO isolate (AJ488834), while 5 clones were 94% identical to PVYC isolates PRI-509 (EU563512) and SON41 (AJ439544). The sequences of the three isolates 138-C, 138-O, and 139-O were submitted to the GenBank with Accession Nos. KT852973, KT852974, and KT852975, respectively. Isolates 138-O and 139-O shared 97.5% nucleotide identity and both displayed 91% and 90% identity with 138-C, respectively. In the phylogenetic reconstructions, 138-O and 139-O grouped tightly within the PVYO strain group while 138-C fell into the PVYC strain group. To confirm the presence of PVYC in the tomato sample 138, a primer specific to the 138-C sequence (CATCCAACCAAACTCTGG) was used with the primer PVY-R and a band of 679 bp was amplified from isolate #138 but not from isolate #139. Apparently, tomatoes in Thika, Kenya, had mixed infection with a potato isolate from the PVYO or PVYN-Wi strain groups, and a pepper isolate from the PVYC strain group. Although PVY is known to occur in potato in Kenya (Muthomi et al. 2009; Were et al. 2013), this is the first report of PVY in tomato in Kenya and first report of a PVYC isolate found in this country. Our results highlight the potential risk of PVY strains to tomato production in Kenya. © 2016, American Phytopathological Society. All rights reserved.
