Characterization of Maize chlorotic mottle virus and Sugarcane mosaic virus causing maize lethal necrosis disease and spatial distribution of their alternative hosts in Kenya

Maize lethal necrosis (MLN) disease caused by a dual infection of maize with Maize chlorotic mottle virus (MCMV) and any cereal potyvirus such as Sugarcane mosaic virus (SCMV), Maize dwarf mosaic virus (MDMV) or Wheat streak mosaic virus (WSMV) was first reported in Kenya in 2011 in Bomet County. This study was aimed at determining the presence and genetic variability of MCMV and SCMV in cereal crops,wild and domesticated grasses and the spatial distribution of alternative hosts in maize production regions of Kenya. Leaf samples of maize, grasses and other cereal crops were collected from fields in Nyamira, Bomet, Vihiga, Makueni and Machakos counties. MCMV and (SCMV) were detected by DAS-ELISA and confirmed by RT-PCR. The PCR products were sequenced in both directions. The resultant sequences were edited and compared with sequences from the Genbank followed by phylogenetic analysis. The distribution of wild grasses harbouring MCMV and SCMV in Kenya was predicted. Six grass weeds tested positive for MCMV and SCMV namely; velvet crabgrass (Digitaria velutina), couch grass (Digitaria abyssinica), star grass (Cynodon dactylon), kikuyu grass (Pennisetum clandestinum) and signal grass (Brachiaria brizantha). Nut grass (Cyperus rotundus tested positive for MCMV alone. Napier grass (Pennisetum purpureum) tested positive for MCMV alone. Sugarcane (Saccharum officinarum L.),finger millet (Eleusine coracana) and sorghum (Sorghum bicolor) tested positive for both MCMV and SCMV. The MCMV isolates nucleotide sequences were 98-100% similar and mostly related to the Kenya and Rwanda isolates (99-100%). SCMV isolates were 93-100% and were most related to China isolate (93-99%). Wild grasses harbouring MCMV and SCMV are spread throughout maize growing regions in Kenya.The results indicate that alternative hosts are important in the epidemiology of MLNcausing viruses and their role should be considered in the development of integrated management strategies for MLN.