Occurrence, molecular identification and phylogenetic analyses of viruses associated with garlic viral complex in Nepal

Garlic is a major spice crop in Nepal. A number of pathogens, including viruses, are known to cause economically important diseases in garlic. Garlic leaves showing leaf curl and mosaic symptoms and thirteen garlic accessions were collected from 12 districts. The accessions were planted under both the field and vector-free conditions. The leaf samples, collected directly from the fields and representative leaf samples from both field and vector-free growing conditions, were subjected to reverse transcription polymerase chain reaction (RT-PCR). Species of Potyvirus [(onion yellow dwarf virus (OYDV) and leek yellow stripe virus (LYSV)], Carlavirus [(shallot latent virus (SLV) and garlic common latent virus (GarCLV)], and Allexivirus [garlic virus A, D, H, and X (GarV-A, -D, -H, and –X)] were detected in mixed infections. Sequence and phylogenetic analyses showed that LYSV, OYDV, and GarCLV were closest to Indian isolates (including one LYSV isolate close to an Iranian isolate), SLV was close to Chinese isolates, and allexiviruses were close to Indian, Korean, and Chinese isolates. To our knowledge, this is the first report of SLV, GarV-A, GarV-D, GarV-H, and GarV-X in Nepal. The findings warrant plant quarantine measures and concerted research for their effective management.