First report of Garlic virus X infecting garlic in India.
During December 2010, garlic plants were observed with mosaic leaf symptoms and stunting in an experimental field at the Indian Agricultural Research Institute, Delhi. Cloves and leaves from 3-month-old symptomatic plants of 5 cultivars (G-282, IC-375416, Ruag, Yamuna Safed and ACC-40) were collected from the field and total RNA was extracted. The presence of Onion yellow dwarf virus and Garlic common latent virus was confirmed by reverse transcription (RT)-PCR in all cultivars, while the presence of Shallot latent virus was only confirmed in cv. G-282 by RT-PCR. Since Allexiviruses are common in garlic, their detection in cloves was confirmed by RT-PCR using primers ALLEX 1 and ALLEX 2. An ∼200-bp amplification product was observed in all five cultivars. To further characterize the Allexivirus in these cultivars, an amplicon of ∼900 bp was amplified, cloned and sequenced. BLAST analysis of the nucleotide sequences from the 5 garlic cultivars showed identity with Garlic virus A (74-83%), Garlic virus E (74-80%), Garlic virus D (76-79%) and Garlic virus X (GarV-X; 75-78%). Since species demarcation in the genus Allexivirus is based on the coat protein gene, another set of primers (5′-MYT KGA GTG GCT VAC ACA YAT-3′ and 5′-ATT RAA GTC GTG RGG ATG CAT-3′) was designed. An ∼1.5-kb amplicon was obtained only in cv. G-282. Sequences (1422 bp) obtained from three clones each from garlic cv. G-282 and Chenopodium amaranticolor were identical and BLAST analysis of the consensus nucleotide sequence showed maximum identity of 75-81% with isolates of GarV-X. This is thought to be the first report of GarV-X in a garlic cultivar from India.