Shallot (Allium cepa var. aggregatum) is a small-bulb onion crop mainly grown in subtropical to temperate regions of the world (Block, 2010;Fritsch & Friesen, 2002). It is consumed for its unique flavour, pungency, and health-enhancing properties (Block, 2010;Fritsch & Friesen, 2002;Shahrajabian et al., 2020). Shallots are predominantly propagated by bulbs, resulting in the accumulation and dissemination of viruses in commercially grown fields and germplasm collections (Katis et al., 2012;Smékalová et al., 2017).The main viruses prevailing in Allium crops are from the genera Potyvirus, Carlavirus, and Allexivirus, which form viral complexes (Katis et al., 2012). Virus infections, particularly by potyviruses like onion yellow dwarf virus (OYDV) and leek yellow stripe virus