Identification of narcissus yellow stripe virus and a closely-related potyvirus isolate in plants of allium carinatum

A survey of varieties and species of ornamental Allium species revealed the presence of multiple viruses, including potyviruses, carlaviruses, and allexiviruses. Most of these viruses have been previously identified in A. sativum (garlic), A. cepa (onion), A. porrum (synonym A. ampeloprasum var. porrum; leek), and/or other edible Allium species. However, two samples of Allium carinatum were found by generic potyvirus PCR and transmission electron microscopy to be infected with potyvirus isolates which were not amplified with primers specific for Leek yellow stripe virus (LYSV) or Onion yellow dwarf virus (OYDV), the potyviruses most commonly found in cultivated Allium spp. These samples also yielded negative results in ELISA tests with LYSV- or OYDV-specific antibodies. Broad spectrum PCR primers for the Nuclear inclusion b to 3’ end (NIb-3’) were then used to amplify and clone this portion of the genome of the potyvirus isolates from A. carinatum. The sequences generated were used to identify one isolate as a strain of Narcissus yellow stripe virus (NYSV), and the other as a potyvirus most closely related to NYSV, but differing sufficiently to be considered as either a novel species (based on current criteria for species boundaries) or a recombinant isolate between NYSV and an unknown parent. However, divergent isolates of NYSV and Narcissus late season yellows virus have been reported from narcissus in Australia, suggesting that an intermediate between these species occurs, which might either be regarded as a third species, or the two species collapsed into one by broadening the species demarcation criteria. Independent of the eventual status of the second isolate, Allium carinatum is a new host of NYSV, which has previously been reported only from Narcissus spp. and Nerine bowdenii.