Complete genome analysis of a divergent isolate of narcissus yellow stripe virus from China

The complete sequence of ZZ-2, a narcissus yellow stripe virus (NYSV) isolate identified from Chinese narcissus sample in China, was determined. Its entire RNA genomes comprised 9654 nucleotides (nt) in length, excluding the 3′-terminal poly(A) tail and encoded a polyprotein of 3105 amino acids (aa), flanked by 5′ and 3′ untranslated regions (UTR) of 130 and 206 nts, respectively. Sequence analyses indicated that ZZ-2 shared highest 94% nt and 97% aa sequence identities with NYSV NY-CB5 and NY-EH173 isolates at the polyprotein level, whereas only 75% nt and 79% aa identities respectively with the representative of NYSV isolate (NYSV-Zhangzhou), which are less than the threshold values of the proposed species demarcation for the genus Potyvirus. However, ZZ-2 shared more than 81%–97% nt and 83%–99% aa sequence identities with all NYSV isolates in the coat protein, respectively, but less than 80% aa sequences with NLSYV isolates. Phylogenetic analysis revealed that ZZ-2 clustered together with NY-CB5 and NY-EH173. This suggests that ZZ-2, NY-CB5 and NY-EH173 represent a divergent group of NYSV isolates but share specific motifs in the cleavage sites at the junction of P1/HC-Pro and P3/6K1, which are differed from those of NLSYV isolates.