Results and analysis
The complete genomic sequence of the virus from mangshi (designed as YMSh-CL isolate) was determined to be 9600 nucleotides (nt) excluding the 3’-terminal poly (A) tail (GenBank accession No. OK073904), flanked by 5’ and 3’ untranslated regions (UTRs) of 136 nt and 170 nt, respectively. The major putative ORF encoding a polyprotein of 3098 amino acid (aa) residues which started at nt 137 and ended at nt 9432. Nine highly conserved proteolytic cleave sites were identical to those of other potyvirus and bioinformatically yielded ten putative mature proteins of P1 (316 aa), HC-Pro (458 aa), P3 (378 aa), 6K1 (51 aa), CI (636 aa), 6K2 (53 aa), VPg (187 aa), NIa-Pro (243 aa), NIb (515 aa) and CP (261 aa), respectively (Fig. 1B). The small ORF (PIPO) within the P3 cistron of potyviruses was identified by the presence of 3007GGAAAAA3014 encoding a protein of 73 aa residues. Most conserved motifs of potyviruses , such as 6I-T-F-G9 and 228H-X12-D-X29-S-G-X18-R-G292 associate with protease activity in P1, the putative zinc finger metal-binding motif of 27C-X8-C-X18-C-X2-C58 related to aphid transmission, and 344C-X72-H417 for protease activity in HC-Pro，106V-L-M-V-E-P-T-R-P-L115，175D-E-C-H178, 202K-V-S-A-T-P-P208, 253L-V-Y-V256, 304V-A-T-N-I-I-E-N-G-V-T-L315 and 348G-E-R-I-Q-R-L-G-R-V-G-R359 related to the potential helicase activity in CI, 46H-X34-D-X67-G-X-C-G-X14-H167 with proteolytic activity in NIa-Pro, 188F-T-A-A-P-I-D194, 202C-V-D-D-F-N207, 244F-D-A-D-G-S249, 306G-N-N-S-G-Q-P-S-T-V-V-D-N-S-L-M-V322 and 350G-D-D352 for RNA-dependant polymerase in NIb were all identified in the virus. Besides, the highly conserve motif of K-I-T-C in HC-Pro involved in aphid transmission, was taken place by 52R-I-T-C55 in the virus, while two other motifs of 310P-T-K312 in HC-Pro and 7D-A-G9 in CP with the similar function, both present in its corresponding location.
The sequences of the virus were pairwise compared with other members of genus Potyvirus available in the GenBank Database, the result showed the virus sharing sequence identity with other members of Potyvirus was 53.0% (onion yellow dwarf virus, OYDV, Accession number NC_005029) to 57.8% (NYSV, Accession number NC_011541) at nt sequence level, and 39.3% (OYDV, NC_005029) to 51.2% (plum pox virus, PPV, NC_001445) at deduce aa sequence level. A maximum-likelihood tree was conducted using the deduced polyprotein sequence and selected members of the genus Potyvirus. The virus was clustered as a single clade between the subgroup of plum pox virus group and that of chilli veinal mottle virus (Fig. 2). These results indicated that the virus should be a novel species of genus Potyvirus and was tentatively named as “Paris mottle associated virus” (PMaV).
Mechanical inoculation proved that Nicotiana benthamiana, N. tobacum, N. glutinosa, N. rustica, N. tabacum var. Xanthi nc, Capsicum annuum, Solanum lycopersicum and Vigna unguiculata are not host plants of PMaV. 33 out of 132 samples from 4 counties of Mangshi, Tengchong, Lijiang, Lushui from Yunnan proved infecting with PaMoV indicting a relatively wide areas of the virus. However, more biological characteristics should be examined in the future for the vector transmission still unknown.