Complete genome and molecular characterization of spiranthes mosaic virus 3 from Phlox paniculata

The first complete genome of spiranthes mosaic virus 3 (SpiMV3, genus Potyvirus, Potyviridae) was determined using high-throughput sequencing (GenBank PQ374234). The virus was detected from a Phlox paniculata plant, displaying severe foliar mosaic, in the Botanical Garden of Lomonosov Moscow State University, Moscow, Russia. The complete SpiMV3 genome comprised 9544 nucleotides (nt), excluding the 3'-terminal poly(A) tail. The large open-reading frame 9258 nt long encoded a polyprotein of 3085 amino acid residues, in which nine putative cleavage sites were identified. BLASTn showed that the complete SpiMV3 genome had the highest identity (66.4%) to Colombian datura potyvirus. Eight more SpiMV3 isolates were found on different phlox cultivars in the Tsitsin Main Botanical Garden, Moscow, by RT-PCR using primers designed based on the complete genome of the Russian SpiMV3 isolate. The coat protein (CP) gene phylogeny showed that known SpiMV3 isolates formed two distinct clusters and were grouped irrespective of their host plant species or geographical origin. The Russian isolates were assigned to one of the clusters. The CP genes of the Russian SpiMV3 isolates shared 94.4-98.1% nucleotide identity to each other, 92.2-96.9% to the rest of the isolates from this group, and 72.7-75.6% to the isolates from another cluster. This is the first report of SpiMV3 from Russia expanding the information on the geographical distribution and genetic diversity of the virus. The complete genome of this virus was sequenced and characterized for the first time.