Molecular epidemiology of Impatiens necrotic spot virus on greenhouse ornamental plants in a local area of Japan

Abstract

Impatiens necrotic spot virus (INSV), belonging to the genus Tospovirus, causes severe damage to greenhouse ornamental plants. We conducted population genetic analyses of INSV isolated from various greenhouse flowers in Iwate Prefecture as a model to elucidate how the virus invaded and spread within a local area of Japan. Forty-two and 30 sequences of the nucleocapsid protein gene (NG) and intergenic regions (IGR), respectively, of the small RNA of the virus were generated from 42 isolates collected from seven greenhouses in three districts, and then they were divided into 10 NG haplotypes and 13 IGR haplotypes. A combined haplotype analysis for the two loci revealed the presence of 14 NG/IGR haplotypes in the region. Genetic structure of the INSV population based on the NG sequences was differentiated according to districts and greenhouses, and 3 major NG haplotypes were predominant in each district. Genetic analysis based on IGR sequences showed that the population structure in some greenhouses consisted of 1 major IGR haplotype and some minor haplotypes with the same NG haplotype. Phylogenetic analysis based on NG and IGR sequences illustrated that INSV haplotypes were clustered according to geographic origin, including the isolates previously reported in Japan and other countries. Host species did not seem to influence the genetic structure of the INSV population. These results suggest that some founder isolates were introduced individually from other epidemic regions to each district in the region through different routes and then spread within the local areas and greenhouses.

Characterization of the first complete genome sequence of an Impatiens necrotic spot orthotospovirus isolate from the United States and worldwide phylogenetic analyses of INSV isolates

“…1 , 2 , 3 ). As indicated by Elliott et al [ 36 ] and Nekoduka et al [ 37 ], our result confirms that INSV isolates do not group phylogenetically based on host species (Figs. 1 , 2 ; Additional file 9 ).…”

“…Availability of genomic sequences from different geographic origin is pivotal to understand INSV genetic diversity and evolution, especially considering that orthotospoviruses have a tripartite genome and can reassort. Furthermore, while for other orthotospoviruses like TSWV, the aa sequence of N is sufficiently diverse to confer phylogenetic character, the INSV-N is highly conserved and it is not phylogenetically informative [ 35 – 37 ]. Genetic analysis can be used to characterize the structure of a virus population in relation to a location or host, and to probe the origin in a population and gene flow across time and space.…”