Viruses Without Borders: Global Analysis of the Population Structure, Haplotype Distribution, and Evolutionary Pattern of Iris Yellow Spot Orthotospovirus (Family Tospoviridae, Genus Orthotospovirus)

Iris yellow spot, caused by Iris yellow spot orthotospovirus (IYSV) (Genus: Orthotospovirus, Family: Tospoviridae), is an important disease of Allium spp. The complete N gene sequences of 142 IYSV isolates of curated sequence data from GenBank were used to determine the genetic diversity and evolutionary pattern. In silico restriction fragment length polymorphism (RFLP) analysis, codon-based maximum likelihood studies, genetic differentiation and gene flow within the populations of IYSV genotypes were investigated. Bayesian phylogenetic analysis was carried out to estimate the evolutionary rate. In silico RFLP analysis of N gene sequences categorized IYSV isolates into two major genotypes viz., IYSV Netherlands (IYSV(NL); 55.63%), IYSV Brazil (IYSV(BR); 38.73%) and the rest fell in neither group [IYSV other (IYSV(other); 5.63%)]. Phylogenetic tree largely corroborated the results of RFLP analysis and the IYSV genotypes clustered into IYSV(NL) and IYSV(BR) genotypes. Genetic diversity test revealed IYSV(other) to be more diverse than IYSV(NL) and IYSV(BR). IYSV(NL) and IYSV(BR) genotypes are under purifying selection and population expansion, whereas IYSV(other) showed decreasing population size and hence appear to be under balancing selection. IYSV(BR) is least differentiated from IYSV(other) compared to IYSV(NL) genotype based on nucleotide diversity. Three putative recombinant events were found in the N gene of IYSV isolates based on RDP analysis, however, RAT substantiated two among them. The marginal likelihood mean substitution rate was 5.08 × 10(–5) subs/site/year and 95% highest posterior density (HPD) substitution rate between 5.11 × 10(–5) and 5.06 × 10(–5). Findings suggest that IYSV continues to evolve using population expansion strategies. The substitution rates identified are similar to other plant RNA viruses.