AUTHOR=Tabassum Afsha , Ramesh S. V. , Zhai Ying , Iftikhar Romana , Olaya Cristian , Pappu Hanu R. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.633710

DOI=10.3389/fmicb.2021.633710

ISSN=1664-302X

ABSTRACT=<p>Iris yellow spot, caused by Iris yellow spot orthotospovirus (IYSV) (Genus: <italic>Orthotospovirus</italic>, Family: <italic>Tospoviridae</italic>), is an important disease of <italic>Allium</italic> 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. <italic>In silico</italic> 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. <italic>In silico</italic> RFLP analysis of N gene sequences categorized IYSV isolates into two major genotypes <italic>viz</italic>., IYSV Netherlands (IYSV<sub><italic>NL</italic></sub>; 55.63%), IYSV Brazil (IYSV<sub><italic>BR</italic></sub>; 38.73%) and the rest fell in neither group [IYSV other (IYSV<sub><italic>other</italic></sub>; 5.63%)]. Phylogenetic tree largely corroborated the results of RFLP analysis and the IYSV genotypes clustered into IYSV<sub><italic>NL</italic></sub> and IYSV<sub><italic>BR</italic></sub> genotypes. Genetic diversity test revealed IYSV<sub><italic>other</italic></sub> to be more diverse than IYSV<sub><italic>NL</italic></sub> and IYSV<sub><italic>BR</italic></sub>. IYSV<sub><italic>NL</italic></sub> and IYSV<sub><italic>BR</italic></sub> genotypes are under purifying selection and population expansion, whereas IYSV<sub><italic>other</italic></sub> showed decreasing population size and hence appear to be under balancing selection. IYSV<sub><italic>BR</italic></sub> is least differentiated from IYSV<sub><italic>other</italic></sub> compared to IYSV<sub><italic>NL</italic></sub> 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<sup>–5</sup> subs/site/year and 95% highest posterior density (HPD) substitution rate between 5.11 × 10<sup>–5</sup> and 5.06 × 10<sup>–5</sup>. Findings suggest that IYSV continues to evolve using population expansion strategies. The substitution rates identified are similar to other plant RNA viruses.</p>