Global analysis of population structure, spatial and temporal dynamics of genetic diversity, and evolutionary lineages of Iris yellow spot virus (Tospovirus: Bunyaviridae)

Determinants of Virus Variation, Evolution, and Host Adaptation

Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.

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.

Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority

TAXONOMY

Iris yellow spot virus (IYSV) is in the genus Tospovirus, family Bunyaviridae, with a single-stranded, tri-segmented RNA genome with an ambisense genome organization. Members of the other genera in the family infect predominantly vertebrates and insects.

GEOGRAPHICAL DISTRIBUTION

IYSV is present in most Allium-growing regions of the world.

PHYSICAL PROPERTIES

Virions are pleomorphic particles of 80-120 nm in size. The particle consists of RNA, protein, glycoprotein and lipids.

GENOME

IYSV shares the genomic features of other tospoviruses: a segmented RNA genome of three RNAs, referred to as large (L), medium (M) and small (S). The L RNA codes for the RNA-dependent RNA polymerase (RdRp) in negative sense. The M RNA uses an ambisense coding strategy and codes for the precursor for the GN /GC glycoprotein in the viral complementary (vc) sense and a non-structural protein (NSm) in the viral (v) sense. The S RNA also uses an ambisense coding strategy with the coat protein (N) in vc sense and a non-structural protein (NSs) in the v sense.

TRANSMISSION

The virus is transmitted by Thrips tabaci Lindeman (Order: Thysanoptera; Family: Thripidae; onion thrips) and with less efficiency by Frankliniella fusca Hinds (tobacco thrips). HOST: IYSV has a relatively broad host range, including cultivated and wild onions, garlic, chives, leeks and several ornamentals. Some weeds are naturally infected by IYSV and may serve as alternative hosts for the virus.

SYMPTOMS

IYSV symptoms in Allium spp. are yellow- to straw-coloured, diamond-shaped lesions on leaves and flowering scapes. Diamond-shaped lesions are particularly pronounced on scapes. As the disease progresses, the lesions coalesce, leading to lodging of the scapes. In seed crops, this could lead to a reduction in yield and quality. Early to mid-season infection in bulb crops results in reduced vigour and bulb size.

CONTROL

Resistant varieties are not available, but a limited number of accessions with field tolerance have been identified. Integrated disease management tactics, including sanitation, crop rotation, thrips management, maintenance of optimal plant vigour, soil fertility, irrigation and physical separation of bulb and seed crops, can mitigate the effect of the disease. Virus code: 00.011.0.85.009 Useful link: http://www.alliumnet.com/.