Variation profile of the orthotospovirus genome

Deepti Nigam, Hernan Garcia-Ruiz

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative-propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations across species. Remarkably, the highest nucleotide variation mapped to the intergenic region of RNA segments S and M, which fold into a hairpin. Secondary structure analyses showed that the hairpin is a dynamic structure with multiple functional shapes formed by stems and loops, contains sites under positive selection and covariable sites. Accumulation and tolerance of mutations in the intergenic region is a general feature of orthotospoviruses and might mediate adaptation to host plants and insect vectors.

Original languageEnglish (US)
Article number521
Pages (from-to)1-28
Number of pages28
Issue number7
StatePublished - Jul 2020


  • Insect vectors
  • Intergenic region
  • RNA secondary structure
  • Single nucleotide polymorphism
  • TSWV
  • Thrips
  • Virus adaptation
  • Virus evolution

ASJC Scopus subject areas

  • Immunology and Allergy
  • Molecular Biology
  • General Immunology and Microbiology
  • Microbiology (medical)
  • Infectious Diseases


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