01 · Research brief
About this project
Sindbis virus is a mosquito-borne alphavirus that causes fever, rash and persistent joint pain in humans, with recurrent outbreaks in Northern Europe and southern Africa. There is no vaccine and no specific antiviral, so treatment is limited to symptom relief.
This project analyses the Sindbis virus genome to identify regions that resist evolutionary change, and asks whether those regions correspond to structured RNA elements. Such regions are of interest because a site the virus cannot easily mutate is a candidate target for sequence-specific antiviral approaches, and because RNA structure in alphavirus genomes has recently been shown to be functionally important even where it is not broadly conserved.
We have assembled 232 complete genomes from NCBI Virus and applied explicit inclusion criteria, excluding 145 sequences annotated with rodent cell-line hosts because culture-passaged virus accumulates adaptations to the cell line rather than to its natural mosquito and bird hosts. The remaining 87 field isolates span 19 countries and seven decades (1963 to 2025) and yield a tree length of approximately 1.0 substitutions per site, which is sufficient evolutionary signal for codon-model analysis.
The specific hypothesis is being finalised against the prior literature and will be fixed and dated before any further analysis is run. All code and data-handling decisions are version-controlled and documented.