Pseudovirus deep mutational scanning of CHIKV envelope proteins

Deep mutational scanning of CHIKV envelope proteins

Interactive visualizations of how mutations to the envelope proteins of the 181/25 strain of Chikungunya virus (CHIKV) affect entry in 293T-Mxra8, 293T-TIM1, and C6/36 cells, as well as Mxra8 binding

Cell entry

Mutation effects on entry in different cells

Differences in cell entry

Compare how mutations affect entry in different cells

Mxra8 binding

Mutation effects on Mxra8 binding (assessed by neutralization by soluble Mxra8)

Structural visualizations

Visualizations of the deep mutational scanning on protein structures

Phylogenetic tree

Interactive phylogenetic tree with deep mutational scanning data

Overview ​

This website provides interactive visualizations and raw data about the effects of mutations to the CHIKV envelope proteins as measured in the pseudovirus deep mutational scanning experiments described in Ju et al (2025). That study measured how mutations to the CHIKV 181/25 envelope proteins affected entry in 293T-Mxra8 cells (human cells expressing the Mxra8 receptor), 293T-TIM1 cells (human cells expressing the TIM1 attachment factor), and C6/36 cells (mosquito cells). It also measured how mutations affect Mxra8 binding.

Because the datasets are so rich, the interactive visualizations here are generally a better way to explore the data than the static figures in the paper. If you just want to examine the effects of specific mutations in each of the three cell lines, this plot will generally be the best one to look at. All the visualizations and data can be accessed by clicking on the gray boxes above for each type of measurement, namely:

  • Cell entry: effects of mutations on entry in 293T-Mxra8, 293T-TIM1, and C6/36 cells.
  • Differences in cell entry: differences in effects of mutations on entry between each pair of cells.
  • Mxra8 binding: effects of mutations on binding to Mxra8, as assessed by pseudovirus neutralization by soluble Mxra8).
  • Structural visualizations: effects of mutations mapped onto three-dimensional structures of the envelope proteins, as rendered by dms-viz.
  • Phylogenetic tree: a Nextstrain phylogenetic tree of the genes encoding the CHIKV envelope proteins with deep mutational scanning phenotypes mapped onto the tips.

See Ju et al (2025) for additional details about the study.

Biosafety ​

The measurements shown on this page were made using pseudovirus deep mutational scanning with lentiviral particles pseudotyped with the envelope proteins from the 181/25 vaccine strain of CHIKV. These pseudoviruses do not encode any viral proteins other than the envelope proteins, and so are only able to undergo a single round of cell entry and are not fully replicative agents capable of spreading or causing disease. They therefore provide a safe way to study mutations to viral entry proteins at biosafety-level-2. In addition, the 181/25 strain of CHIKV from which the envelope proteins studied here are derived is an attenuated vaccine strain that has been safety tested in humans.

Numerical data, additional plots, and computer code ​

Links to the deep mutational scanning measurements in numerical form (eg, as CSVs) are included on each of the main pages above (eg, the cell entry page has links to the CSV files with the raw data on how mutations affect cell entry).

For more detailed documentation of the analysis (including additional interactive plots and links to CSVs) as automatically generated by dms-vep-pipeline-3, see the Appendix.

The full computer code, processed data, and analysis pipeline is available on GitHub at https://github.com/dms-vep/CHIKV-181-25-E-DMS.