CHIKVnext: Molecular epidemiology of Chikungunya virus

Michael T. Wolfinger^1,2

<sub>¹Department of Theoretical Chemistry, University of Vienna, Vienna, Austria

²Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria</sub>

This repository contains a nextstrain community build of Chikungunya virus (CHIKV) that is accessible here. Alternatively, you can drag & drop the CHIKV.json file directly at auspice.us.

Data in this community build rely on publicly available CHIKV genomes from NCBI Genbank. New releases are published on an irregular basis when a reasonable amount of novel sequences are available.

Documentation

This repository includes comprehensive documentation to help you understand and work with the CHIKV build:

• BUILD.md - Complete guide to the build process, dependencies, and how to reproduce the analysis
• DATA.md - Documentation of data files, formats, and how to access sequence data
• CONTRIBUTING.md - Guidelines for contributing to the project and getting help

Quick links:

• How to reproduce the analysis
• Dependencies and installation
• Data sources and formats
• How to contribute
• Nextstrain documentation

Citation

If you use data provided in this repository in your own work please link back to this site and cite the following publications - Thank you!

• Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
  Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, and Michael T. Wolfinger
  Genes, 12(2):239, Feb 2021. DOI:10.3390/genes12020239 PMCID:PMC7914560

• Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture
  Adriano de Bernardi Schneider, Roman Ochsenreiter, Reilly Hostager, Ivo L. Hofacker, Daniel Janies, and Michael T. Wolfinger
  Viruses, 11:798, Aug 2019. DOI:10.3390/v11090798 PMCID:PMC6784101