Genomics of Chikungunya Virus

Chikungunya (CHIKV) has been the cause of multiple outbreaks and infects greater than one million people every year. CHIKV was originally identified on the Asian continent, which has subsequently spread to other areas around the world—including the Western Hemisphere. CHIKV infection is generally acute with symptoms including: dehydration, headache, vomiting, myalgia, arthralgia, fever, rash, abdominal pain, and retro-orbital pain. Infected patients are at-risk for long-term joint stiffness and pain, which increases the need to better understand the sequence diversity of these viruses and how any viral mutations affect the severity of disease in the human host.

This project produced data demonstrating that 185 CHIKV sequences associated with the 2014 Caribbean outbreak segregate into 2 well-supported clades, that multiple phylogenetic subclades are associated with clinical phenotypes, and that multiple international transmission events were observed. This study makes an important contribution towards a better understanding of viral evolution, transmission dynamics, and intra-host sequence diversity. We believe that our data and the associated analysis will be of broad interest and of use to those in the fields of virology, phylogenetics, epidemiology, and vaccine development.


PLoS neglected tropical diseases. 2018-07-30; 12.7: e0006670.
Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic
Tan Y, Pickett BE, Shrivastava S, Gresh L, Balmaseda A, Amedeo P, Hu L, Puri V, Fedorova NB, Halpin RA, LaPointe MP, Cone MR, Heberlein-Larson L, Kramer LD, Ciota AT, Gordon A, Shabman RS, Das SR, Harris E
PMID: 30059496
Journal of virology. 2016-12-01; 90.23: 10600-10611.
Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus
Chen R, Puri V, Fedorova N, Lin D, Hari KL, Jain R, Rodas JD, Das SR, Shabman RS, Weaver SC
PMID: 27654297


This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Award Number U19AI110819.

Principal Investigator

Key Staff

  • Torrey Williams


Sustainable Sciences Institute (Nicaragua)

National Virology Laboratory of Nicaragua

Florida Bureau of Public Health Laboratories

New York State Department of Health

University of Michigan

University of California, Berkeley

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