title: Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus.
abstract: Since the India and Indian Ocean outbreaks of 2005 and 2006, the global distribution of chikungunya virus (CHIKV) and the locations of epidemics have dramatically shifted. First, the Indian Ocean lineage (IOL) caused sustained epidemics in India and has radiated to many other countries. Second, the Asian lineage has caused frequent outbreaks in the Pacific islands and in 2013 was introduced into the Caribbean, followed by rapid spread to nearly all of the neotropics. Further, CHIKV epidemics, as well as exported cases, have been reported in central Africa after a long period of perceived silence. To understand these changes and to anticipate the future of the virus, the exact distribution, genetic diversity, transmission routes, and future epidemic potential of CHIKV require further assessment. To do so, we conducted the most comprehensive phylogenetic analysis to date, examined CHIKV evolution and transmission, and explored distinct genetic factors associated with the emergence of the East/Central/South African (ECSA) lineage, the IOL, and the Asian lineage. Our results reveal contrasting evolutionary patterns among the lineages, with growing genetic diversities observed in each, and suggest that CHIKV will continue to be a major public health threat with the potential for further emergence and spread.
  
  
  OBJECTIVE
  Chikungunya fever is a reemerging infectious disease that is transmitted by Aedes mosquitoes and causes severe health and economic burdens in affected populations. Since the unprecedented Indian Ocean and Indian subcontinent outbreaks of 2005 and 2006, CHIKV has further expanded its geographic range, including to the Americas in 2013. Its evolution and transmission during and following these epidemics, as well as the recent evolution and spread of other lineages, require optimal assessment. Using newly obtained genome sequences, we provide a comprehensive update of the global distribution of CHIKV genetic diversity and analyze factors associated with recent outbreaks. These results provide a solid foundation for future evolutionary studies of CHIKV that can elucidate emergence mechanisms and also may help to predict future epidemics.
authors.affiliation: Institute of Human Infections and Immunology and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA.
authors.forename: Rubing
authors.initials: R
authors.lastname: Chen
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Vinita
authors.initials: V
authors.lastname: Puri
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Nadia
authors.initials: N
authors.lastname: Fedorova
authors.affiliation: CBio Inc., Fremont, California, USA.
authors.forename: David
authors.initials: D
authors.lastname: Lin
authors.affiliation: CBio Inc., Fremont, California, USA.
authors.forename: Kumar L
authors.initials: KL
authors.lastname: Hari
authors.affiliation: CBio Inc., Fremont, California, USA.
authors.forename: Ravi
authors.initials: R
authors.lastname: Jain
authors.affiliation: University of Antioquia, Medellín, Colombia.
authors.forename: Juan David
authors.initials: JD
authors.lastname: Rodas
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Suman R
authors.identifier: http://orcid.org/0000-0003-2496-9724
authors.initials: SR
authors.lastname: Das
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Reed S
authors.initials: RS
authors.lastname: Shabman
authors.affiliation: Institute of Human Infections and Immunology and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA sweaver@utmb.edu.|Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Weaver
mesh_terms: D020121:5' Untranslated Regions; D000330:Aedes / Q000821:virology; D000349:Africa / Q000453:epidemiology; D000569:Americas / Q000453:epidemiology; D000818:Animals; D001208:Asia / Q000453:epidemiology; D065632:Chikungunya Fever / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D002646:Chikungunya virus / Q000145:classification* / Q000235:genetics*; D058872:Epidemics; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D007194:India / Q000453:epidemiology; D007303:Insect Vectors / Q000821:virology; D010802:Phylogeny
chemical_list: D020121:5' Untranslated Regions