title: Chikungunya Virus Sequences Across the First Epidemic in Nicaragua, 2014-2015.
abstract: Chikungunya is caused by the mosquito-borne arthrogenic alphavirus, chikungunya virus (CHIKV). Chikungunya was introduced into the Americas in late 2013 and Nicaragua in mid-2014. Here, we sequenced five imported and 30 autochthonous Nicaraguan CHIKV from cases identified in the first epidemic in the country between August 2014 and April 2015. One full-length and two partial genomic sequences were obtained by deep sequencing; Sanger methodology yielded 33 E1 sequences from five imported and 28 autochthonous cases. Phylogenetic analysis indicates that Nicaraguan CHIKV all belonged to the Asian genotype, Caribbean clade. Moreover, E1 gene sequences revealed accumulation of mutations in later months of the epidemic, including four silent mutations in 11 autochthonous cases and three non-synonymous mutations in three autochthonous cases. No mutations contributing to increased transmissibility by Aedes albopictus were identified in the E1 gene. This represents the most comprehensive set of CHIKV sequences available from the Americas to date.
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Chunling
authors.initials: C
authors.lastname: Wang
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Saira
authors.initials: S
authors.lastname: Saborio
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Lionel
authors.initials: L
authors.lastname: Gresh
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Meghana
authors.initials: M
authors.lastname: Eswarappa
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Diane
authors.initials: D
authors.lastname: Wu
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Andrew
authors.initials: A
authors.lastname: Fire
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Poornima
authors.initials: P
authors.lastname: Parameswaran
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California.
authors.forename: Angel
authors.initials: A
authors.lastname: Balmaseda
authors.affiliation: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua; Department of Genetics and Department of Pathology, Stanford University, Stanford, California eharris@berkeley.edu.
authors.forename: Eva
authors.initials: E
authors.lastname: Harris
mesh_terms: D065632:Chikungunya Fever / Q000453:epidemiology* / Q000821:virology*; D002646:Chikungunya virus / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D058872:Epidemics; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D009527:Nicaragua / Q000453:epidemiology; D010802:Phylogeny; D011159:Population Surveillance; D012367:RNA, Viral / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D012367:RNA, Viral