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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.
Financial support: Funding for this study came from the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (R01AI099631 to Angel Balmaseda), with support for deep sequencing assay development from NIAID/PSWRCE grant U54AI065359 (Poornima Parameswaran and Andrew Fire).
Authors' addresses: Chunling Wang, Meghana Eswarappa, Poornima Parameswaran, and Eva Harris, Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, E-mails: firstname.lastname@example.org, email@example.com, firstname.lastname@example.org, and email@example.com. Saira Saborio and Angel Balmaseda, Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua, E-mails: firstname.lastname@example.org and email@example.com. Lionel Gresh, Sustainable Sciences Institute, Managua, Nicaragua, E-mail: firstname.lastname@example.org. Diane Wu and Andrew Fire, Department of Genetics, Stanford University, Stanford, CA, and Department of Pathology, Stanford University, Stanford, CA, E-mails: email@example.com and firstname.lastname@example.org.