Genomic epidemiology of Chikungunya virus in Colombia reveals genetic variability of strains and multiple geographic introductions in outbreak, 2014 (original) (raw)

Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. this study aimed to determine the genetic diversity and phylogenetic relationships of CHIKVs in Colombia. A descriptive and retrospective study was carried out using sera of patients infected with Chikungunya during the outbreak in Colombia. the whole genomes of CHIKV (n = 16) were sequenced with an Illumina Hi-seq 2500 and were assembled using the Iterative Virus Assembler software. A Bayesian inference phylogenetic analysis was carried out with 157 strains of worldwide origin. the Colombian CHIKV sequences were grouped in the Asian genotype; however, three independent phylogenetic subclades were observed, probably the result of three separate introductions from Panama, Nicaragua, and St. Barts. Each subclade showed several different non-synonymous mutations (nsP2-A153V; nsp2-Y543H; nsp2-G720A; nsP3-L458P; Capside R78Q), that may have functional consequences for CHIKV biology and pathogenesis. These same mutations may affect the efficacy of potential CHIKV vaccines. Chikungunya virus (CHIKV) is an alphavirus of the Togaviridae family, that is transmitted by the bite of mosquitoes of the species Aedes aegypti and A. albopictus 1. CHIKV is considered a public health problem due to its rapid spread and high morbidity 2. It causes a febrile illness accompanied by maculopapular rash and severe joint pain that can last for months or years 1. The incapacitating nature of the disease has caused a substantial economic burden and collapse in health systems 1. The local transmission of CHIKV has been reported in more than 100 countries and territories in Asia, Africa, Europe, and the Americas 1. According to the World Health Organization (WHO), between December 2013, and 2017, the islands of the Caribbean and the Americas registered >2,5 million suspected and confirmed 3. The study of whole genome sequences of CHIKV isolates from different regions of the world has facilitated an understanding of the evolutionary history of this virus 4. The first phylogenetic studies of CHIKV identified three geographically associated genotypes: West Africa (WA), East/Central/South Africa (ECSA) and Asia (AS) 5. However, in the years 2005-2006 a new descendant from the ECSA, the Indian Ocean lineage (IOL) was described 6. IOL developed a higher affinity for the Aedes albopictus vector, resulting from the E1-A226V, E2-I211T, E1-T98A and E2-L210Q mutations 2 , and was associated with the massive epidemics of 2005-2006 in the Indian Ocean Islands and the Indian subcontinent 6,7. Since the outbreaks in India and the Indian Ocean,