Phylogenetic analysis of Chikungunya virus in Colombia: Evidence of purifying selection in the E1 gene.
BACKGROUND
Chikungunya virus (CHIKV) is a single-stranded positive sense RNA virus that belongs to the Alphavirus genus of the family Togaviridae. Its genome is 11.8 kb in length, and three genotypes have been identified worldwide: Asian, East/Central/South African (ECSA) and West African. Chikungunya fever is an acute febrile disease transmitted by Aedes spp. that usually presents with polyarthralgia and cutaneous eruption. Following introduction of the virus to the Americas in 2013, the first cases in Colombia occurred in September of 2014, and they reached a cumulative total of 399,932 cases by June of 2015.


OBJECTIVE
To identify the genotype or genotypes responsible for the current epidemic in Colombia and to describe the genetic variability of the virus in the country.


METHODS
Serum samples from patients presenting with symptoms compatible with Chikungunya fever during 2014-2015 were selected for the study. RT-PCR products of the E1 gene from these samples were used for sequencing and subsequent phylogenetic and adaptive evolution analyses.


RESULTS
The study identified only the presence of the Asian genotype in Colombia. Comparing the Colombian sequences with other sequences from the Americas revealed an average of 0.001 base substitutions per site, with 99.7% and 99.9% nucleotide identity and 99.9% amino acid identity. The adaptive evolution analysis indicated that the E1 gene is under strong purifying selection.


CONCLUSIONS
The first epidemic of Chikunguya fever in Colombia was caused by the circulation of the virus Asian genotype. Further genotypic surveillance of the virus in Colombia is required to detect possible changes in its epidemiology, fitness and pathogenicity.
Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia. klaiton@ins.gov.co.
Katherine
K
Laiton-Donato
José A
JA
Usme-Ciro
Angélica
A
Rico
Lissethe
L
Pardo
Camilo
C
Martínez
Daniela
D
Salas
Susanne
S
Ardila
Andrés
A
Páez
D000330:Aedes / Q000821:virology*; D018354:Alphavirus Infections / Q000453:epidemiology* / Q000473:pathology; D000569:Americas; D000818:Animals; D065632:Chikungunya Fever / Q000453:epidemiology / Q000821:virology*; D002646:Chikungunya virus; D003105:Colombia; D004196:Disease Outbreaks; D005838:Genotype; D006801:Humans
Chikungunya virus; Colombia; genotype; molecular epidemiology; phylogeny; surveillance