title: Evidence for homologous recombination in Chikungunya Virus.
abstract: Chikungunya Virus (CHIKV), a mosquito-transmitted alphavirus, causes acute fever and joint pain in humans. Recently, endemic CHIKV infection outbreaks have jeopardized public health in wider geographical regions. Here, we analyze the phylogenetic associations of CHIKV and explore the potential recombination events on 152 genomic isolates deposited in GenBank database. The CHIKV genotypes [West African, Asian, East/Central/South African (ECSA)], and a clear division of ECSA clade into three sub-groups (I-II-III), were defined by Bayesian analysis; similar results were obtained using E1 gene sequences. A nucleotide identity-based approach is provided to facilitate CHIKV classification within ECSA clade. Using seven methods to detect recombination, we found a statistically significant event (p-values range: 1.14×10(-7)-4.45×10(-24)) located within the nsP3 coding region. This finding was further confirmed by phylogenetic networks (PHI Test, p=0.004) and phylogenetic tree incongruence analysis. The recombinant strain, KJ679578/India/2011 (ECSA III), derives from viruses of ECSA III and ECSA I. Our study demonstrates that recombination is an additional mechanism of genetic diversity in CHIKV that might assist in the cross-species transmission process.
authors.affiliation: Virology Area, School of Biochemistry and Pharmaceutical Sciences, National University of Rosario, Suipacha 531, 2000 Rosario, Argentina.
authors.forename: Pablo E
authors.initials: PE
authors.lastname: Casal
authors.affiliation: Virology Area, School of Biochemistry and Pharmaceutical Sciences, National University of Rosario, Suipacha 531, 2000 Rosario, Argentina; Human Virology Group, IBR-CONICET/National University of Rosario, Suipacha 570, 2000 Rosario, Argentina.
authors.forename: Diego
authors.initials: D
authors.lastname: Chouhy
authors.affiliation: Human Virology Group, IBR-CONICET/National University of Rosario, Suipacha 570, 2000 Rosario, Argentina.
authors.forename: Elisa M
authors.initials: EM
authors.lastname: Bolatti
authors.affiliation: Virology Area, School of Biochemistry and Pharmaceutical Sciences, National University of Rosario, Suipacha 531, 2000 Rosario, Argentina.
authors.forename: Germán R
authors.initials: GR
authors.lastname: Perez
authors.affiliation: Human Virology Group, IBR-CONICET/National University of Rosario, Suipacha 570, 2000 Rosario, Argentina.
authors.forename: Emma J
authors.initials: EJ
authors.lastname: Stella
authors.affiliation: Virology Area, School of Biochemistry and Pharmaceutical Sciences, National University of Rosario, Suipacha 531, 2000 Rosario, Argentina; Human Virology Group, IBR-CONICET/National University of Rosario, Suipacha 570, 2000 Rosario, Argentina. Electronic address: giri@ibr-conicet.gov.ar.
authors.forename: Adriana A
authors.initials: AA
authors.lastname: Giri
mesh_terms: D001499:Bayes Theorem; D002646:Chikungunya virus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D059765:Homologous Recombination; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D014759:Viral Envelope Proteins
keywords: Bayesian phylogeny; Chikungunya Virus; Complete ORFs/E1 gene; East/Central/South African clade; Nucleotide identity classification; Recombination