Evolutionary rates and timescale comparison of Chikungunya viruses inferred from the whole genome/E1 gene with special reference to the 2005-07 outbreak in the Indian subcontinent
Autor(es): Cherian Sarah S, Walimbe Atul M, Jadhav Santosh M, Gandhe Swati S, Hundekar Supriya L, Mishra Akhilesh C, Arankalle Vidya A
Resumo: Chikungunya (CHIK) virus reemerged during 2005-07 as an important pathogen causing massive disease outbreaks affecting India - several countries of the Indian Ocean. Knowledge of the evolutionary rates - divergence times of the CHIK virus may help to better underst- the disease epidemiology. Considering the limited availability of such information, we estimated the substitution rates - the ancestral times for all the CHIK genotypes - also the time to the most recent common ancestor (tMRCA) of the 2005-07 isolates. Using whole genomes - partial E1 gene datasets, we applied the Bayesian Markov Chain Monte Carlo (MCMC) framework that explicitly accounts for lineage-specific evolutionary rates through the use of 'relaxed' molecular clock models. Under a constant population relaxed clock model, the evolutionary timescale of CHIK viruses in this study was estimated to be in the last 300 years. The progenitor of the 2005-07 viruses was found to have existed around 9 years ago, - to have originated from Central Africa. The presence of a strain in India in 2000 that bears 99% identity with a Ug-an strain of 1982, which correlates with the tMRCA of the Indian - Indian Ocean isolates, confirms our earlier report that the progenitor of the 2005-07 isolates originates from Ug-a's neighbourhood. The 'A226V' mutation that existed in the Indian Ocean isolates since late 2005 was found to occur only in the 2007 isolate from India. The study confirms the epidemiological data, specifically with regard to the re-emergence of CHIKV - throws light on the evolutionary dynamics of CHIK viruses.
Palavras-Chave: Chikungunya virus; Evolutionary rates; Divergence times; Bayesian; MCMC; tMRCA; India
Imprenta: Infection, Genetics and Evolution, v. 9, n. 1, p. 16-23, 2009
Identificador do objeto digital: 10.1016/j.meegid.2008.09.004
Descritores: Chikungunya virus - Genome ; Chikungunya virus - Pathogenesis ; Chikungunya virus - Proteins ; Chikungunya virus - Viral infections ; Chikungunya Virus - Virus ; Chikungunya virus - Epidemiology ; Chikungunya virus - Public health
Data de publicação: 2009
