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Bayesian coalescent inference of hepatitis A virus populations: evolutionary rates and patterns

¹ Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
² Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC H3G 1Y6, Canada
³ Laboratorio de Organización y Evolución del Genoma, Instituto de Biología, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay

Correspondence
Juan Cristina
cristina{at}cin.edu.uy

Hepatitis A virus (HAV) is a hepatotropic member of the family Picornaviridae. Previous studies suggested that HAV may evolve more slowly than other members of the family. To estimate HAV substitution rates precisely, we used a Bayesian Markov chain Monte Carlo (MCMC) approach on temporally sampled HAV VP1 full-length sequences from strains isolated in France. A mean rate of evolutionary change of 9.76x10^–4 nucleotide substitution per site per year was found. The results also revealed that the synonymous rate found for HAV is lower than that of other members of the family. Bayesian skyline plots revealed a sharp decline in the effective number of infections in 1996, coinciding with the introduction of HAV vaccine.

A table showing the origins of French genotype IA HAV strains is available with the online version of this paper.

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