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Viruses 2011, 3(2), 83-101; doi:10.3390/v3020083
Article

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

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Received: 3 December 2010; in revised form: 6 January 2011 / Accepted: 6 January 2011 / Published: 25 January 2011
(This article belongs to the Special Issue Virus Dynamics and Evolution)
Download PDF [221 KB, uploaded 25 January 2011]
Abstract: Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements.
Keywords: hepatitis B virus; molecular clock; Bayesian phylogenetics hepatitis B virus; molecular clock; Bayesian phylogenetics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Harrison, A.; Lemey, P.; Hurles, M.; Moyes, C.; Horn, S.; Pryor, J.; Malani, J.; Supuri, M.; Masta, A.; Teriboriki, B.; Toatu, T.; Penny, D.; Rambaut, A.; Shapiro, B. Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation. Viruses 2011, 3, 83-101.

AMA Style

Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A, Shapiro B. Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation. Viruses. 2011; 3(2):83-101.

Chicago/Turabian Style

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth. 2011. "Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation." Viruses 3, no. 2: 83-101.


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