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

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

Serological HCV results by age.

<p>Abbreviations: yrs, years; sampled, number sampled; +ve, number of serologically positive samples;</p>*<p>, participants sex was not recorded; U/N, age not recorded.</p

Serological HCV results by country.

<p>Abbreviations: %, percentage; CI, Confidence Interval.</p

Serological HCV results by town in Papua New Guinea.

<p>Abbreviations: %, percentage; CI, Confidence Interval.</p

Primers.

<p>Primers used in RT-PCR, and PCR reactions of the 5′UTR and NS5B region of HCV and the nested amplifications of the IL28B SNPs. Genotype 7 is in quotations as it is yet to be confirmed as a new genotype. TaqMan SNP typing for rs8099917 was conducted using custom Assays-on-Demand products from Applied Biosystems (C__11710096_10) and verified with the listed primers, using standard PCR and sequencing techniques.</p