Hepatitis B Virus: Alternative phylogenetic hypotheses and its impact on molecular evolution inferences.

Characterizing molecular evolution patterns of the Hepatitis B Virus (HBV) is important for a better understanding of the natural history of this infection. However, several molecular evolution estimates are conditioned on tree topology. There is no consensus about the phylogenetic relationships of HBV genotypes, and different studies often find alternative topologies. While most studies consider HBV genotypes F and H as sister to all other human genotypes, a recent study suggested an alternative HBV phylogeny that indicates an accelerated substitution rate for HBV-F/H partially driven by positive selection. In this study, we evaluate the impact of alternative HBV topologies on inferences of HBV phylogeny, rate acceleration, and positive selection on the HBV-F/H branch. Our results indicate that under certain methodological approaches alternative HBV topologies are equally likely. Considering phylogenetic uncertainty, there is no evidence that HBV-F/H had an accelerated substitution rate, even though inferences of positive selection are robust to alternative background topologies. Our results further suggest that, under reasonable assumptions, HBV-F/H most likely represents the sister lineage to all other human/ape HBV genotypes. Understanding the full range of likely topologies will be crucial for elaborating, testing, and refining hypothesis about the evolutionary HBV origins in our species.

High prevalence of HBV/A1 subgenotype in native south Americans may be explained by recent economic developments in the Amazon.

Native American populations present the highest prevalence of Hepatitis B Virus (HBV) infection in the Americas, which may be associated to severe disease outcomes. Ten HBV genotypes (A­J) have been described, displaying a remarkable geographic structure, which most likely reflects historic patterns of human migrations. In this study, we characterize the HBV strains circulating in a historical sample of Native South Americans to characterize the historical viral dynamics in this population. The sample consisted of 1070 individuals belonging to 38 populations collected between 1965 and 1997. Presence of HBV DNA was checked by quantitative real-time PCR, and determination of HBV genotypes and subgenotypes was performed through sequencing and phylogenetic analysis of a fragment including part of HBsAg and Pol coding regions (S/Pol). A Bayesian Skyline Plot analysis was performed to compare the viral population dynamics of HBV/A1 strains found in Native Americans and in the general Brazilian population. A total of 109 individuals were positive for HBV DNA (~ 10%), and 70 samples were successfully sequenced and genotyped. Subgenotype A1 (HBV/A1), related to African populations and the African slave trade, was the most prevalent (66­94%). The Skyline Plot analysis showed a marked population expansion of HBV/A1 in Native Americans occurring more recently (1945­1965) than in the general Brazilian population. Our results suggest that historic processes that contributed to formation of HBV/A1 circulating in Native American are related with more recent migratory waves towards the Amazon basin, which generated a different viral dynamics in this region.

Origin of HBV and its arrival in the Americas--the importance of natural selection on time estimates.

BACKGROUND: The strong geographic structure shown by the global pattern of HBV lineages suggests an ancient origin for this virus; however, estimates based on the molecular clock suggest a very recent origin for the Native American genotypes F and H. In this study, we contribute to this debate by estimating the divergence times of genotypes F and H and by discussing how evolutionary rates estimated from recent samples may underestimate the divergence time of more ancient nodes in HBV phylogenies. METHODS: A total of 108 complete HBV genotype F and H genomes were compared to 44 reference genomes from other genotypes. Time estimates were based on a Bayesian method with evolutionary rates taken from the literature. To assess the pattern of substitutions in recent versus old branches we mapped the phylogenetic distribution of all mutations occurring in genotypes F and H using a maximum likelihood approach and compared the number of synonymous and non-synonymous mutations in young and old branches of HBV genotype F and H phylogeny using a χ² test. RESULTS: Estimated divergence times between genotypes F and H depend heavily on the evolutionary rate. While fast rates suggest a recent separation of these genotypes (approximately 800 years ago), slow rates suggest an earlier divergence (up to approximately 13,000 years ago). There is a clear excess of non-synonymous substitutions in the most recent branches of HBV phylogeny (P=4.87×10⁻¹5), most likely suggesting the action of purifying selection. CONCLUSIONS: These results suggest that rates estimated based on recent samples will overestimate the evolutionary rate and underestimate the coalescence times for ancient nodes in HBV phylogeny.