Abstract
Despite its wide spread and high prevalence in sub-Saharan Africa, hepatitis B virus genotype E (HBV/E) has a surprisingly low genetic diversity, indicating an only recent emergence of this genotype in the general African population. Here, we performed extensive phylogeographic analyses, including Bayesian MCMC modeling. Our results indicate a mutation rate of 1.9×10−4 substitutions per site and year (s/s/y) and confirm a recent emergence of HBV/E, most likely within the last 130 years, and only after the transatlantic slave-trade had come to an end. Our analyses suggest that HBV/E originated from the area of Nigeria, before rapidly spreading throughout sub-Saharan Africa. Interestingly, viral strains found in Haiti seem to be the result of multiple introductions only in the second half of the 20th century, corroborating an absence of a significant number of HBV/E strains in West Africa several centuries ago. Our results confirm that the hyperendemicity of HBV(E) in today's Africa is a recent phenomenon and likely the result of dramatic changes in the routes of viral transmission in a relatively recent past.
Highlights
Hepatitis B virus (HBV), a major public health burden, is a partially double-stranded circular DNA virus of,3.2 kb
The authors linked the global spread of HBV to human migratory patterns to estimate a global evolution during the past 34,000 years and found a long-term substitution rate of 2.261026 s/s/y on the S-gene which is almost 100 times slower than previous estimates. Based on this mutation rate, the tMRCA of genotype E was estimated to be 6000 years. We address these apparent discrepancies and provide evidence that hepatitis B virus genotype E (HBV/E) has only recently been introduced into the general West African population
Substitution rates and tMRCA To estimate the time of evolution from a most recent common ancestor and assess the nucleotide substitution rates, we performed Bayesian coalescent analyses on 167 HBV/E fulllength and 454 S-gene strains
Summary
Hepatitis B virus (HBV), a major public health burden, is a partially double-stranded circular DNA virus of ,3.2 kb. Because of differences in the computational approach as well as the dataset, large differences of nucleotide substitution rates were observed, ranging from ,1024 to 1025 substitutions per site and year (s/s/y) [16,17,18,19,20,21] As most of these studies were based on repeated sampling in the same chronic carriers of the virus or on viral strains collected from mother child pairs, the observed substitution rates are largely indicative of short evolutionary rates and may not necessarily reflect general longer term evolutionary rates. A substitution rate of 3.261024 was reported for a small HBV/E dataset [15] All of these studies indicate an only recent introduction and a short time of evolution of HBV/E in the general population of sub-Saharan Africa
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