Bayesian Inference of the Evolution of HBV/E

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.

High prevalence and diversity of hepatitis B and hepatitis delta virus in Gabon

“…Our identification of HBV‐E confirms previous studies showing that genotype E circulates in Gabon, improving evidence of its endemicity in Western and central Africa. Furthermore, high sequence similarity to other HBV‐E strains from this area corroborates previous findings of low genetic diversity across a wide area in West Africa, suggesting its recent emergence . Though we found HBV‐E across all provinces in Gabon, its predominance in the North of the country could indicates that it may have recently been introduced from this Western region of the continent.…”

“…HBV subgenotype A4, reported regionally in Cameroon 44 TA B L E 2 ( Continued) area in West Africa, suggesting its recent emergence. 46,47 Though we found HBV-E across all provinces in Gabon, its predominance in the North of the country could indicates that it may have recently been introduced from this Western region of the continent.…”

Genotypes and Genetic Variability of Hepatitis B Virus

“…However, as a result of the constraints of the overlapping open reading frames and the presence of secondary RNA structures, such as epsilon, coded by nonoverlapping regions, the mutation rate of the various regions of the HBV genome varies [1,2]. The HBV genome has been estimated to evolve at an error rate of approximately 10 -3 to 10 -6 nucleotide substitutions/site/year [3,4,5,6,7,8,9]. To date, based on an intergroup divergence >7.5% across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A-I [10,11,12], with a putative 10th genotype, ‘J', isolated from a single individual [13].…”

“…This genotype is endemic in western, central Africa, with a low genetic diversity, intimating a recent emergence of 200 years or less [4]. As opposed to subgenotype A1, which was dispersed by the slave trade [18], genotype E is rarely found outside Africa, except in individuals of African descent, further supporting its recent emergence after the forced migrations of slavery.…”

“…As opposed to subgenotype A1, which was dispersed by the slave trade [18], genotype E is rarely found outside Africa, except in individuals of African descent, further supporting its recent emergence after the forced migrations of slavery. Using Bayesian inference, a median time of evolution from a most recent common ancestor (tMRCA) of 130 years has been calculated [4]. This differs from a tMRCA of 6,000 years estimated by others [8].…”