The hepatitis B virus - Insights into genetic variability, evolution and Bayesian phylogeographic inference

Project: Dissertation

Layman's description

Hepatitis B infection is a major global health problem with more than a quarter of a billion people living with chronic carriership and with almost 800000 casualties per year due to liver complications caused by the disease; this despite the fact that a vaccine has been available since 1982 and is part of the vaccination program in large parts of the world. Thus there is a long way to go to eradicate the disease and an important step along that way is to increase the understanding of the genetic variability of the virus, its evolutionary rate and which factors are involved in the spread and expansion of the disease. These are key factors both for further vaccine development and for the understanding of what kind of preventive measures need to be taken to limit the spread to uninfected individuals.

In terms of genome size, the hepatitis B virus is the smallest virus known to infect humans and its compactness with multiple overlapping reading frames puts restraints on the emergence of mutations. In addition, the chronic infection can be divided into different phases characterized by large differences in both infectivity and mutation rate. This makes both short- and long-term evolution of hepatitis B difficult to describe. In the papers included in this thesis we aimed to investigate genetic variation within the precore and core promoter region and to describe the origin, spread and diversification of HBV genotype A.

We described a novel insertion in precore causing a frameshift and the abolishment of HBeAg secretion because of a resulting premature stop codon. The sequence material originated in a patient from whom we had serum collected throughout the process of seroconversion. Viral load decreased by three logs and ALT values normalized concomitantly with the emergence of the mutated variant which could be detected early during the process as a minor variant along with the wildtype. The position of the insertion lies within the functionally important encapsidation signal necessary for the packaging of the HBV genome into core particles. Prediction of the structure of the encapsidation signal in the mutant was performed and revealed that functionally important parts of the structure remained intact.

The variability in the core promoter and precore region was described in paper II. Genotypes A-D were studied and mutations were found to occur at key positions as A1762T, G1764A, G1896A and G1899A. The proportions of strains originating in seroconverted patients differed between the four genotypes. A number of rare mutations were found, notably the double mutations C1857T along with G1897A and C1856T together with G1898A.

The evolution, global transmission and expansion of HBV/A has previously been described using a variety of different phylogenetic approaches. The main differences lie in the choice of method for calibrating the molecular clock – the correlation of the observed root-to tip divergence in the tree with units of time. We used a GenBank dataset supplemented with sequence material from the early 70’s and a tip-dating approach with a local clock model that allowed for rate variation between lineages. We showed that the deeper temporal distribution the added sequence material provided was necessary for a statistically robust calculation of tMRCA and evolutionary rate and conversely that the HBV/A material presently available in GenBank contained an insufficient temporal signal. The main finding in our study indicated a diversification of HBV/A in East Africa/Asia, Europe and West Africa in the 19th century followed by a rapid expansion during the mid-20th century. Hepatitis B quasi-subgenotype A3 has previously been proposed to have been introduced to Haiti through the trans-Atlantic slave trade, but our study indicated that these strains appear to have been introduced later in an historical context similar to that describing how HIV was introduced to the Americas.
Effective start/end date2012/03/012018/03/09