Full Genome Amplification and Quasispecies Reconstruction of the Hepatitis B Virus from Next Generation Sequencing Data

Abstract

The Hepatitis B Virus (HBV) is a DNA virus that infects most vertebrates and is part of the Hepadnaviridae family. Transmission of HBV occurs through bodily fluids such as blood and sexual contact. HBV targets the liver cells of mammals, including humans, and can result in acute or chronic infections. The virus replicates within host liver cells by reverse transcription of an RNA intermediate and also integrates into the host genome. HBV undergoes high mutation rates due to its error-prone replication, leading to a diverse population of viral variants. Consequently, It has several genotypes (A to J). In chronic infections, HBV forms a complex mixture of viral variants within the host, known as a quasispecies consisting of major, intermediate, and minor variants. As selection occurs on the entire viral population, and progresses over the course of infection, the dynamics of viral evolution cannot be understood from the fittest strain alone. Therefor, quasispecies reconstructions present a unique avenue to gain novel insights into the emergence of novel strains. This research seeks to enhance our understanding of HBV quasispecies dynamics.