Hepatitis delta virus Raw sequence reads

The hepatitis delta virus (HDV) genome is comprised of a single-stranded circular RNA molecule, approximately 1700 nucleotides in length, with high intermolecular self-complementarity, giving rise to a rod-like structure. Only 1 open reading frame (ORF) of HDV genome is transcribed, and codes for a protein, the hepatitis delta antigen (HDAg), existing in 2 isoforms: the small (S-HDAg) isoform consisting of 195 amino acids (aa) and the long (L-HDAg) with 214 aa. This virus replicates by a double-rolling-circle model, which involves the host RNA polymerase II and generates a concatemer of complimentary copy of the genome, known as the antigenome. The individual antigenomic molecules are obtained through a self-cleavage process led by the viral ribozyme, and are used as a template for the genomic RNA, through another process of rolling circle amplification, or enter into the translation process by producing HDAg.Although the HDV genome replicates through the cellular RNA polymerase II, it shows a high genetic variability, high rate of evolution (1.2x10-3 to 9.5x10-3 nt substitutions_site_year). The aim of this project is to use next-generation sequencing technologies to analyze the variability of HDV genome in regions relevant for its replication, such as the ribozyme or the HDAg ORF.