title: A bioinformatics pipeline for the analyses of viral escape dynamics and host immune responses during an infection.
abstract: Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno-virology of viral infections, as these allow fast and cheap generation of genomic data. However, due to the large volumes of data generated, a thorough understanding of the biological and immunological significance of such information is often difficult. This paper proposes a pipeline that allows visualization and statistical analysis of viral mutations that are associated with immune escape. Taking next generation sequencing data from longitudinal analysis of HCV viral genomes during a single HCV infection, along with antigen specific T-cell responses detected from the same subject, we demonstrate the applicability of these tools in the context of primary HCV infection. We provide a statistical and visual explanation of the relationship between cooccurring mutations on the viral genome and the parallel adaptive immune response against HCV.
authors.affiliation: Inflammation and Infection Research Centre, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Preston
authors.identifier: 0000-0002-2849-9216
authors.initials: P
authors.lastname: Leung
authors.affiliation: Inflammation and Infection Research Centre, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Rowena
authors.initials: R
authors.lastname: Bull
authors.affiliation: Inflammation and Infection Research Centre, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lloyd
authors.affiliation: Inflammation and Infection Research Centre, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Fabio
authors.initials: F
authors.lastname: Luciani
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016679:Genome, Viral / Q000235:genetics; D015658:HIV Infections / Q000235:genetics / Q000821:virology; D016174:Hepacivirus / Q000235:genetics; D006526:Hepatitis C / Q000235:genetics / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics*; D009154:Mutation; D012984:Software