Evolutionary dynamics of hepatitis C virus during very early infections

Speaker: Fabio Luciani

Affiliation: Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales

Time: Monday 30/05/2011 from 14:00 to 15:00

Venue: Access Grid UWS. Presented from Parramatta (EB.1.32), accessible from Campbelltown (26.1.50) and Penrith (Y239).

Abstract: Background and aims Primary hepatitis C virus (HCV) infection typically manifests asymptomatically, and most commonly evolves into chronic infection via a complex interplay between rapid viral evolution and host immune selective pressures. The characteristics of transmitted virus(es) and early viral dynamics remain incompletely defined. Here, full genome amplification and next generation sequencing (NGS) are employed to quantify HCV evolution in very early infection.

Methods Ten subjects recruited in a prospective cohort of high risk HCV uninfected prisoners were identified with initial viraemia prior to ultimate seroconversion. Blood samples were collected every second week for 24 weeks before viral clearance (n=3D5) or chronicity (n=3D5). Viral RNA was extracted for cDNA synthesis of the full-length genome, amplified by nested PCR and subjected to NGS (Roche 454). Bayesian statistics was applied - and validated with positive controls - to eliminate NGS errors and to reconstruct 3-5 kb region of the HCV genome from short NGS reads. Re-constructed sequences of HCV quasi-species were used to measure selective pressure. Phylogenetic and statistical analyses (BEAST) were used to estimate the time of the infection and to quantify the number of transmitted (founder) viruses for each subject.

Results Here, very early HCV infection was studied longitudinally from pre-seroconversion until resolution of outcome by means of a full genome viral evolution analysis in four subjects infected via injection drug use =96 two infections resulted in clearance, two were persistent. By means of next generation sequencing (NGS) and corroborative standard cloning, single nucleotide polymorphisms (SNPs) across the entire HCV genome were identified with population frequencies as low as 1%. Viral haplotypes were constructed to infer the sequence of founder viruses and build time-measured phylogenies. Two sequential bottleneck events were identified: the first was associated with transmission, with only 1-3 viruses successfully initiating infection in the new host; the second occurred approximately 100 days post-infection, around the time of seroconversion. In cases resulting in chronic infection, the declining viremia and diversity was followed by emergence of a new variant evolving from one of the founder viruses, showing that chronic infection is characterized by a selective sweep with a small number of mutated residues reaching fixation. Some of these mutations occurred in known targets of CD8 cytotoxic T cell and neutralizing antibody responses.

Conclusions: This work provides the first genome-wide investigation of viral evolution and immune response in very early HCV infection, suggesting early and rapid evolution of HCV under strong host selective pressure.

Biography: Fabio Luciani, PhD in theoretical biology, Masters in Theoretical Physics. His research interests are in evolutionary dynamics of infectious diseases, biostatistics, mathematical models in complex system. He is an NHMRC training fellow at the UNSW.