Tracking HCV protease population diversity during transmission and susceptibility of founder populations to antiviral therapy

Abstract

Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity. In all transmissions, a genetic bottleneck was observed, although diverse viral populations were transmitted in each case. A low frequency cloud of mutations (<1%) was detectable in the donor inoculum and recipient mice, with single nucleotide variants (SNVs) > 1% restricted to a subset of nucleotides. The population of SNVs >1% was reduced upon transmission while the low frequency SNV cloud remained stable. Fixation of multiple identical synonymous substitutions was apparent in independent transmissions, and no evidence for reversion of T-cell epitopes was observed. In addition, susceptibility of founder populations to antiviral therapy was assessed. Animals were treated with protease inhibitor (PI) monotherapy to track resistance associated substitution (RAS) emergence. Longitudinal analyses revealed a decline in population diversity under therapy, with no detectable RAS >1% prior to therapy commencement. Despite inoculation from a common source and identical therapeutic regimens, unique RAS emergence profiles were identified in different hosts prior to and during therapeutic failure, with complex mutational signatures at protease residues 155, 156 and 168 detected. Together these analyses track viral population complexity at high-resolution in the human-liver chimeric mouse model post-transmission and under therapeutic intervention, revealing novel insights into the evolutionary processes which shape viral protease population composition at various critical stages of the viral life-cycle.

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

“…The evolvability of SARS-CoV-2 spike protein RBD in the presence of nAbs depends on both the mutation rate in the presence of selection pressure and the mutational tolerance of the spike protein. The mutation rate of SARS-CoV-2 is in line with that of other single-strand RNA viruses, [ 28 ], and is relatively high when compared against some members of this group (such as Hepatitis C) for which evolution has practical clinical consequences ( S1 Table ) [ 29 , 30 ]. Mutation rates themselves are evolvable and may increase over time due to natural selection [ 31 ].…”

Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein

“…Mutation rates for RNA viruses in general are among the highest known (on the order of 10 −6 per base per viral replication cycle). When compared against many other RNA viruses, such as Hepatitis C, for which evolution has practical clinical consequences, SARS-CoV-2 has a relatively high evolutionary rate (Table S1) ( 32, 33 ). As mentioned earlier, the currently estimated mutation rate for SARS-CoV-2 is in the context of neutral genetic drift ( 20 ).…”

Animal Models to Study Hepatitis C Virus Infection

“…Next to chimpanzees, this human liver chimeric mouse model is also attractive for monitoring HCV drug resistance ( 118 ). Our laboratory has particular interest in this matter and showed that the combination of DAAs with entry inhibitors restricts the breakthrough of DAA-resistant viruses ( 119 , 120 ). Finally, the uPA-SCID mouse model is also applicable for studies concerning malaria, which is caused by the parasite Plasmodium falciparum , and the study of the hepatitis E virus (HEV) ( 121 – 125 ).…”