Intra-host analysis of hepaciviral glycoprotein evolution reveals signatures associated with viral persistence and clearance

Abstract

Even 30 years after the discovery of the hepatitis C virus (HCV) in humans there is still no vaccine available. Reasons for this include the high mutation rate of HCV, which allows the virus to escape immune recognition, and the absence of an immunocompetent animal model for vaccine development. Phylogenetically distinct hepaciviruses (genus Hepacivirus, family Flaviviridae) have been isolated from diverse species, each with a narrow host range: the equine hepacivirus (EqHV) is the closest known relative of HCV. In this study we used amplicon-based deep-sequencing to investigate the viral intra-host population composition of the genomic regions encoding the surface glycoproteins E1 and E2. Patterns of E1E2 substitutional evolution were compared in longitudinally sampled EqHV-positive sera of naturally and experimentally infected horses and HCV-positive patients. Intra-host virus diversity was higher in chronically than in acutely infected horses, a pattern which was similar in the HCV infected patients. However, overall glycoprotein variability was higher in HCV compared to EqHV. Additionally, selection pressure in HCV populations was higher, especially within the N-terminal region of E2, corresponding to the hypervariable region 1 (HVR1) in HCV. An alignment of glycoprotein sequences from diverse hepaciviruses identified the HVR1 as unique characteristic of HCV: hepaciviruses from non-human species lack this region. Together, these data indicate that EqHV infection of horses could represent a powerful surrogate animal model to gain insights into hepaciviral evolution and HCVs HVR1-mediated immune evasion strategy.

Experimental cross-species infection of donkeys with equine hepacivirus and analysis of host immune signatures

“…Model systems, such as the EqHV infections in equids, could help understand viral and host determinants required for species barrier crossing. For instance, recently, a study about intra-host diversity of EqHV and HCV shed light into viral determinants important for persistent hepacivirus infection and indicated the hypervariable region 1 in HCV as an important determinant in infecting the human population [ 33 ]. Furthermore, a previous study by Hoffmann et al 2020 found a divergent EqHV sequence in donkeys that differed by 22% from the reference strain which could have an impact on EqHV diagnostics in donkeys [ 34 ].…”

SARS-CoV-2 entry route impacts a range of downstream viral and cellular processes

“…Upon transmission, fixation of mutations in RNA virus populations can occur through founder effect (limited genetic variability in the inoculum) or selective sweeps (an advantageous phenotype is swept to fixation) (For examples see ( Gömer et al, 2022 ) and ( Brown et al, 2012 )). As the dynamics of early innate immune activation differs between viral entry routes, we hypothesized that the resulting contrasting selective environments, in which early viral replication occurs, could influence the frequency or fixation of mutations in the cellular viral population.…”

An Equine Model for Vaccination against a Hepacivirus: Insights into Host Responses to E2 Recombinant Protein Vaccination and Subsequent Equine Hepacivirus Inoculation

“…The reasons for the apparent failure of the vaccine in Vaccine Pony 4 are not known. Investigation of the EqHV viral intrahost population composition of the genomic regions encoding E1 and E2 in experimentally infected horses revealed low bottleneck severity and high heterogeneity of the virus populations initiating infection [ 42 ]. Furthermore, intra-host viral diversification was observed over time [ 42 ].…”

“…Investigation of the EqHV viral intrahost population composition of the genomic regions encoding E1 and E2 in experimentally infected horses revealed low bottleneck severity and high heterogeneity of the virus populations initiating infection [ 42 ]. Furthermore, intra-host viral diversification was observed over time [ 42 ]. Although intra-host heterogeneity of EqHV was shown to be less pronounced than for HCV [ 42 ], the potential roles in reducing vaccine effectiveness and inducing varied immune responses among hosts warrant consideration.…”

“…Furthermore, intra-host viral diversification was observed over time [ 42 ]. Although intra-host heterogeneity of EqHV was shown to be less pronounced than for HCV [ 42 ], the potential roles in reducing vaccine effectiveness and inducing varied immune responses among hosts warrant consideration.…”