Difference of Intrahost Dynamics of the Second Human Pegivirus and Hepatitis C Virus in HPgV-2/HCV-Coinfected Patients

Abstract

BackgroundThe second human pegivirus (HPgV-2) and hepatitis C virus (HCV) belong to the Flaviviridae family and share some common genome features. However, the two viruses exhibit significantly different genetic diversity. The comparison of intrahost dynamics of HPgV-2 and HCV that mainly reflect virus-host interactions is needed to elucidate their intrahost difference of genetic diversity and the possible mechanisms.MethodsIntrahost single nucleotide variations (iSNVs) were identified by means of next-generation sequencing from both cross-sectional and longitudinal samples from HPgV-2- and HCV-coinfected patients. The levels of human cytokines were quantified in the patient before and after HCV elimination by the treatment of direct-acting antivirals (DAA).ResultsUnlike HCV, the viral sequences of HPgV-2 are highly conserved among HPgV-2-infected patients. However, iSNV analysis confirmed the intrahost variation or quasispecies of HPgV-2. Almost all iSNVs of HPgV-2 did not accumulate or transmit within host over time, which may explain the highly conserved HPgV-2 consensus sequence. Intrahost variation of HPgV-2 mainly causes nucleotide transition in particular at the 3rd codon position and synonymous substitutions, indicating purifying or negative selection posed by host immune system. Cytokine data further indicate that HPgV-2 infection alone may not efficiently stimulate innate immune responses since proinflammatory cytokine expression dramatically decreased with elimination of HCV.ConclusionThis study provided new insights into the intrahost genomic variations and evolutionary dynamics of HPgV-2 as well as the impact of host immune selection and virus polymerase on virus evolution. The different genetic diversity of HPgV-2 and HCV makes HPgV-2 a potential new model to investigate RNA virus diversity and the mechanism of viral polymerase in modulating virus replication.

RNA-Dependent RNA Polymerase of the Second Human Pegivirus Exhibits a High-Fidelity Feature

“…Our previous studies showed that sofosbuvir can inhibit HCV replication but not HPgV-2 replication ( 13 , 14 ). Sofosbuvir is a uridine analog and a nucleotide inhibitor (NI) of RdRp for the treatment of chronic HCV infection ( 21 – 23 ).…”

“…Forberg et al suggested that the relationship between HPgV-2 and HCV is commensal but not dependent ( 12 ). It is hypothesized that, with reliance on HCV, HPgV-2 would be under minimal selective pressure and maintain its sequence fidelity within the host ( 13 ). We emphasize that as the fidelity of HPgV-2 RdRp was evaluated only in in vitro polymerase assays, our results may not completely reflect the true behavior of HPgV-2 RdRp in vivo.…”

“…In contrast to HCV and the first human pegivirus (HPgV-1, or GBV-C), HPgV-2 exhibits minimal genetic diversity, and identity of HPgV-2 genetic sequences collected from different countries or regions is as high as 94%, while both HCV and HPgV-1 have multiple genotypes and subtypes ( 12 ). In addition, HPgV-2 shows a significantly lower level of quasispecies and intrahost variation than HCV ( 13 ). The high conservation of the HPgV-2 genome may be related to inefficient innate immune responses and low immune selection pressures ( 12 , 13 ).…”

“…In addition, HPgV-2 shows a significantly lower level of quasispecies and intrahost variation than HCV ( 13 ). The high conservation of the HPgV-2 genome may be related to inefficient innate immune responses and low immune selection pressures ( 12 , 13 ). Previous studies suggest that HPgV-2 may be an ancient and stable virus with many fewer mutations.…”

“…Moreover, our previous studies indicated that direct-acting antiviral (DAA) treatment, such as the nucleotide inhibitor (NI) sofosbuvir targeting viral RdRp, could eliminate HCV but not HPgV-2 infection ( 13 , 14 ). The preclinical assessments and clinical analysis of sofosbuvir trials have shown that mutations in HCV RdRp lead to a decrease in drug susceptibility ( 15 – 18 ) and that the drug resistance is closely related to RdRp fidelity ( 19 , 20 ).…”