Molecular determinants of mouse adaptation of rat hepacivirus
Lack of immunocompetent animal models for hepatitis C virus (HCV) impedes vaccine development and studies of  immune responses. Norway rat hepacivirus (NrHV) infection in rats shares HCV-defining characteristics, including hepatotropism, chronicity, immune responses, and aspects of pathology. To exploit genetic variants and research tools, we previously adapted NrHV to prolonged infection in laboratory mice. Through intrahepatic RNA inoculation of molecular clones of identified variants, we here characterized four mutations in the envelope proteins responsible for mouse adaptation, including one disrupting a glycosylation site. These mutations led to high titer viremia, similar to that observed in rats. In 4-week-old mice, infection was cleared after around 5 weeks compared to 2-3 weeks for non-adapted virus. In contrast, the mutations led to persistent but attenuated infection in rats, and they partially reverted accompanied by an increase in viremia. Attenuated infection in rat but not mouse hepatoma cells demonstrated that the characterized mutations were indeed mouse adaptive rather than generally enhancing fitness in both cell lines, and that species determinants and not immune interactions were responsible for attenuation in rats. Unlike persistent NrHV infection in rats, acute resolving infection in mice was not associated with development of neutralizing antibodies. Finally, infection of scavenger receptor B-I (SR-BI) knockout mice suggested that adaptation to mouse SR-BI was not a primary function of the identified mutations. Rather, the virus may have adapted to lower dependency on SR-BI, thereby potentially surpassing species-specific differences. In conclusion, we identified specific determinants of NrHV mouse adaptation, suggesting species-specific interactions during entry. Overall design: Mice and rats were infected by intrahepatic inoculation of 10 µg in vitro-transcribed viral genomic RNA. Blood samples were collected at the indicated timepoints and viral RNA was extracted form blood sera using TRIzol. The whole viral ORF was reverse-transcribed by RT-PCR using the Maxima H Minus Reverse Transcriptase. The resulting cDNA was purified and libraries were prepared using the NebNext Ultra II FS DNA Library Prep Kit for Illumina. Libraries were quantified using Qubit and pooled at equimolar concentration. Deep sequencing was performed on an Illumina MiSeq instrument.