miRNA independent hepacivirus variants suggest a strong evolutionary pressure to maintain miR-122 dependence.

• Main Authors: Yingpu Yu, Troels K H Scheel, Joseph M Luna, Hachung Chung, Eiko Nishiuchi, Margaret A Scull, Natalia Echeverría, Inna Ricardo-Lax, Amit Kapoor, W Ian Lipkin, Thomas J Divers, Douglas F Antczak, Bud C Tennant, Charles M Rice
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2017-10-01
• Series: PLoS Pathogens
• Online Access: https://doi.org/10.1371/journal.ppat.1006694
• ISSN: 1553-7366; 1553-7374

Hepatitis C virus (HCV) requires the liver specific micro-RNA (miRNA), miR-122, to replicate. This was considered unique among RNA viruses until recent discoveries of HCV-related hepaciviruses prompting the question of a more general miR-122 dependence. Among hepaciviruses, the closest known HCV relative is the equine non-primate hepacivirus (NPHV). Here, we used Argonaute cross-linking immunoprecipitation (AGO-CLIP) to confirm AGO binding to the single predicted miR-122 site in the NPHV 5'UTR in vivo. To study miR-122 requirements in the absence of NPHV-permissive cell culture systems, we generated infectious NPHV/HCV chimeric viruses with the 5' end of NPHV replacing orthologous HCV sequences. These chimeras were viable even in cells lacking miR-122, although miR-122 presence enhanced virus production. No other miRNAs bound this region. By random mutagenesis, we isolated HCV variants partially dependent on miR-122 as well as robustly replicating NPHV/HCV variants completely independent of any miRNAs. These miRNA independent variants even replicate and produce infectious particles in non-hepatic cells after exogenous delivery of apolipoprotein E (ApoE). Our findings suggest that miR-122 independent HCV and NPHV variants have arisen and been sampled during evolution, yet miR-122 dependence has prevailed. We propose that hepaciviruses may use this mechanism to guarantee liver tropism and exploit the tolerogenic liver environment to avoid clearance and promote chronicity.