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

Research output: Contribution to journalJournal articleResearchpeer-review

  • Yingpu Yu
  • Scheel, Troels Kasper Høyer
  • Joseph M. Luna
  • Hachung Chung
  • Eiko Nishiuchi
  • Margaret A. Scull
  • Natalia Echeverría
  • Inna Ricardo-Lax
  • Amit Kapoor
  • Ian W. Lipkin
  • Thomas J. Divers
  • Douglas F. Antczak
  • Bud C. Tennant
  • Charles M. Rice

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.

Original languageEnglish
Article numbere1006694
JournalPLOS Pathogens
Issue number10
Number of pages21
Publication statusPublished - 2017

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