Discovery of 5’ NAD capped viral RNAs reveals evolutionary divergent 5’ metabolite capping across hepaciviruses
Hepatitis C virus (HCV), an important pathogen and prototype hepacivirus, 5’ caps its RNA with flavin adenine dinucleotide (FAD); no other 5’ metabolite capped viral RNAs have been identified. Here, we establish NADzymeID, allowing specific identification of 5’ nicotinamide adenine dinucleotide (NAD). Using NADzymeID, we find that Norway rat hepacivirus 1 (NrHV-1) and related hepaciviruses use 5’ NAD capping, whereas the closest relatives of HCV use 5’ FAD, thereby revealing evolutionary divergence of 5’ capping. NrHV-1 replication is attenuated in absence of NAD, and NrHV-1 is cleared more rapidly in mice with reduced intrahepatic NAD levels. As observed for 5’ FAD, 5’ NAD protects viral RNA from RIG-I mediated innate immune sensing. Thus, despite evolutionary divergence, metabolite capping generally confers evasion of innate immune responses. These represent the first examples of 5’ NAD capping for viruses, providing tools also to investigate the elusive function of cellular 5’ metabolite caps. Larsen et al. demonstrate that one clade of hepaciviruses use FAD and the other use NAD to protect their RNA genomes by 5’ metabolite capping and facilitate innate immune evasion. The study provides the first examples of viral 5’NAD RNA capping.
Authors
- Troels K. H. Scheel (ORCID: https://orcid.org/0000-0003-1545-4067)
- Sonja Fernbach (ORCID: https://orcid.org/0000-0002-3362-3832)
- Helena D. Tjørnelund (ORCID: https://orcid.org/0000-0001-8648-3266)
- Jonas T. Treebak (ORCID: https://orcid.org/0000-0003-1488-7012)
- Kenn Holmbeck (ORCID: https://orcid.org/0000-0002-4472-3257)
- Louise Nielsen
- Jens Bukh (ORCID: https://orcid.org/0000-0002-7815-4806)
- Anna V. Sherwood (ORCID: https://orcid.org/0000-0001-7153-8420)
- Caroline E. Thorselius (ORCID: https://orcid.org/0009-0002-0668-1348)
- Helena S. Larsen
- Jeppe Vinther (ORCID: https://orcid.org/0000-0002-3847-3853)
- Santseharay Ramírez (ORCID: https://orcid.org/0000-0003-3699-1814)
- Raphael Wolfisberg (ORCID: https://orcid.org/0000-0002-6191-2084)
- Anna S. Hassing (ORCID: https://orcid.org/0000-0003-1650-8784)
- Sabina Chubanava (ORCID: https://orcid.org/0000-0002-5842-2623)
- Amal Al‐Chaer
- Matthew J. Kennedy (ORCID: https://orcid.org/0009-0007-6343-1528)
- Eva Jakljevič (ORCID: https://orcid.org/0000-0003-3657-1254)
- Lizandro R. Rivera-Rangel
- Paula H. Faller
- Cathrine B. Vågbø
- Nicola Rose
- Line A. Ryberg
Institutions
- University of Copenhagen (DK)
- Central Norway Regional Health Authority (NO)
- Novo Nordisk Foundation (DK)
- Copenhagen University Hospital (DK)
- National Institute for Biological Standards and Control (GB)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-06-29
- DOI
- https://doi.org/10.1038/s41467-026-74886-0
- Primary Topic
- Hepatitis C virus research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- McGill University
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Novo Nordisk
- Helse Midt-Norge
- Norges Forskningsråd
- Novo Nordisk Foundation Center for Basic Metabolic Research
- Centro de Investigação em Biomedicina