Viral RNA Families
A project to provide a comprehensive collection of viral RNA secondary structure families for the virology community.
- Goal
- Expand Rfam's coverage of viral ncRNA families by incorporating new and updated families identified through whole-genome alignment analysis.
- Status
- Ongoing — Coronaviridae families complete (release 14.2); Hepacivirus families updated through release 14.10; Flaviviridae families added in release 14.9. Further virus families are in progress.
- Collaborators
- Manja Marz and the European Virus Bioinformatics Centre (EVBC), Friedrich Schiller University Jena
Coronaviridae RNA Families
In release 14.2 we created 10 families representing the complete 5'- and 3'-UTRs for Alpha-, Beta-, Gamma-, and Deltacoronaviruses, plus a specialised set for the subgenus Sarbecovirus (SARS-CoV-1 and SARS-CoV-2). Four existing non-UTR families were also updated.
SARS-CoV-2 coronavirus. Genome: OX309346.1 (29,903 nt), RNA structures: 3. Generated with RD2T and Rfam. See preprint: https://doi.org/10.64898/2026.05.10.724034 [1]
| Accession ↕ | Rfam ID ↕ | Description | Sequences ↕ | Species ↕ |
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Hepacivirus RNA Families
In release 14.8, four new Hepatitis C RNA families were added and five existing families updated (with four families removed: RF02585, RF02586, RF02587, RF02588). In release 14.10, nine HCV families were further refined to better reflect their secondary structures.
Rfam 15.0 created 5 new Hepatitis C virus (HCV) families (RF04305–RF04309).
Hepatitis C virus (HCV). Genome: NC_038882.1 (9,646 nt), RNA structures: 12. Generated with RD2T and Rfam. See preprint: https://doi.org/10.64898/2026.05.10.724034
| Accession ↕ | Rfam ID ↕ | Description | Sequences ↕ | Species ↕ |
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Flaviviridae RNA Families
Added in release 14.9, these families cover the major Flavivirus clades including mosquito-borne, tick-borne, insect-specific, and no-known-vector viruses, as well as Pestivirus families.
In Rfam 15.1, we updated and included new Pestivirus genus RNAs, comprising four new 3′UTR RNAs and an updated Pestivirus internal ribosome entry site (IRES, RF00209) [2][3]. Family RF04322 (Pestivirus-3UTR-stem-SLI) includes stem-loop I, which is conserved throughout all Pestivirus genomes, while RF04323 (Pestivirus-3UTR-SLIV-SLII-BVDV-1), RF04324 (Pestivirus-3UTR-SLIV-SLIII-SLII-CSFV), and RF04325 (Pestivirus-3UTR-SLIII-scrofae) are clade-specific families. All are included in clan CL00151.
| Accession ↕ | Rfam ID ↕ | Description | Sequences ↕ | Species ↕ |
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Work in Progress
We are working on adding families from additional virus families, including Filoviridae (e.g. Ebolavirus) and Rhabdoviridae (e.g. Rabies viruses). Contact Rfam if you are interested in a specific virus family or have feedback about this project.
Publications
- Muston P, Triebel S, Nawrocki E, Ontiveros-Palacios N, Jandalala I, Sweeney B, Bateman A, Marz M, Petrov AI, Madrigal P (2026) Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT. bioRxiv 2026.05.10.724034. doi: 10.64898/2026.05.10.724034
- Triebel S, Eulenfeld T, Ontiveros-Palacios N, Sweeney B, Tautz N, Marz M (2025) First full-genome alignment representative for the genus Pestivirus. RNA. doi: 10.1261/rna.080732.125
- Ontiveros-Palacios N, Cooke E, Nawrocki EP, Triebel S, Marz M, Rivas E, Griffiths-Jones S, Petrov AI, Bateman A, Sweeney B (2025) Rfam 15: RNA families database in 2025. Nucleic Acids Res 53(D1):D258–D267. doi: 10.1093/nar/gkae1023
- Triebel S, Lamkiewicz K, Ontiveros N, Sweeney B, Stadler PF, Petrov AI, Niepmann M, Marz M (2024) Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Sci Rep 14(1):15145. doi: 10.1038/s41598-024-62897-0
- Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI (2021) Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res 49(D1):D192–D200. doi: 10.1093/nar/gkaa1047
- R2DT (2024) Viral genomes. https://docs.r2dt.bio/en/latest/viral-genomes.html
