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Ribozyviria

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Ribozyviria
A ribbon diagram of a hepatitis D virus ribozyme
Ribbon diagram of a self-cleaved form of the genomic HDV ribozyme
Virus classification Edit this classification
(unranked): Virus
Realm: Ribozyviria
Family: Kolmioviridae
Genera

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Ribozyviria is a realm of animal viruses. Viruses in the realm are characterized by the presence of ribozymes in the genome that are involved in replication. They encode one protein, DAg, which associates with the single-stranded, negative-sense RNA genome, forming a rod-shaped ribonucleoprotein (RNP) complex. The RNP complex is surrounded by an envelope that has spike proteins from a helper virus. The best-studied ribozyvirian is the hepatitis D virus (HDV), and its helper virus is the hepatitis B virus. Because of the dependency on helper viruses, ribozyvirians infect the same cells as their helper viruses.

Ribozyvirians infect cells by attaching to the surface with helper virus-derived spike proteins on the surface of the envelope. The envelope fuses with the cell membrane, releasing the RNP into the cell, where it moves to the nucleus for replication. A host RNA polymerase replicates the genome in a double rolling circle process, during which individual progeny genomes are excised from strands of numerous consecutive genomes by viral ribozymes. The DAg protein is translated from messenger RNA and binds to the genome. Envelopes are then obtained before progeny viruses leave the cell.

Ribozyvirians infect a variety of animals, including amphibians, birds, fish, insects, mammals, and reptiles. In humans, HDV causes the liver disease hepatitis D, with symptoms such as cirrhosis, hepatitis, and liver cancer. The origin of ribozyvirians is unclear, but they have been proposed to originate from an escaped gene from a cellular host or mis-spliced RNA. HDV was the first virus of the realm to be discovered, in 1977, and was the only known ribozyvirian for about 40 years. Starting in the late 2010s, other members began to be discovered, and in 2021, both the realm Ribozyviria and its sole family, Kolmioviridae, were established.

Classification

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Ribozyviria contains one family, Kolmioviridae, with no intermediate taxa between the ranks of realm and family.[1] Kolmioviridae contains 11 genera:[2]

Characteristics

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Genome and proteins

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Ribozyvirians have negative-sense single-stranded RNA (–ssRNA) genomes that are about 1.5–1.7 kilobases in length. The genome is a non-segmented, covalently-closed circular RNA (cccRNA) molecule that organizes into a rod-like shape due to a high amount of self-complementarity. Their genomes contain at least two ribozymes: one on the genomic (negative-sense) strand, and one on the antigenomic (positive-sense) strand.[4][5] The only protein encoded by ribozyvirians is the delta antigen (DAg),[6] encoded in the antigenome.[7] Some deltaviruses express two forms of DAg,[6] called small delta antigen (S-DAg) and large delta antigen (L-DAg).[8] L-DAg is almost identical to S-DAg; the only difference is that L-DAg contains 19 or 20 additional amino acid residues,[7] created by genome editing by the host.[9]

Structure

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A diagram of hepatitis D virions
A diagram of hepatitis D virion structure. It makes its own ribozyme proteins, while the envelope proteins derive from a helper virus, the hepatitis B virus.

The structure of ribozyvirians has only been detailed for deltaviruses.[10] The extracellular particles (virions) of deltaviruses are roughly spherical, pleomorphic in shape and about 36–43 nanometers in diameter. Virions consist of a rod-shaped genomic ribonucleoprotein (RNP) complex surrounded by a viral envelope with spikes derived from a helper virus. The RNP complex consists of the genome and the nucleoprotein DAg, which associates with the genome.[8][9][11] The quantity of S-DAg and L-DAg bound to the genome is variable, but there is about a 70 to 1 protein:RNA ratio.[9] DAg has an alpha-helical fold and forms into complexes of eight DAg proteins (octamers), and it is believed that the genome wraps around these octamers.[12]

Life cycle

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The replication process of ribozyvirians is only known for deltaviruses. They enter host cells by attaching to receptors on the cell surface with their envelope proteins, which are derived from helper viruses. Because of this dependency on helper viruses, ribozyvirians infect the same cells as their helper viruses. After attachment, the envelope fuses with the host cell membrane, releasing the RNP complex into the cell. There, the RNP moves to the cell nucleus, where the genome is replicated.[13][14] The genome is replicated during a double rolling circle process by a host DNA-directed RNA polymerase II enzyme. During replication, ribozymes in the antigenome and genome cleave concatemers of linear antigenomes and genomes and ligate (i.e., connect) individual linear progeny strands into a circular form.[11][13][14]

DAg facilitates the recruitment of chromatin remodeling complexes and the host RNA polymerase II,[12] which begins the replication process by progressing in a loop around the genome, producing a continuous, linear strand of numerous copies (a concatemer) of the antigenome. Ribozymes in the antigenome self-cleave the concatemer to produce individual linear antigenomes. These strands ligate to produce circular antigenomic molecules. The circular antigenome is then replicated in the same manner as the genome, creating a concatemer of genomic strands. Ribozymes in the genome self-cleave this concatemer to produce individual linear genomes, which are ligated into circular genomic molecules.[15]

Messenger RNA (mRNA) encoding DAg is transcribed from the negative-sense genome. Expression of DAg induces packaging of RNPs into envelopes made from the Golgi apparatus. These envelopes contain proteins of the helper virus and facilitate budding from the surface of the cell.[12][13] For deltaviruses, the envelope of hepatitis B virus (HBV) is recruited through farnesylation, which is a post-translational attachment of a hydrophobic molecule to a cysteine residue at the end (C-terminus) of L-DAg's amino acid sequence. This facilitates an interaction between the RNP and the HBV envelope to recruit the envelope.[16] Only genomic RNA molecules that fold into a rod-shape and have DAgs bound to them are packaged into virions. Antigenomes (i.e., positive-sense strands) are not found in virions.[14]

Dependency on helper viruses

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All ribozyvirians are believed to be dependent on evolutionarily unrelated helper viruses to complete their life cycle,[17] as autonomous ribozyvirians that do not rely on helper viruses have not been discovered.[12] Identified helper viruses include hepatitis B virus for deltaviruses and arenaviruses for daletviruses.[12][18] Other potential helper viruses include flaviviruses, herpesviruses, poxviruses, and retroviruses.[19]

Distribution

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Ribozyvirians are found in a variety of animals, including amphibians, birds, fish, insects, reptiles, mammals such as rodents, as well as in humans.[11][20] Specific species include common vampire bats, groundhogs, white-tailed deer, white-rumped munias, yellow-bellied tits, Australian zebra finches, and the fungus-growing termite Odontotermes wallonensis.[17] In addition to animals, metagenomic searches have identified ribozyvirian-like cccRNAs that encode homologs of DAg replicating in what are likely unicellular eukaryotes, suggesting a wider host range than what is known.[12]

Phylogenetics

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Ribozyvirians are not related to other –ssRNA viruses, which share common ancestry as they all encode RNA-dependent RNA polymerases. Some characteristics of ribozyvirians are similar to viroids, virusoids, and other replicons, such as genome structure, RNA transcription by means of a host DNA-directed RNA polymerase II, the presence of ribozymes, and RNA-to-RNA double rolling circle replication. The evolutionary origins of ribozyvirians and viroids, however, is unclear, as is their relationship with each other.[21][22] It has been proposed that ribozyvirians originate as an escaped gene from a cellular host, or as a result of mis-spliced RNA, from an ancient animal host or from a plant that transmitted the ancestral virus to animals.[23]

Within the family Kolmioviridae, genera are distinguished by the amino acid sequence similarity of the DAg protein. Viruses with less than or equal to 60% sequence similarity are assigned to different genera.[24] A phylogenetic tree of ribozyvirian genera based on the DAg protein is shown hereafter:[2]

Ribozyviria / Kolmioviridae

Interactions with hosts

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Among ribozyvirians, only deltaviruses (i.e., HDV) are known to cause disease.[17] In humans, they primarily infect liver cells[25] and can cause hepatitis D,[11][26] with symptoms such as cirrhosis, hepatitis, and liver cancer.[25] Deltaviruses infect an estimated 10–20 million people worldwide, about 5% of hepatitis B virus carriers.[27] HDV is entirely dependent on hepatitis B virus proteins for replication,[28] but it can also use flavivirus, hepacivirus, and vesiculovirus glycoproteins in place of HBV proteins.[29]

History

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The first ribozyvirian discovered was the hepatitis D virus.[30] The delta antigen HDAg was discovered in 1977[26] by Italian virologist Mario Rizzetto and his colleagues[31] and was initially thought to be an antigen of the hepatitis B virus. Further research showed that HDAg was associated with a separate virus, HDV.[28] For about 40 years, HDV was the only known ribozyvirian. Other ribozyvirians started to be discovered in the late 2010s.[30] In 2021, both Ribozyviria and its sole family, Kolmioviridae, were established.[1][32]

Etymology

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Ribozyviria takes the first part of its name from the word "ribozyme", a core characteristic of viruses in the realm. The second part, -viria, is the suffix used for virus realms.[20][32] The sole family in the realm, Kolmioviridae, derives the first part of its name from the Finnish word "kolmio", meaning triangle, a reference to the Greek letter Δ spelled out in the name of the genus Deltavirus. The second part is the suffix used for virus families, -viridae.[1][20]

See also

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References

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  1. 1 2 3 "Taxon Details: Kolmioviridae". International Committee on Taxonomy of Viruses. Archived from the original on 23 January 2026. Retrieved 16 April 2026.
  2. 1 2 Kuhn et al. 2024, sec. "Relationships within the family".
  3. ↑ "Species List: Kolmioviridae". International Committee on Taxonomy of Viruses. Retrieved 16 April 2026.
  4. ↑ Kuhn et al. 2024, secs. "Summary", "Nucleic acid".
  5. ↑ ICTV Taxonomy Profile: Deltavirus, sec. "Nucleic acid".
  6. 1 2 Kuhn et al. 2024, sec. "Proteins".
  7. 1 2 ICTV Taxonomy Profile: Deltavirus, sec. "Proteins".
  8. 1 2 ICTV Taxonomy Profile: Deltavirus, sec. "Morphology".
  9. 1 2 3 Condezo & San Martín 2024, p. 524.
  10. ↑ Kuhn et al. 2024, sec. "Morphology".
  11. 1 2 3 4 Kuhn et al. 2024, sec. "Summary".
  12. 1 2 3 4 5 6 Krupovic & Koonin 2026, sec. "Small realms Adnaviria and Ribozyviria".
  13. 1 2 3 Kuhn et al. 2024, sec. "Genome organization and replication".
  14. 1 2 3 ICTV Taxonomy Profile: Deltavirus, sec. "Genome organization and replication".
  15. ↑ "Symmetric Rolling Circle Replication". ViralZone. Swiss Institute of Bioinformatics. Archived from the original on 15 February 2026. Retrieved 16 April 2026.
  16. ↑ Condezo & San Martín 2024, pp. 524–525.
  17. 1 2 3 Kuhn et al. 2024, sec. "Biology".
  18. ↑ Hepojoki et al. 2020, pp. 4–5.
  19. ↑ Pérez-Vargas et al. 2021, sec. "Candidate Helper Viruses".
  20. 1 2 3 Hepojoki et al. 2020, p. 5.
  21. ↑ Kuhn et al. 2024, sec. "Relationships with other taxa".
  22. ↑ Pérez-Vargas et al. 2021, sec. "Phylogeny".
  23. ↑ Pérez-Vargas et al. 2021, secs. "Current Hypotheses of HDV Origin", "Conclusions".
  24. ↑ Kuhn et al. 2024, sec. "Genus demarcation criteria".
  25. 1 2 ICTV Taxonomy Profile: Deltavirus, sec. "Biology".
  26. 1 2 Lampertico et al. 2023, sec. "Summary".
  27. ↑ Lampertico et al. 2023, secs. "Summary", "Epidemiology of HDV infection".
  28. 1 2 Pérez-Vargas et al. 2021, sec. "Introduction".
  29. ↑ Hepojoki et al. 2020, p. 4.
  30. 1 2 Pérez-Vargas et al. 2021, sec. "Discovery of HDV-Like Viruses".
  31. ↑ Da, Heller & Koh 2019, sec. "Introduction".
  32. 1 2 "Taxon Details: Ribozyviria". International Committee on Taxonomy of Viruses. Archived from the original on 12 October 2026. Retrieved 16 April 2026.

Books

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  • Condezo GN, San Martín C (2024). "Maturation of Viruses". In Mateau MG (ed.). Structure and Physics of Viruses. Springer Cham. pp. 524–525. ISBN 978-3-031-65186-1.

Journal articles

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Other

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