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Viruses
v.10(12); 2018 Dec
PMC6315422
Published online 2018 Dec 17. doi: 10.3390/v10120720
1 WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; gro.ertnecazneulfni@truH.noreA
2 Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ua.gro.hm@retteN.snaH (H.J.N.); ua.gro.lrdiv@nhojelttiL.teragraM (M.L.); ua.gro.lrdiv@neuY.ylliL (L.Y.)
3 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; ua.ude.yendys@ihS.gnaM (M.S.); ua.ude.yendys@nede.sj (J.-S.E.); ua.ude.yendys@semloH.drawdE (E.C.H.)
4 Centre for Integrative Ecology, Deakin University, Geelong, VIC 3220, Australia; ua.ude.nikaed@nessaalK.lecraM
* Correspondence: gro.ertnecazneulfni@elliw.ellehcim ; Tel.: +61-3-9342-9303
Received 2018 Nov 9; Accepted 2018 Dec 9.
Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/ ).
GUID: 23B978F0-E3AE-4F2E-ADD3-84981854EBA2
Keywords: co-evolution, dabbling duck, hepatitis D virus, phylogeny
1. Taylor J., Pelchat M. Origin of hepatitis Delta virus. Future Microbiol. 2010; 5 :393–402. doi: 10.2217/fmb.10.15. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
2. Taylor J.M., Purcell R.H., Farci P. Hepatitis D (D) virus. In: Knipe D.M., Howley P.M., editors. Fields Virology. Lippincott Williams & Wilkins; Philadelphia, PA, USA: 2013. pp. 2222–2241. [ Google Scholar ]
3. Wedemeyer H., Manns M.P. Epidemiology, pathogenesis and management of hepatitis D: Update and challenges ahead. Nat. Rev. Gastroenterol. Hepatol. 2010; 7 :31–40. doi: 10.1038/nrgastro.2009.205. [ PubMed ] [ CrossRef ] [ Google Scholar ]
4. WHO Hepatitis D Fact Sheet. [(accessed on 24 February 2018)]; 2017 Available online: http://www.who.int/mediacentre/factsheets/hepatitis-d/en/
5. Le Gal F., Gault E., Ripault M.P., Serpaggi J., Trinchet J.C., Gordien E., Deny P. Eighth major clade for hepatitis Delta virus. Emerg. Infect. Dis. 2006; 12 :1447–1450. doi: 10.3201/eid1209.060112. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
6. Littlejohn M., Locarnini S., Yuen L. Origins and evolution of hepatitis B virus and hepatitis D virus. Cold Spring Harb. Perspect. Med. 2016; 6 :a021360. doi: 10.1101/cshperspect.a021360. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
7. Brazas R., Ganem D. Delta-interacting protein and the origin of hepatitis Delta antigen-Response. Science. 1997; 276 :825. [ Google Scholar ]
8. Long M., de Souza S.J., Gilbert W. Delta-interacting protein and the origin of hepatitis Delta antigen. Science. 1997; 276 :824–825. doi: 10.1126/science.276.5313.824. [ PubMed ] [ CrossRef ] [ Google Scholar ]
9. Brazas R., Ganem D. A cellular homolog of hepatitis Delta antigen: Implications for viral replication and evolution. Science. 1996; 274 :90–94. doi: 10.1126/science.274.5284.90. [ PubMed ] [ CrossRef ] [ Google Scholar ]
10. Salehi-Ashtiani K., Luptak A., Litovchick A., Szostak J.W. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science. 2006; 313 :1788–1792. doi: 10.1126/science.1129308. [ PubMed ] [ CrossRef ] [ Google Scholar ]
11. Taylor J.M. Host RNA circles and the origin of hepatitis Delta virus. World J. Gastroenterol. 2014; 20 :2971–2978. doi: 10.3748/wjg.v20.i11.2971. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
12. Shi M., Lin X.D., Tian J.H., Chen L.J., Chen X., Li C.X., Qin X.C., Li J., Cao J.P., Eden J.S., et al. Redefining the invertebrate RNA virosphere. Nature. 2016; 540 :539–543. doi: 10.1038/nature20167. [ PubMed ] [ CrossRef ] [ Google Scholar ]
13. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., et al. Full-length transcriptome assembly from RNA-SEQ data without a reference genome. Nat. Biotechnol. 2011; 29 :644–652. doi: 10.1038/nbt.1883. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
14. Buchfink B., Xie C., Huson D.H. Fast and sensitive protein alignment using diamond. Nat. Methods. 2015; 12 :59–60. doi: 10.1038/nmeth.3176. [ PubMed ] [ CrossRef ] [ Google Scholar ]
15. Chapman J.R., Helin A.S., Wille M., Atterby C., Jarhult J.D., Fridlund J.S., Waldenstrom J. A panel of stably expressed reference genes for real-time qPCR gene expression studies of mallards ( Anas platyrhynchos ) PLoS ONE. 2016; 11 :e0149454. doi: 10.1371/journal.pone.0149454. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
16. Remmert M., Biegert A., Hauser A., Soding J. Hhblits: Lightning-fast iterative protein sequence searching by hmm-hmm alignment. Nat. Methods. 2011; 9 :173–175. doi: 10.1038/nmeth.1818. [ PubMed ] [ CrossRef ] [ Google Scholar ]
17. Katoh K., Standley D.M. Mafft multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013; 30 :772–780. doi: 10.1093/molbev/mst010. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
18. Capella-Gutierrez S., Silla-Martinez J.M., Gabaldon T. Trimal: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009; 25 :1972–1973. doi: 10.1093/bioinformatics/btp348. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
19. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of phyml 3.0. Syst. Biol. 2010; 59 :307–321. doi: 10.1093/sysbio/syq010. [ PubMed ] [ CrossRef ] [ Google Scholar ]
20. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31 :3406–3415. doi: 10.1093/nar/gkg595. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
21. Webb C.H.T., Luptak A. HDV-like self-cleaving ribozymes. RNA Biol. 2011; 8 :719–727. doi: 10.4161/rna.8.5.16226. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
22. Byun Y., Han K. Pseudoviewer3: Generating planar drawings of large-scale RNA structures with pseudoknots. Bioinformatics. 2009; 25 :1435–1437. doi: 10.1093/bioinformatics/btp252. [ PubMed ] [ CrossRef ] [ Google Scholar ]
23. Wolf E., Kim P.S., Berger B. Multicoil: A program for predicting two- and three-stranded coiled coils. Protein Sci. 1997; 6 :1179–1189. doi: 10.1002/pro.5560060606. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
24. Wang K.S., Choo Q.L., Weiner A.J., Ou J.H., Najarian R.C., Thayer R.M., Mullenbach G.T., Denniston K.J., Gerin J.L., Houghton M. Structure, sequence and expression of the hepatitis Delta (delta) viral genome. Nature. 1986; 323 :508–514. doi: 10.1038/323508a0. [ PubMed ] [ CrossRef ] [ Google Scholar ]
25. Hetzel U., Szirovicza L., Smura T., Prähauser B., Vapalahti O., Kipar A., Hepojoki J. Identification of a novel deltavirus in boa constrictor. BioRxiv Preprint. 2018 doi: 10.1101/429753. [ CrossRef ] [ Google Scholar ]
26. Perrotta A.T., Been M.D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis Delta-virus RNA. Nature. 1991; 350 :434–436. doi: 10.1038/350434a0. [ PubMed ] [ CrossRef ] [ Google Scholar ]
27. Kozak M. Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie. 1994; 76 :815–821. doi: 10.1016/0300-9084(94)90182-1. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
28. Proudfoot N.J. Ending the message: Poly(a) signals then and now. Genes Dev. 2011; 25 :1770–1782. doi: 10.1101/gad.17268411. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
29. Hsieh S.Y., Taylor J. Regulation of polyadenylation of hepatitis Delta virus antigenomic RNA. J. Virol. 1991; 65 :6438–6446. [ PMC free article ] [ PubMed ] [ Google Scholar ]
30. Casey J.L., Bergmann K.F., Brown T.L., Gerin J.L. Structural requirements for RNA editing in hepatitis Delta virus: Evidence for a uridine-to-cytidine editing mechanism. Proc. Natl. Acad. Sci. USA. 1992; 89 :7149–7153. doi: 10.1073/pnas.89.15.7149. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
31. Glenn J.S., Watson J.A., Havel C.M., White J.M. Identification of a prenylation site in delta-virus large antigen. Science. 1992; 256 :1331–1333. doi: 10.1126/science.1598578. [ PubMed ] [ CrossRef ] [ Google Scholar ]
32. Xia Y.P., Lai M.M. Oligomerization of hepatitis Delta antigen is required for both the trans-activating and trans-dominant inhibitory activities of the delta antigen. J. Virol. 1992; 66 :6641–6648. [ PMC free article ] [ PubMed ] [ Google Scholar ]
33. Lazinski D.W., Taylor J.M. Relating structure to function in the hepatitis Delta virus antigen. J. Virol. 1993; 67 :2672–2680. [ PMC free article ] [ PubMed ] [ Google Scholar ]
34. Huang W.H., Chen C.W., Wu H.L., Chen P.J. Post-translational modification of delta antigen of hepatitis D virus. Curr. Top. Microbiol. 2006; 307 :91–112. [ PubMed ] [ Google Scholar ]
35. Lai M.M.C. RNA replication without RNA-dependent RNA polymerase: Surprises from hepatitis Delta virus. J. Virol. 2005; 79 :7951–7958. doi: 10.1128/JVI.79.13.7951-7958.2005. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
Articles from Viruses are provided here courtesy of Multidisciplinary Digital Publishing Institute (MDPI)
1. Taylor J., Pelchat M. Origin of hepatitis Delta virus. Future Microbiol. 2010; 5 :393–402. doi: 10.2217/fmb.10.15. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
2. Taylor J.M., Purcell R.H., Farci P. Hepatitis D (D) virus. In: Knipe D.M., Howley P.M., editors. Fields Virology. Lippincott Williams & Wilkins; Philadelphia, PA, USA: 2013. pp. 2222–2241. [ Google Scholar ] [ Ref list ]
3. Wedemeyer H., Manns M.P. Epidemiology, pathogenesis and management of hepatitis D: Update and challenges ahead. Nat. Rev. Gastroenterol. Hepatol. 2010; 7 :31–40. doi: 10.1038/nrgastro.2009.205. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
4. WHO Hepatitis D Fact Sheet. [(accessed on 24 February 2018)]; 2017 Available online: http://www.who.int/mediacentre/factsheets/hepatitis-d/en/ [ Ref list ]
5. Le Gal F., Gault E., Ripault M.P., Serpaggi J., Trinchet J.C., Gordien E., Deny P. Eighth major clade for hepatitis Delta virus. Emerg. Infect. Dis. 2006; 12 :1447–1450. doi: 10.3201/eid1209.060112. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
6. Littlejohn M., Locarnini S., Yuen L. Origins and evolution of hepatitis B virus and hepatitis D virus. Cold Spring Harb. Perspect. Med. 2016; 6 :a021360. doi: 10.1101/cshperspect.a021360. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
7. Brazas R., Ganem D. Delta-interacting protein and the origin of hepatitis Delta antigen-Response. Science. 1997; 276 :825. [ Google Scholar ] [ Ref list ]
8. Long M., de Souza S.J., Gilbert W. Delta-interacting protein and the origin of hepatitis Delta antigen. Science. 1997; 276 :824–825. doi: 10.1126/science.276.5313.824. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
9. Brazas R., Ganem D. A cellular homolog of hepatitis Delta antigen: Implications for viral replication and evolution. Science. 1996; 274 :90–94. doi: 10.1126/science.274.5284.90. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
10. Salehi-Ashtiani K., Luptak A., Litovchick A., Szostak J.W. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science. 2006; 313 :1788–1792. doi: 10.1126/science.1129308. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
11. Taylor J.M. Host RNA circles and the origin of hepatitis Delta virus. World J. Gastroenterol. 2014; 20 :2971–2978. doi: 10.3748/wjg.v20.i11.2971. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
12. Shi M., Lin X.D., Tian J.H., Chen L.J., Chen X., Li C.X., Qin X.C., Li J., Cao J.P., Eden J.S., et al. Redefining the invertebrate RNA virosphere. Nature. 2016; 540 :539–543. doi: 10.1038/nature20167. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
13. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., et al. Full-length transcriptome assembly from RNA-SEQ data without a reference genome. Nat. Biotechnol. 2011; 29 :644–652. doi: 10.1038/nbt.1883. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
14. Buchfink B., Xie C., Huson D.H. Fast and sensitive protein alignment using diamond. Nat. Methods. 2015; 12 :59–60. doi: 10.1038/nmeth.3176. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
15. Chapman J.R., Helin A.S., Wille M., Atterby C., Jarhult J.D., Fridlund J.S., Waldenstrom J. A panel of stably expressed reference genes for real-time qPCR gene expression studies of mallards ( Anas platyrhynchos ) PLoS ONE. 2016; 11 :e0149454. doi: 10.1371/journal.pone.0149454. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
16. Remmert M., Biegert A., Hauser A., Soding J. Hhblits: Lightning-fast iterative protein sequence searching by hmm-hmm alignment. Nat. Methods. 2011; 9 :173–175. doi: 10.1038/nmeth.1818. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
17. Katoh K., Standley D.M. Mafft multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013; 30 :772–780. doi: 10.1093/molbev/mst010. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
18. Capella-Gutierrez S., Silla-Martinez J.M., Gabaldon T. Trimal: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009; 25 :1972–1973. doi: 10.1093/bioinformatics/btp348. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
19. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of phyml 3.0. Syst. Biol. 2010; 59 :307–321. doi: 10.1093/sysbio/syq010. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
20. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31 :3406–3415. doi: 10.1093/nar/gkg595. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
21. Webb C.H.T., Luptak A. HDV-like self-cleaving ribozymes. RNA Biol. 2011; 8 :719–727. doi: 10.4161/rna.8.5.16226. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
22. Byun Y., Han K. Pseudoviewer3: Generating planar drawings of large-scale RNA structures with pseudoknots. Bioinformatics. 2009; 25 :1435–1437. doi: 10.1093/bioinformatics/btp252. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
23. Wolf E., Kim P.S., Berger B. Multicoil: A program for predicting two- and three-stranded coiled coils. Protein Sci. 1997; 6 :1179–1189. doi: 10.1002/pro.5560060606. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
24. Wang K.S., Choo Q.L., Weiner A.J., Ou J.H., Najarian R.C., Thayer R.M., Mullenbach G.T., Denniston K.J., Gerin J.L., Houghton M. Structure, sequence and expression of the hepatitis Delta (delta) viral genome. Nature. 1986; 323 :508–514. doi: 10.1038/323508a0. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
25. Hetzel U., Szirovicza L., Smura T., Prähauser B., Vapalahti O., Kipar A., Hepojoki J. Identification of a novel deltavirus in boa constrictor. BioRxiv Preprint. 2018 doi: 10.1101/429753. [ CrossRef ] [ Google Scholar ] [ Ref list ]
26. Perrotta A.T., Been M.D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis Delta-virus RNA. Nature. 1991; 350 :434–436. doi: 10.1038/350434a0. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
27. Kozak M. Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie. 1994; 76 :815–821. doi: 10.1016/0300-9084(94)90182-1. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
28. Proudfoot N.J. Ending the message: Poly(a) signals then and now. Genes Dev. 2011; 25 :1770–1782. doi: 10.1101/gad.17268411. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
29. Hsieh S.Y., Taylor J. Regulation of polyadenylation of hepatitis Delta virus antigenomic RNA. J. Virol. 1991; 65 :6438–6446. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
30. Casey J.L., Bergmann K.F., Brown T.L., Gerin J.L. Structural requirements for RNA editing in hepatitis Delta virus: Evidence for a uridine-to-cytidine editing mechanism. Proc. Natl. Acad. Sci. USA. 1992; 89 :7149–7153. doi: 10.1073/pnas.89.15.7149. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
31. Glenn J.S., Watson J.A., Havel C.M., White J.M. Identification of a prenylation site in delta-virus large antigen. Science. 1992; 256 :1331–1333. doi: 10.1126/science.1598578. [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
32. Xia Y.P., Lai M.M. Oligomerization of hepatitis Delta antigen is required for both the trans-activating and trans-dominant inhibitory activities of the delta antigen. J. Virol. 1992; 66 :6641–6648. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
33. Lazinski D.W., Taylor J.M. Relating structure to function in the hepatitis Delta virus antigen. J. Virol. 1993; 67 :2672–2680. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
34. Huang W.H., Chen C.W., Wu H.L., Chen P.J. Post-translational modification of delta antigen of hepatitis D virus. Curr. Top. Microbiol. 2006; 307 :91–112. [ PubMed ] [ Google Scholar ] [ Ref list ]
35. Lai M.M.C. RNA replication without RNA-dependent RNA polymerase: Surprises from hepatitis Delta virus. J. Virol. 2005; 79 :7951–7958. doi: 10.1128/JVI.79.13.7951-7958.2005. [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ] [ Ref list ]
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