Natural occurrence and characterization of two internal ribosome entry site elements in a novel virus, canine picodicistrovirus, in the picornavirus-like superfamily

Journal of Virology

Volumn 86, Issue 5, 2012, Pages 2797-2808

  Woo, Patrick C Y ^a,b   Lau, Susanna K P ^a,b   Choi, Garnet K Y ^b   Huang, Yi ^b   Teng, Jade L L ^b   Tsoi, Hoi Wah ^b   Tse, Herman ^a,b   Yeung, Man Lung ^a,b   Chan, Kwok Hung ^b   Jin, Dong Yan ^b   Yuen, Kwok Yung ^a,b  

^a THE UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HELICASE; POLYPROTEIN; RNA DIRECTED RNA POLYMERASE; SINGLE STRANDED RNA; VIRUS RNA;

5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DICISTROVIRIDAE; DNA SEQUENCE; DOG; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PICORNAVIRUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; DISEASE RESERVOIRS; DOGS; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; PHYLOGENY; PICORNAVIRIDAE; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, VIRAL;

CANIS FAMILIARIS; DICISTROVIRIDAE; PICORNAVIRIDAE; RNA VIRUSES;

EID: 84863229705     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.05481-11     Document Type: Article

References (60)

1. Anisimova M, Gascuel O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55:539-552.
2. Bazan JF, Fletterick RJ. 1988. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc. Natl. Acad. Sci. U. S. A. 85:7872-7876.
3. Belsham GJ. 2009. Divergent picornavirus IRES elements. Virus Res. 139: 183-192.
4. Bonning BC, Miller WA. 2010. Dicistroviruses. Annu. Rev. Entomol. 55:129-150.
5. Chan CP, et al. 2006. Modulation of the unfolded protein response by the severe acute respiratory syndrome coronavirus spike protein. J. Virol. 80: 9279-9287.
6. Chen YP, Siede R. 2007. Honey bee viruses. Adv. Virus Res. 70:33-80.
7. Chow M, et al. 1987. Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature 327:482-486.
8. Choy EY, Kok KH, Tsao SW, Jin DY. 2008. Utility of Epstein-Barr virus-encoded small RNA promoters for driving the expression of fusion transcripts harboring short hairpin RNAs. Gene Ther. 15:191-202.
9. Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1165.
10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Fernández-Miragall O, Lopez de Quinto S, Martinez-Salas E. 2009. Relevance ofRNAstructure for the activity of picornavirus IRES elements. Virus Res. 139:172-182.
12. Gorbalenya AE, Donchenko AP, Blinov VM, Koonin EV. 1989. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett. 243:103-114.
13. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM. 1989. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17:4713-4730.
14. Gorbalenya AE, Koonin EV, Lai MM. 1991. Putative papain-related thiol proteases of positive-strand RNA viruses. Identification of rubi- and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi-, alpha- and coronaviruses. FEBS Lett. 288:201-205.
15. Gorbalenya AE, Koonin EV, Wolf YI. 1990. A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett. 262:145-148.
16. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
17. Hämmerle T, Molla A, Wimmer E. 1992. Mutational analysis of the proposed FG loop of poliovirus proteinase 3C identifies amino acids that are necessary for 3CD cleavage and might be determinants of a function distinct from proteolytic activity. J. Virol. 66:6028-6034.
18. Hanzlik TN, Zeddam JL, Gordon KHJ, Christian PD. 1999. A new view of small RNA viruses of insects. Pestic. Outlook 10:22-26.
19. Harvala H, Simmonds P. 2009. Human parechoviruses: biology, epidemiology and clinical significance. J. Clin. Virol. 45:1-9.
20. Hellen CU, de Breyne S. 2007. A distinct group of hepacivirus/pestiviruslike internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination. J. Virol. 81:5850-5863.
21. Hughes PJ, Stanway G. 2000. The 2A proteins of three diverse picornaviruses are related to each other and to the H-rev107 family of proteins involved in the control of cell proliferation. J. Gen. Virol. 81:201-207.
22. Jang SK, Pestova TV, Hellen CU, Witherell GW, Wimmer E. 1990. Cap-independent translation of picornavirus RNAs: structure and function of the internal ribosomal entry site. Enzyme 44:292-309.
23. Kamer G, Argos P. 1984. Primary structural comparison of RNAdependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res. 12:7269-7282.
24. Kapoor A, et al. 2011. Characterization of a canine homolog of human Aichivirus. J. Virol. 85:11520-11525.
25. Klein J. 2009. Understanding the molecular epidemiology of foot-andmouth- disease virus. Infect. Genet. Evol. 9:153-161.
26. Koonin EV, Wolf YI, Nagasaki K, Dolja VV. 2008. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat. Rev. Microbiol. 6:925-939.
27. Krous HF, Langlois NE. 2010. Ljungan virus: a commentary on its association with fetal and infant morbidity and mortality in animals and humans. Birth Defects Res. A Clin. Mol. Teratol. 88:947-952.
28. Lau SK, et al. 2010. Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, selflimiting infection that allows recombination events. J. Virol. 84:2808-2819.
29. Lau SK, et al. 2010. Coexistence of different genotypes in the same bat and serological characterization of Rousettus bat coronavirus HKU9 belonging to a novel Betacoronavirus subgroup. J. Virol. 84:11385-11394.
30. Lau SK, et al. 2011. Complete genome analysis of three novel picornaviruses from diverse bat species. J. Virol. 85:8819-8828.
31. Lau SK, et al. 2005. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. U. S. A. 102:14040-14045.
32. Lau SK, et al. 2007. Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology 367: 428-439.
33. Lau SK, et al. 2010. Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China. Virology 404:106-116.
34. Lau SK, et al. 2012. Identification of a novel feline picornavirus from the domestic cat. J. Virol. 86:395-405.
35. Lau SK, et al. 2007. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J. Clin. Microbiol. 45:3655-3664.
36. Li L, et al. 2011. Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses. J. Gen. Virol. 92:2534-2541.
37. Lightner DV. 1996. Epizootiology, distribution and the impact on international trade of two penaeid shrimp viruses in the Americas. Rev. Sci. Tech. 15:579-601.
38. Lightner DV, et al. 1997. Risk of spread of penaeid shrimp viruses in the Americas by the international movement of live and frozen shrimp. Rev. Sci. Tech. 16:146-160.
39. Malnou CE, Poyry TA, Jackson RJ, Kean KM. 2002. Poliovirus internal ribosome entry segment structure alterations that specifically affect function in neuronal cells: molecular genetic analysis. J. Virol. 76:10617-10626.
40. Marti GA, et al. 2009. Prevalence and distribution of parasites and pathogens of triatominae from Argentina, with emphasis on Triatoma infestans and Triatoma virus TrV. J. Invertebr. Pathol. 102:233-237.
41. Molla A, Jang SK, Paul AV, Reuer Q, Wimmer E. 1992. Cardioviral internal ribosomal entry site is functional in a genetically engineered dicistronic poliovirus. Nature 356:255-257.
42. Murphy FA, Gibbs EPJ, Horzinek MC, Studdert MJ. 1999. Veterinary virology, 3rd ed. Academic Press, San Diego, CA.
43. Muscio OA, La Torre JL, Scodeller EA. 1988. Characterization of Triatoma virus, a picorna-like virus isolated from the triatomine bug Triatoma infestans. J. Gen. Virol. 69(Pt. 11):2929-2934.
44. Reuter G, Boros A, Pankovics P. 2011. Kobuviruses-a comprehensive review. Rev. Med. Virol. 21:32-41.
45. Rhoades RE, Tabor-Godwin JM, Tsueng G, Feuer R. 2011. Enterovirus infections of the central nervous system. Virology 411:288-305.
46. Roberts PJ, Belsham GJ. 1995. Identification of critical amino acids within the foot-and-mouth disease virus leader protein, a cysteine protease. Virology 213:140-146.
47. Ryan MD, Flint M. 1997. Virus-encoded proteinases of the picornavirus super-group. J. Gen. Virol. 78(Pt. 4):699-723.
48. Scotti PD, Longworth JF, Plus N, Croizier G, Reinganum C. 1981. The biology and ecology of strains of an insect small RNA virus complex. Adv. Virus Res. 26:117-143.
49. Solomon T, et al. 2010. Virology, epidemiology, pathogenesis, and control of enterovirus 71. Lancet Infect. Dis. 10:778-790.
50. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
51. Tsukiyama-Kohara K, Iizuka N, Kohara M, Nomoto A. 1992. Internal ribosome entry site within hepatitis C virus RNA. J. Virol. 66:1476 - 1483.
52. Whitton JL, Cornell CT, Feuer R. 2005. Host and virus determinants of picornavirus pathogenesis and tropism. Nat. Rev. Microbiol. 3:765-776.
53. Woo PC, Huang Y, Lau SK, Yuen KY. 2010. Coronavirus genomics and bioinformatics analysis. Viruses 2:1804-1820.
54. Woo PC, et al. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79:884-895.
55. Woo PC, et al. 2010. Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae. J. Gen. Virol. 91:2433-2448.
56. Woo PC, et al. 2009. Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J. Virol. 83:908-917.
57. Woo PC, et al. 2005. Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J. Infect. Dis. 192:1898-1907.
58. Yip CC, Lau SK, Woo PC, Chan KH, Yuen KY. 2011. Complete genome sequence of a coxsackievirus A22 strain in Hong Kong reveals a natural intratypic recombination event. J. Virol. 85:12098-12099.
59. Yu Y, et al. 2011. The mechanism of translation initiation on Aichivirus RNA mediated by a novel type of picornavirus IRES. EMBO J. 30:4423-4436.
60. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.