Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease: Implications for vector development in human gene therapy

Virology

Volumn 332, Issue 1, 2005, Pages 114-129

  Purkayastha, Anjan ^a,b,c   Su, Jing ^a,b,c   Carlisle, Steve ^d   Tibbetts, Clark ^b,c   Seto, Donald ^a,b,c  

^a GEORGE MASON UNIVERSITY   (United States)

^b HQ USAF Surgeon General Office   (United States)

^c Epidem Outbreak Survlnc Consortium   (United States)

^d Commonwealth Biotechnologies Inc (CBI) ^*  (United States)

Author keywords

Acute respiratory disease; HAdV B1 species; Human adenovirus type 7; Human gene therapy vector

Indexed keywords

DNA VACCINE;

ACCURACY; ACUTE RESPIRATORY TRACT DISEASE; ARTICLE; BIOINFORMATICS; BIOTECHNOLOGY; CHIMPANZEE; COMPARATIVE STUDY; DNA SEQUENCE; EPIDEMIC; GENE SEQUENCE; GENE THERAPY; GENE VECTOR; GENOME; GENOMICS; HUMAN; HUMAN ADENOVIRUS; MEDICAL TECHNOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL;

ADENOVIRUS INFECTIONS, HUMAN; ADENOVIRUSES, HUMAN; AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENE THERAPY; GENETIC VECTORS; GENOME, VIRAL; HUMANS; MOLECULAR SEQUENCE DATA; RESPIRATORY TRACT INFECTIONS; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

ADENOVIRIDAE; HUMAN ADENOVIRUS; HUMAN ADENOVIRUS TYPE 7; PAN TROGLODYTES;

EID: 12344262517     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2004.10.041     Document Type: Article

References (75)

1. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 3 1990 403 410
2. M. Basnight Jr., N.G. Rogers, C.J. Gibbs Jr., and D.C. Gajdusek Characterization of four new adenovirus serotypes isolated from chimpanzee tissue explants Am. J. Epidemiol. 94 2 1971 166 171
3. T.O. Berge, B. England, C. Mauris, H.E. Shuey, and E.H. Lennette Etiology of acute respiratory disease among service personnel at Fort Ord, California Am. J. Hyg. 62 3 1955 283 294
4. M. Berriman, and K. Rutherford Viewing and annotating sequence data with Artemis Brief. Bioinform. 4 2 2003 124 132
5. J. Besemer, and M. Borodovsky Heuristic approach to deriving models for gene finding Nucleic Acids Res. 27 19 1999 3911 3920
6. M.H. Binger, and S.J. Flint Accumulation of early and intermediate mRNA species during subgroup C adenovirus productive infections Virology 136 2 1984 387 403
7. R.M. Chanock, W. Ludwig, R.J. Heubner, T.R. Cate, and L.W. Chu Immunization by selective infection with type 4 adenovirus grown in human diploid tissue cultures: I. Safety and lack of oncogenicity and tests for potency in volunteers JAMA 195 6 1966 445 452
8. L. Crawford-Miksza, and D.P. Schnurr Analysis of 15 adenovirus hexon proteins reveals the location and structure of seven hypervariable regions containing serotype-specific residues J. Virol. 70 3 1996 1836 1844
9. L.K. Crawford-Miksza, R.N. Nang, and D.P. Schnurr Strain variation in adenovirus serotypes 4 and 7a causing acute respiratory disease J. Clin. Microbiol. 37 4 1999 1107 1112
10. R. Crespo, H.L. Shivaprasad, R. Droual, R.P. Chin, P.R. Woolcock, and T.E. Carpenter Inclusion body tracheitis associated with avian adenovirus in turkeys Avian Dis. 42 3 1998 589 596
11. A. Dan, P. Elo, B. Harrach, Z. Zadori, and M. Benko Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs Virus Genes 22 2 2001 175 179
12. A.J. Davison, E.A. Telford, M.S. Watson, K. McBride, and V. Mautner The DNA sequence of adenovirus type 40 J. Mol. Biol. 234 4 1993 1308 1316
13. A.J. Davison, K.M. Wright, and B. Harrach DNA sequence of frog adenovirus J. Gen. Virol. 81 Pt. 10 2000 2431 2439
14. A.J. Davison, M. Benko, and B. Harrach Genetic content and evolution of adenoviruses J. Gen. Virol. 84 Pt. 11 2003 2895 2908
15. C. Defer, M.T. Belin, M.L. Caillet-Boudin, and P. Boulanger Human adenovirus-host cell interactions: comparative study with members of subgroups B and C J. Virol. 64 8 1990 3661 3673
16. F. Deryckere, and H.G. Burgert Early region 3 of adenovirus type 19 (subgroup D) encodes an HLA-binding protein distinct from that of subgroups B and C J. Virol. 70 5 1996 2832 2841
17. D.D. Erdman, W. Xu, S.I. Gerber, G.C. Gray, D. Schnurr, A.E. Kajon, and L.J. Anderson Molecular epidemiology of adenovirus type 7 in the United States, 1966-2000 Emerging Infect Dis. 8 3 2002 269 277
18. S.L. Farkas, M. Benko, P. Elo, K. Ursu, A. Dan, W. Ahne, and B. Harrach Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus J. Gen. Virol. 83 Pt. 10 2002 2403 2410
19. R.L. Finnen, J.F. Biddle, and J. Flint Truncation of the human adenovirus type 5 L4 33-kDa protein: evidence for an essential role of the carboxy-terminus in the viral infectious cycle Virology 289 2 2001 388 399
20. J. Flint, and T. Shenk Viral transactivating proteins Annu. Rev. Genet. 31 1997 177 212
21. F. Gao, E. Bailes, D.L. Robertson, Y. Chen, C.M. Rodenburg, S.F. Michael, L.B. Cummins, L.O. Arthur, M. Peeters, G.M. Shaw, P.M. Sharp, and B.H. Hahn Origin of HIV-1 in the chimpanzee Pan troglodytes Nature 397 6718 1999 436 441
22. C.A. Gaydos, and J.C. Gaydos Adenovirus vaccines in the U.S. military Mil. Med. 160 6 1995 300 304
23. T.B. Hasson, P.D. Soloway, D.A. Ornelles, W. Doerfler, and T. Shenk Adenovirus L1 52- and 55-kilodalton proteins are required for assembly of virions J. Virol. 63 9 1989 3612 3621
24. B.W. Hayes, G.C. Telling, M.M. Myat, J.F. Williams, and S.J. Flint The adenovirus L4 100-kilodalton protein is necessary for efficient translation of viral late mRNA species J. Virol. 64 6 1990 2732 2742
25. J. Hierholzer Adenoviruses E.H. L.D. Lennette E.T. Lennette Diagnostic Procedures for Viral, Rickettsial and Chlamydial Infections 7th ed. 1995 American Public Health Association Washington 169 188
26. W.D. Hillis, A.W. Holmes, and V. Davison Serologic characterization of adenoviruses isolated from chimpanzees associated with viral hepatitis Proc. Soc. Exp. Biol. Med. 129 2 1968 366 369
27. V.M. Hirsch, R.A. Olmsted, M. Murphey-Corb, R.H. Purcell, and P.R. Johnson An African primate lentivirus (SIVsm) closely related to HIV-2 Nature 339 6223 1989 389 392
28. J.S. Hong, K.G. Mullis, and J.A. Engler Characterization of the early region 3 and fiber genes of Ad7 Virology 167 2 1988 545 553
29. T.M. Horton, A.E. Tollefson, W.S. Wold, and L.R. Gooding A protein serologically and functionally related to the group C E3 14,700-kilodalton protein is found in multiple adenovirus serotypes J. Virol. 64 3 1990 1250 1255
30. J. Howitt, C.W. Anderson, and P. Freimuth Adenovirus interaction with its cellular receptor CAR W. Doerfler P. Böhm Adenoviruses: Model and Vectors in Virus-Host Interactions 2003 Springer Berlin 331 364
31. A. Kajon, and G. Wadell Genome analysis of South American adenovirus strains of serotype 7 collected over a 7-year period J. Clin. Microbiol. 32 9 1994 2321 2323
32. A.H. Kidd, D. Garwicz, and M. Oberg Human and simian adenoviruses: phylogenetic inferences from analysis of VA RNA genes Virology 207 1 1995 32 45
33. G.M. Kovacs, S.E. LaPatra, J.C. D'Halluin, and M. Benko Phylogenetic analysis of the hexon and protease genes of a fish adenovirus isolated from white sturgeon (Acipenser transmontanus) supports the proposal for a new adenovirus genus Virus Res. 98 1 2003 27 34
34. K.P. Lauer, I. Llorente, E. Blair, J. Seto, V. Krasnov, A. Purkayastha, S.E. Ditty, T.L. Hadfield, C. Buck, C. Tibbetts, and D. Seto Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1 J. Gen. Virol. 85 Pt. 9 2004 2615 2625
35. C.T. Le, G.C. Gray, and S.K. Poddar A modified rapid method of nucleic acid isolation from suspension of matured virus: applied in restriction analysis of DNA from an adenovirus prototype strain and a patient isolate J. Med. Microbiol. 50 6 2001 571 574
36. K.N. Leppard E4 gene function in adenovirus, adenovirus vector and adeno-associated virus infections J. Gen. Virol. 78 Pt. 9 1997 2131 2138
37. Q.G. Li, and G. Wadell Analysis of 15 different genome types of adenovirus type 7 isolated on five continents J. Virol. 60 1 1986 331 335
38. Q.G. Li, and G. Wadell The degree of genetic variability among adenovirus type 4 strains isolated from man and chimpanzee Arch. Virol. 101 1-2 1988 65 77
39. Q. Li, and G. Wadell Genetic variability of hexon loops 1 and 2 between seven genome types of adenovirus serotype 7 Arch. Virol. 144 9 1999 1739 1749
40. M.B. Mathews, and T. Shenk Adenovirus virus-associated RNA and translation control J. Virol. 65 11 1991 5657 5662
41. F.M. Munoz, P.A. Piedra, and G.J. Demmler Disseminated adenovirus disease in immunocompromised and immunocompetent children Clin. Infect. Dis. 27 5 1998 1194 1200
42. E.A. Oosterom-Dragon, and H.S. Ginsberg Characterization of two temperature-sensitive mutants of type 5 adenovirus with mutations in the 100,000-dalton protein gene J. Virol. 40 2 1981 491 500
43. A. Purkayastha, S.E. Ditty, J. Su, J. McGraw, T.L. Hadfield, C. Tibbetts, and D. Seto Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease (ARD). Implications for gene therapy and vaccine vector development J. Virol. 2004 (in press)
44. S.E. Raper, N. Chirmule, F.S. Lee, N.A. Wivel, A. Bagg, G.P. Gao, J.M. Wilson, and M.L. Batshaw Fatal systemic inflammatory response syndrome in a ornithine transcarbamylase deficient patient following adenoviral gene transfer Mol. Genet. Metab. 80 1-2 2003 148 158
45. M. Rosa-Calatrava, L. Grave, F. Puvion-Dutilleul, B. Chatton, and C. Kedinger Functional analysis of adenovirus protein IX identifies domains involved in capsid stability, transcriptional activity, and nuclear reorganization J. Virol. 75 15 2001 7131 7141
46. W.P. Rowe, R.J. Huebner, L.K. Gilmore, R.H. Parrott, and T.G. Ward Isolation of a cytopathic agent from human adenoids undergoing spontaneous degradation in tissue culture Proc. Soc. Exp. Biol. Med. 84 1953 570 573
47. W.P. Rowe, J.W. Hartley, and R.J. Huebner Serotype composition of the adenovirus group Proc. Soc. Exp. Biol. Med. 97 2 1958 465 470
48. S. Roy, G. Gao, Y. Lu, X. Zhou, M. Lock, R. Calcedo, and J.M. Wilson Characterization of a family of chimpanzee adenoviruses and development of molecular clones for gene transfer vectors Hum. Gene Ther. 15 5 2004 519 530
49. Y.J. Ruan, C.L. Wei, A.L. Ee, V.B. Vega, H. Thoreau, S.T. Su, J.M. Chia, P. Ng, K.P. Chiu, L. Lim, T. Zhang, C.K. Peng, E.O. Lin, N.M. Lee, S.L. Yee, L.F. Ng, R.E. Chee, L.W. Stanton, P.M. Long, and E.T. Liu Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection Lancet 361 9371 2003 1779 1785
50. J.J. Rux, P.R. Kuser, and R.M. Burnett Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution X-ray crystallographic, molecular modeling, and sequence-based methods J. Virol. 77 17 2003 9553 9566
51. M. Ryan, G. Gray, A. Hawksworth, M. Malasig, M. Hudspeth, and S. Poddar The Naval Health Research Center Respiratory Disease Laboratory Mil. Med. 165 7 Suppl. 2 2000 32 34
52. M.A.K. Ryan, G.C. Gray, M.D. Malasig, L.N. Binn, L.V. Asher, D. Cute, S.C. Kehl, B.E. Dunn, and A.J. Yund Two fatal cases of adenovirus-related illness in previously healthy young adults-Illinois, 2000 Morb. Mortal. Wkly. Rep. 50 26 2001 553 555
53. M.A. Ryan, G.C. Gray, B. Smith, J.A. McKeehan, A.W. Hawksworth, and M.D. Malasig Large epidemic of respiratory illness due to adenovirus types 7 and 3 in healthy young adults Clin. Infect. Dis. 34 5 2002 577 582
54. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 4 1987 406 425
55. C. San Martin, and R.M. Burnett Structural studies on adenoviruses W.a.B.P. Doerfler Adenoviruses: Model and Vectors in Virus-Host Interactions 2003 Sringer Berlin 57 94
56. K.L. Sargent, R.A. Meulenbroek, and R.J. Parks Activation of adenoviral gene expression by protein IX is not required for efficient virus replication J. Virol. 78 10 2004 5032 5037
57. H. Schmitz, R. Wigand, and W. Heinrich Worldwide epidemiology of human adenovirus infections Am. J. Epidemiol. 117 4 1983 455 466
58. T. Shenk Adenoviridae: the viruses and their replication B. Fields D.M. Knipe P.M. Howley Fields Virology 3rd ed. 1996 Lippincott-Raven Philadelphia 2111 2148
59. J.P. Slattery, G. Franchini, and A. Gessain Genomic evolution, patterns of global dissemination, and interspecies transmission of human and simian T-cell leukemia/lymphotropic viruses Genome Res. 9 6 1999 525 540
60. K.F. Soike, J.D. Douglas, H. Plager, and F. Coulston Further studies of the viruses of the chimpanzee: II. Viral infection in recently imported chimpanzees captured in Africa Exp. Mol. Pathol. 11 3 1969 333 339
61. D. Stone, A. Furthmann, V. Sandig, and A. Lieber The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11 Virology 309 1 2003 152 165
62. S.M. Temperley, and R.T. Hay Recognition of the adenovirus type 2 origin of DNA replication by the virally encoded DNA polymerase and preterminal proteins EMBO J. 11 2 1992 761 768
63. O. Tokunaga, M. Shinagawa, and R. Padmanabhan Physical mapping of the genome and sequence analysis at the inverted terminal repetition of adenovirus type 4 DNA Gene 18 3 1982 329 334
64. F.H. Top Jr., E.L. Buescher, W.H. Bancroft, and P.K. Russell Immunization with live types 7 and 4 adenovirus vaccines: II. Antibody response and protective effect against acute respiratory disease due to adenovirus type 7 J. Infect. Dis. 124 2 1971 155 160
65. F.H. Top Jr., R.A. Grossman, P.J. Bartelloni, H.E. Segal, B.A. Dudding, P.K. Russell, and E.L. Buescher Immunization with live types 7 and 4 adenovirus vaccines: I. Safety, infectivity, antigenicity, and potency of adenovirus type 7 vaccine in humans J. Infect. Dis. 124 2 1971 148 154
66. G. Wadell, and T.M. Varsanyi Demonstration of three different subtypes of adenovirus type 7 by DNA restriction site mapping Infect. Immun. 21 1 1978 238 246
67. G. Wadell, T.M. Varsanyi, A. Lord, and R.N. Sutton Epidemic outbreaks of adenovirus 7 with special reference to the pathogenicity of adenovirus genome type 7b Am. J. Epidemiol. 112 5 1980 619 628
68. G. Wadell, M.K. Cooney, A. da Costa Linhares, L. de Silva, M.L. Kennett, R. Kono, R. Gui-Fang, K. Lindman, J.P. Nascimento, and B.D. Schoub Molecular epidemiology of adenoviruses: global distribution of adenovirus 7 genome types J. Clin. Microbiol. 21 3 1985 403 408
69. T.J. Wickham, P. Mathias, D.A. Cheresh, and G.R. Nemerow Integrins alpha v beta 3 and alpha v beta 5 promote adenovirus internalization but not virus attachment Cell 73 2 1993 309 319
70. W.S. Wold, and L.R. Gooding Region E3 of adenovirus: a cassette of genes involved in host immunosurveillance and virus-cell interactions Virology 184 1 1991 1 8
71. R.F. Yeh, L.P. Lim, and C.B. Burge Computational inference of homologous gene structures in the human genome Genome Res. 11 5 2001 803 816
72. P.R. Yew, X. Liu, and A.J. Berk Adenovirus E1B oncoprotein tethers a transcriptional repression domain to p53 Genes Dev. 8 2 1994 190 202
73. C.S. Young The structure and function of the adenovirus major late promoter Curr. Top. Microbiol. Immunol. 272 2003 213 249
74. W. Zhang, J.A. Low, J.B. Christensen, and M.J. Imperiale Role for the adenovirus IVa2 protein in packaging of viral DNA J. Virol. 75 21 2001 10446 10454
75. Y.L. Zu, Y. Takamatsu, M.J. Zhao, T. Maekawa, H. Handa, and S. Ishii Transcriptional regulation by a point mutant of adenovirus-2 E1a product lacking DNA binding activity J. Biol. Chem. 267 28 1992 20181 20187