1887

Journal of General Virology header logo

Volume 85, Issue 9

Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1 Free

Abstract

The 36 001 base pair DNA sequence of human adenovirus serotype 1 (HAdV-1) has been determined, using a ‘leveraged primer sequencing strategy’ to generate high quality sequences economically. This annotated genome (GenBank AF534906) confirms anticipated similarity to closely related species C (formerly subgroup), human adenoviruses HAdV-2 and -5, and near identity with earlier reports of sequences representing parts of the HAdV-1 genome. A first round of HAdV-1 sequence data acquisition used PCR amplification and sequencing primers from sequences common to the genomes of HAdV-2 and -5. The subsequent rounds of sequencing used primers derived from the newly generated data. Corroborative re-sequencing with primers selected from this HAdV-1 dataset generated sparsely tiled arrays of high quality sequencing ladders spanning both complementary strands of the HAdV-1 genome. These strategies allow for rapid and accurate low-pass sequencing of genomes. Such rapid genome determinations facilitate the development of specific probes for differentiation of family, serotype, subtype and strain (e.g. pathogen genome signatures). These will be used to monitor epidemic outbreaks of acute respiratory disease in a defined test bed by the Epidemic Outbreak Surveillance (EOS) project.

  • Received:
  • Accepted:
  • Published Online:
SGM
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.80118-0
2004-09-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/85/9/vir852615.html?itemId=/content/journal/jgv/10.1099/vir.0.80118-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
     [Google Scholar]
  2. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
     [Google Scholar]
  3. Benko M., Harrach B. 2003; Molecular evolution of adenoviruses. In Adenoviruses: Model and Vectors in Virus–Host Interactions pp  3–35 Edited by Doerfler W., Bohm P. Berlin: Springer;
     [Google Scholar]
  4. Benko M., Harrach B., Russell W. C. 2000; The Adenoviridae . In Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses pp  227–238 Edited by van Regenmortel M. H. V., Fauquet C. M., Bishop G. H. L., Carstens E. B., Estes M. K., Lemon S. M., Maniloff J., Mayo M. A., McGeoch D. J., Pringle C. R., Wickner R. B. San Diego: Academic Press;
     [Google Scholar]
  5. Berriman M., Rutherford K. 2003; Viewing and annotating sequence data with Artemis. Brief Bioinform 4:124–132 [CrossRef]
     [Google Scholar]
  6. Besemer J., Borodovsky M. 1999; Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920 [CrossRef]
     [Google Scholar]
  7. Binger M. H., Flint S. J. 1984; Accumulation of early and intermediate mRNA species during subgroup C adenovirus productive infections. Virology 136:387–403 [CrossRef]
     [Google Scholar]
  8. Buescher E. L. 1967; Respiratory disease and the adenoviruses. Med Clin North Am 51:769–779
     [Google Scholar]
  9. Chroboczek J., Bieber F., Jacrot B. 1992; The sequence of the genome of adenovirus type 5 and its comparison with the genome of adenovirus type 2. Virology 186:280–285 [CrossRef]
     [Google Scholar]
  10. Concino M., Goldman R. A., Caruthers M. H., Weinmann R. 1984; Point mutations of the adenovirus major late promoter with different transcriptional efficiencies in vitro . J Biol Chem 258:8493–8496
     [Google Scholar]
  11. Dan A., Elo P., Harrach B., Zadori Z., Benko M. 2001; Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs. Virus Genes 22:175–179 [CrossRef]
     [Google Scholar]
  12. Davison A. J., Telford E. A., Watson M. S., McBride K., Mautner V. 1993; The DNA sequence of adenovirus type 40. J Mol Biol 234:1308–1316 [CrossRef]
     [Google Scholar]
  13. Davison A. J., Benko M., Harrach B. 2003; Genetic content and evolution of adenoviruses. J Gen Virol 84:2895–2908 [CrossRef]
     [Google Scholar]
  14. De Jong R. N., Van Der Vliet P. C., Brenkman A. B. 2003; Adenovirus DNA replication: protein priming, jumping back and the role for the DNA binding protein DBP. In Adenoviruses: Model and Vectors in Virus–Host Interactions pp  187–211 Edited by Doerfler W., Bohm P. Berlin: Springer;
     [Google Scholar]
  15. Dudding B. A., Wagner S. C., Zeller J. A., Gmelich J. T., French G. R., Top F. H. Jr 1972; Fatal pneumonia associated with adenovirus type 7 in three military trainees. N Engl J Med 286:1289–1292 [CrossRef]
     [Google Scholar]
  16. Evans J. D., Hearing P. 2002; Adenovirus replication. In Adenoviral Vectors for Gene Therapy pp  39–70 Edited by Curiel D. T., Douglas J. T. San Diego: Academic Press;
     [Google Scholar]
  17. Flint J., Shenk T. 1997; Viral transactivating proteins. Annu Rev Genet 31:177–212 [CrossRef]
     [Google Scholar]
  18. Gao W., Robbins P. D., Gambotto A. 2003; Human adenovirus type 35: nucleotide sequence and vector development. Gene Ther 10:1941–1949 [CrossRef]
     [Google Scholar]
  19. Gray G. C., Goswami P. R., Malasig M. D., Hawksworth A. W., Trump D. H., Ryan M. A., Schnurr D. P. 2000; Adult adenovirus infections: loss of orphaned vaccines precipitates military respiratory disease epidemics. For the Adenovirus Surveillance Group. Clin Infect Dis 31:663–670 [CrossRef]
     [Google Scholar]
  20. Hasson T. B., Soloway P. D., Ornelles D. A., Doerfler W., Shenk T. 1989; Adenovirus L1 52- and 55-kilodalton proteins are required for assembly of virions. J Virol 63:3612–3621
     [Google Scholar]
  21. Hatfield L., Hearing P. 1991; Redundant elements in the adenovirus type 5 inverted terminal repeat promote bidirectional transcription in vitro and are important for virus growth in vivo . Virology 184:265–276 [CrossRef]
     [Google Scholar]
  22. Hatfield L., Hearing P. 1993; The NFIII/OCT-1 binding site stimulates adenovirus DNA replication in vivo and is functionally redundant with adjacent sequences. J Virol 67:3931–3939
     [Google Scholar]
  23. Hayes B. W., Telling G. C., Myat M. M., Williams J. F., Flint S. J. 1990; The adenovirus L4 100-kilodalton protein is necessary for efficient translation of viral late mRNA species. J Virol 64:2732–2742
     [Google Scholar]
  24. Hillemann M. R., Werner J. R. 1954; Recovery of new agent from patients with acute respiratory illness. Proc Soc Exp Biol Med 85:183–188 [CrossRef]
     [Google Scholar]
  25. Horton T. M., Tollefson A. E., Wold W. S., Gooding L. R. 1990; A protein serologically and functionally related to the group C E3 14, 700-kilodalton protein is found in multiple adenovirus serotypes. J Virol 64:1250–1255
     [Google Scholar]
  26. Howitt J., Anderson C. W., Freimuth P. 2003; Adenovirus interaction with its cellular receptor CAR. In Adenoviruses: Model and Vectors in Virus–Host Interactions pp  331–364 Edited by Doerfler W., Bohm P. Berlin: Springer;
     [Google Scholar]
  27. Huang X. 1994; On global sequence alignment. Comput Appl Biosci 10:227–235
     [Google Scholar]
  28. Lee R. F., Concino M. F., Weinmann R. 1988; Genetic profile of the transcriptional signals from the adenovirus major late promoter. Virology 165:51–56 [CrossRef]
     [Google Scholar]
  29. Leegwater P. A., van Driel W., van der Vliet P. C. 1985; Recognition site of nuclear factor I, a sequence-specific DNA-binding protein from HeLa cells that stimulates adenovirus DNA replication. EMBO J 4:1515–1521
     [Google Scholar]
  30. Leong K., Lee W., Berk A. J. 1990; High-level transcription from the adenovirus major late promoter requires downstream binding sites for late phase-specific factors. J Virol 64:51–60
     [Google Scholar]
  31. Leppard K. N. 1997; E4 gene function in adenovirus, adenovirus vector and adeno-associated virus infections. J Gen Virol 78:2131–2138
     [Google Scholar]
  32. Mathews M. B., Shenk T. 1991; Adenovirus virus-associated RNA and translation control. J Virol 65:5657–5662
     [Google Scholar]
  33. Mei Y. F., Skog J., Lindman K., Wadell G. 2003; Comparative analysis of the genome organization of human adenovirus 11, a member of the human adenovirus species B, and the commonly used human adenovirus 5 vector, a member of species C. J Gen Virol 84:2061–2071 [CrossRef]
     [Google Scholar]
  34. Mul Y. M., Verrijzer C. P., van der Vliet P. C. 1990; Transcription factors NFI and NFIII/oct-1 function independently, employing different mechanisms to enhance adenovirus DNA replication. J Virol 64:5510–5518
     [Google Scholar]
  35. Oosterom-Dragon E. A., Ginsberg H. S. 1981; Characterization of two temperature-sensitive mutants of type 5 adenovirus with mutations in the 100,000-dalton protein gene. J Virol 40:491–500
     [Google Scholar]
  36. Parks C. L., Shenk T. 1997; Activation of the adenovirus major late promoter by transcription factors MAZ and Sp1. J Virol 71:9600–9607
     [Google Scholar]
  37. Pruijn G. J., van Miltenburg R. T., Claessens J. A., van der Vliet P. C. 1988; Interaction between the octamer-binding protein nuclear factor III and the adenovirus origin of DNA replication. J Virol 62:3092–3102
     [Google Scholar]
  38. Reach M., Xu L.-X., Young C. S. H. 1991; Transcription from the adenovirus major late promoter uses redundant activating elements. EMBO J 10:3439–3446
     [Google Scholar]
  39. Roberts R. J., Akusjarvi G., Alestrom P., Gelinas R. E., Gingeras T. R., Sciaky D., Pettersson U. 1986; A consensus sequence for the adenovirus-2 genome. In Adenovirus DNA pp  1–51 Edited by Doerfler W. Boston: Martinus Nijhoff;
     [Google Scholar]
  40. Rowe W. P., Huebner R. J., Gilmore L. K., Parrot R. H., Ward T. G. 1953; Isolation of a cytopathogenic agent from human adenoids undergoing spontaneous degradation in tissue culture. Proc Soc Exp Biol Med 84:570–573 [CrossRef]
     [Google Scholar]
  41. Russell W. C. 2000; Update on adenovirus and its vectors. J Gen Virol 81:2573–2604
     [Google Scholar]
  42. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B. 2000; Artemis: sequence visualization and annotation. Bioinformatics 16:944–945 [CrossRef]
     [Google Scholar]
  43. Rux J. J., Kuser P. R., Burnett R. M. 2003; Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution X-ray crystallographic, molecular modeling, and sequence-based methods. J Virol 77:9553–9566 [CrossRef]
     [Google Scholar]
  44. Ryan M. A. K., Gray G. C., Malasig M. D., Binn L. N., Asher L. V., Cute D., Kehl S. C., Dunn B. E., Yund A. J. 2001; Two fatal cases of adenovirus-related illness in previously healthy young adults - Illinois, 2000. Morb Mortal Wkly Rep 50:553–555
     [Google Scholar]
  45. San Martin C., Burnett R. M. 2003; Structural studies on adenoviruses. In Adenoviruses: Model and Vectors in Virus–Host Interactions pp  57–94 Edited by Doerfler W., Bohm P. Berlin: Springer;
     [Google Scholar]
  46. Scarpini C., Arthur J., Efstathiou S., McGrath Y., Wilkinson G. 1999; Herpes simplex virus and adenovirus vectors. In DNA Viruses, a Practical Approach pp  267–306 Edited by Cann A. J. New York: Oxford University Press;
     [Google Scholar]
  47. Schwartz S., Zhang Z., Frazer K. A., Smit A., Riemer C., Bouck J., Gibbs R., Hardison R., Miller W. 2000; PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 10:577–586 [CrossRef]
     [Google Scholar]
  48. Seto D., Koop B. F., Deshpande P., Howard S., Seto J., Wilk E., Wang K., Hood L. 1994; Organization, sequence, and function of 34·5 kb of genomic DNA encompassing several murine T-cell receptor α / δ variable gene segments. Genomics 20:258–266 [CrossRef]
     [Google Scholar]
  49. Sprengel J., Schmitz B., Heuss-Neitzel D., Zock C., Doerfler W. 1994; Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis. J Virol 68:379–389
     [Google Scholar]
  50. Stone D., Furthmann A., Sandig V., Lieber A. 2003; The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11. Virology 309:152–165 [CrossRef]
     [Google Scholar]
  51. Sugarman B. J., Hutchins B. M., McAllister D. L., Lu F., Thomas B. K. 2003; The complete nucleotide acid sequence of the adenovirus type 5 reference material (ARM) genome. Bioprocessing J September/October27–32
     [Google Scholar]
  52. Temperley S. M., Hay R. T. 1992; Recognition of the adenovirus type 2 origin of DNA replication by the virally encoded DNA polymerase and preterminal proteins. EMBO J 11:761–768
     [Google Scholar]
  53. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustalx windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882
     [Google Scholar]
  54. Vogels R., Zuijdgeest D., van Rijnsoever R. 20 other authors 2003; Replication-deficient human adenovirus type 35 vectors for gene transfer and vaccination: efficient human cell infection and bypass of preexisting adenovirus immunity. J Virol 77:8263–8271 [CrossRef]
     [Google Scholar]
  55. Wadell G. 1984; Molecular epidemiology of human adenoviruses. Curr Top Microbiol Immunol 110:191–220
     [Google Scholar]
  56. Wickham T. J., Mathias P., Cheresh D. A., Nemerow G. R. 1993; Integrins α v β 3 and α v β 5 promote adenovirus internalization but not virus attachment. Cell 73:309–319 [CrossRef]
     [Google Scholar]
  57. Wold W. S. M., Gooding L. R. 1991; Region E3 of adenovirus: a cassette of genes involved in host immunosurveillance and virus–cell interactions. Virology 184:1–8 [CrossRef]
     [Google Scholar]
  58. Yeh R. F., Lim L. P., Burge C. B. 2001; Computational inference of homologous gene structures in the human genome. Genome Res 11:803–816 [CrossRef]
     [Google Scholar]
  59. Yew P. R., Liu X., Berk A. J. 1994; Adenovirus E1B oncoprotein tethers a transcriptional repression domain to p53. Genes Dev 8:190–202 [CrossRef]
     [Google Scholar]
  60. Young C. S. H. 2003; The structure and function of the adenovirus major late promoter. In Adenoviruses: Model and Vectors in Virus–Host Interactions pp  213–249 Edited by Doerfler W., Bohm P. Berlin: Springer;
     [Google Scholar]
  61. Zafar N., Mazumder R., Seto D. 2001; Comparisons of gene colinearity in genomes using GeneOrder2.0. Trends Biochem Sci 26:514–516 [CrossRef]
     [Google Scholar]
  62. Zhang W., Low J. A., Christensen J. B., Imperiale M. J. 2001; Role for the adenovirus IVa2 protein in packaging of viral DNA. J Virol 75:10446–10454 [CrossRef]
     [Google Scholar]
  63. Zu Y. L., Takamatsu Y., Zhao M. J., Maekawa T., Handa H., Ishii S. 1992; Transcriptional regulation by a point mutant of adenovirus-2 E1a product lacking DNA-binding activity. J Biol Chem 267:20181–20187
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.80118-0
Loading
Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1
J. Gen. Virol. 85, 2615 (2004); https://doi.org/10.1099/vir.0.80118-0
/content/journal/jgv/10.1099/vir.0.80118-0
/content/journal/jgv/10.1099/vir.0.80118-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error