Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence

Journal of General Virology

Volumn 92, Issue 6, 2011, Pages 1251-1259

  Kaneko, Hisatoshi ^a   Aoki, Koki ^b   Ishida, Susumu ^b   Ohno, Shigeaki ^b   Kitaichi, Nobuyoshi ^b,c   Ishiko, Hiroaki ^d   Fujimoto, Tsuguto ^e   Ikeda, Yoshifumi ^f   Nakamura, Masako ^g   Gonzalez, Gabriel ^h   Koyanagi, Kanako O ^h   Watanabe, Hidemi ^h   Suzutani, Tatsuo ^a  

^a FUKUSHIMA MEDICAL UNIVERSITY   (Japan)

^b HOKKAIDO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c HEALTH SCIENCES UNIVERSITY OF HOKKAIDO   (Japan)

^d LSI MEDIENCE CORPORATION   (Japan)

^e NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

^f Hiroshima City Institute of Public Health   (Japan)

^g Fukui Prefectural Institute of Public Health and Environmental Science   (Japan)

^h HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; VIRUS DNA;

ADENOVIRUS; ADENOVIRUS 53; ARTICLE; DNA VIRUS; JAPAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; STRAIN IDENTIFICATION; VIRUS GENOME; VIRUS RECOMBINANT; VIRUS TYPING;

ADENOVIRUS INFECTIONS, HUMAN; ADENOVIRUSES, HUMAN; GENOME, VIRAL; HUMANS; JAPAN; KERATOCONJUNCTIVITIS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

HUMAN ADENOVIRUS; HUMAN ADENOVIRUS D;

EID: 79956310781     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.030361-0     Document Type: Article

References (37)

1. Adrian, T., Bastian, B., Benoist, W., Hierholzer, J. C. & Wigand, R. (1985). Characterization of adenovirus 15/H9 intermediate strains. Intervirology 23, 15-22.
2. Aoki, K. & Tagawa, Y. (2002). A twenty-one year surveillance of adenoviral conjunctivitis in Sapporo, Japan. Int Ophthalmol Clin 42, 49-54.
3. Aoki, K., Ishiko, H., Konno, T., Shimada, Y., Hayashi, A., Kaneko, H., Ohguchi, T., Tagawa, Y., Ohno, S. & Yamazaki, S. (2008). Epidemic keratoconjunctivitis due to the novel hexon-chimeric-intermediate 22,37/H8 human adenovirus. J Clin Microbiol 46, 3259-3269.
4. Aoki, K., Kaneko, H., Kitaichi, N., Ohguchi, T., Tagawa, Y. & Ohno, S. (2011). Clinical features of adenoviral conjunctivitis at the early stage of infection. Jpn J Ophthalmol 55, 11-15.
5. Benko, M., Harrach, B., Both, G. W., Russell, W. C., Adair, B. M., Adam, E., de Jong, J. C., Hess, M., Johnson, M. & other authors (2005). Family Adenoviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 213-228. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego, CA: Elsevier Academic Press.
6. Engelmann, I., Madisch, I., Pommer, H. & Heim, A. (2006). An outbreak of epidemic keratoconjunctivitis caused by a new intermediate adenovirus 22/H8 identified by molecular typing. Clin Infect Dis 43, e64-e66.
7. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
8. Gibbs, M. J., Armstrong, J. S. & Gibbs, A. J. (2000). Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573-582.
9. Ishiko, H. & Aoki, K. (2009). Spread of epidemic keratoconjunctivitis due to a novel serotype of human adenovirus in Japan. J Clin Microbiol 47, 2678-2679.
10. Ishiko, H., Shimada, Y., Konno, T., Hayashi, A., Ohguchi, T., Tagawa, Y., Aoki, K., Ohno, S. & Yamazaki, S. (2008). Novel human adenovirus causing nosocomial epidemic keratoconjunctivitis. J ClinMicrobiol 46, 2002-2008.
11. Jones, M. S., Harrach, B., Ganac, R. D., Gozum, M. M., Dela Cruz, W. P., Riedel, B., Pan, C., Delwart, E. L. & Schnurr, D. P. (2007). New adenovirus species found in a patient presenting with gastroenteritis. J Virol 81, 5978-5984.
12. Kaneko, H., Iida, T., Aoki, K., Ohno, S. & Suzutani, T. (2005). Sensitive and rapid detection of herpes simplex virus and varicella-zoster virus DNA by loop-mediated isothermal amplification. J Clin Microbiol 43, 3290-3296.
13. Kaneko, H., Iida, T., Ishiko, H., Ohguchi, T., Ariga, T., Tagawa, Y., Aoki, K., Ohno, S. & Suzutani, T. (2009). Analysis of the complete genome sequence of epidemic keratoconjunctivitis-related human adenovirus type 8, 19, 37 and a novel serotype. J GenVirol 90, 1471-1476.
14. Kaneko, H., Suzutani, T., Aoki, K., Kitaichi, N., Ishida, S., Ishiko, H., Ohashi, T., Okamoto, S., Nakagawa, H. & other authors (2011a). Epidemiological and virological features of epidemic keratoconjunctivitis due to new human adenovirus type 54 in Japan. Br J Ophthalmol 95, 32-36.
15. Kaneko, H., Aoki, K., Ohno, S., Ishiko, H., Fujimoto, T., Kikuchi, M., Harada, S., Gonzalez, G., Koyanagi, K. O. & other authors (2011b). Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan. J Clin Microbiol 49, 484-490.
16. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
17. Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. & Ray, S. C. (1999). Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152-160.
18. Lukashev, A. N., Ivanova, O. E., Eremeeva, T. P. & Iggo, R. D. (2008). Evidence of frequent recombination among human adenoviruses. J Gen Virol 89, 380-388.
19. Madisch, I., Harste, G., Pommer, H. & Heim, A. (2005). Phylogenetic analysis of the main neutralization and hemagglutination determinants of all human adenovirus prototypes as a basis for molecular classification and taxonomy. J Virol 79, 15265-15276.
20. Martin, D. & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562-563.
21. Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C. (2005a). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98-102.
22. Martin, D. P., Williamson, C. & Posada, D. (2005b). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260-262.
23. Noda, M., Miyamoto, Y., Ikeda, Y., Matsuishi, T. & Ogino, T. (1991). Intermediate human adenovirus type 22/H10,19,37 as a new etiological agent of conjunctivitis. J Clin Microbiol 29, 1286-1289.
24. Padidam, M., Sawyer, S. & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218-225.
25. Posada, D. & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98, 13757-13762.
26. Robinson, C. M., Shariati, F., Gillaspy, A. F., Dyer, D. W. & Chodosh, J. (2008). Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism. BMC Genomics 9, 213.
27. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
28. Shinagawa, M., Matsuda, A., Ishiyama, T., Goto, H. & Sato, G. (1983). A rapid and simple method for preparation of adenovirus DNA from infected cells. Microbiol Immunol 27, 817-822.
29. Smith, J. M. (1992). Analyzing the mosaic structure of genes. J Mol Evol 34, 126-129.
30. Swenson, P. D., Wadell, G., Allard, A. & Hierholzer, J. C. (2003). Adenoviruses. In Manual of Clinical Microbiology, 8th edn, vol. 2, pp. 1404-1417. Edited by P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller & R. H. Yolken. Washington, DC: American Society for Microbiology.
31. Tabbara, K. F., Omar, N., Hammouda, E., Akanuma, M., Ohguchi, T., Ariga, T., Tagawa, Y., Kitaichi, N., Ishida, S. & other authors (2010). Molecular epidemiology of adenoviral keratoconjunctivitis in Saudi Arabia. Mol Vis 16, 2132-2136.
32. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
33. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
34. Walsh, M. P., Chintakuntlawar, A., Robinson, C. M., Madisch, I., Harrach, B., Hudson, N. R., Schnurr, D., Heim, A., Chodosh, J. & other authors (2009). Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis. PLoS ONE 4, e5635.
35. Walsh, M. P., Seto, J., Jones, M. S., Chodosh, J., Xu, W. & Seto, D. (2010). Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol 48, 991-993.
36. Wold, W. S. M. & Horwitz, M. S. (2007). Adenoviruses. In Fields Virology, 5th edn, vol. 2, pp. 2395-2436. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman & S. E. Straus. Philadelphia, PA: Lippincott Williams & Wilkins.
37. Yang, Z., Zhu, Z., Tang, L., Wang, L., Tan, X., Yu, P., Zhang, Y., Tian, X., Wang, J. & other authors (2009). Genomic analyses of recombinant adenovirus type 11a in China. J Clin Microbiol 47, 3082-3090.