Characterization of a highly divergent TT virus genome

References

1. 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 Research 25:3389–3402
   [Google Scholar]
2. Boom R., Sol C. J. A., Salimans M. M. M., Jansen C. L., Wertheim-van Dillen P. M. E., van der Noordaa J. 1990; Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28:495–503
   [Google Scholar]
3. Coombs N. J., Gough A. C., Primrose J. N. 1999; Optimization of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Research 27:12–14
   [Google Scholar]
4. Erker J. C., Leary T. P., Desai S. M., Chalmers M. L., Mushahwar I. K. 1999; Analyses of TT virus full-length genomic sequences. Journal of General Virology 80:1743–1750
   [Google Scholar]
5. Felsenstein J. 1993 PHYLIP (phylogeny inference package) v3.5c Department of Genetics, University of Washington; Seattle, USA:
   [Google Scholar]
6. Hijikata M., Takahashi K., Mishiro S. 1999; Complete circular DNA genome of a TT virus variant (isolate name SANBAN) and 44 partial ORF2 sequences implicating a great degree of diversity beyond genotypes. Virology 260:17–22
   [Google Scholar]
7. Jaeger J. A., Turner D. H., Zuker M. 1989; Improved predictions of secondary structures for RNA. Proceedings of the National Academy of Sciences, USA 86:7706–7710
   [Google Scholar]
8. Kozak M. 1986; Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292
   [Google Scholar]
9. Leary T. P., Erker J. C., Chalmers M. L., Desai S. M., Mushahwar I. K. 1999; Improved detection systems for TT virus reveal high prevalence in humans, non-human primates and farm animals. Journal of General Virology 80:2115–2120
   [Google Scholar]
10. Miyata H., Tsunoda H., Kazi A., Yamada A., Khan M. A., Murakami J., Kamahora T., Shiraki K., Hino S. 1999; Identification of a novel GC-rich 113-nucleotide region to complete the circular, single-stranded DNA genome of TT virus, the first human circovirus. Journal of Virology 73:3582–3586
    [Google Scholar]
11. Morozov I., Sirinarumitr T., Sorden S. D., Halbur P. G., Morgan M. K., Yoon K.-J., Paul P. S. 1998; Detection of a novel strain of porcine circovirus in pigs with postweaning multisystemic wasting syndrome. Journal of Clinical Microbiology 36:2535–2541
    [Google Scholar]
12. Mulyanto M., Hijikata M., Matsushita M., Ingkokusmo G., Widjaya A., Sumarsidi D., Kanai K., Ohta Y., Mishiro S. 2000; TT virus (TTV) genotypes in native and non-native prostitutes of Irian Jaya, Indonesia: implication for non-occupational transmission. Archives of Virology 145:63–72
    [Google Scholar]
13. Mushahwar I. K., Erker J. C., Muerhoff A. S., Leary T. P., Simons J. N., Birkenmeyer L. G., Chalmers M. L., Pilot-Matias T. J., Desai S. M. 1999; Molecular and biophysical characterization of TT virus: evidence for a new virus family infecting humans. Proceedings of the National Academy of Sciences, USA 96:3177–3182
    [Google Scholar]
14. Nishizawa T., Okamoto H., Konishi K., Yoshizawa H., Miyakawa Y., Mayumi M. 1997; A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochemical and Biophysical Research Communications 241:92–97
    [Google Scholar]
15. Nishizawa T., Okamoto H., Tsuda F., Aikawa T., Sugai Y., Konishi K., Akahane Y., Ukita M., Tanaka T., Miyakawa Y., Mayumi M. 1999; Quasispecies of TT virus (TTV) with sequence divergence in hypervariable regions of the capsid protein in chronic TTV infection. Journal of Virology 73:9604–9608
    [Google Scholar]
16. Okamoto H., Akahane Y., Ukita M., Fukuda M., Tsuda F., Miyakawa Y., Mayumi M. 1998; Fecal excretion of a nonenveloped DNA virus (TTV) associated with posttransfusion non A-G hepatitis. Journal of Medical Virology 56:128–132
    [Google Scholar]
17. Okamoto H., Takahashi M., Nishizawa T., Ukita M., Fukuda M., Tsuda F., Miyakawa Y., Mayumi M. 1999a; Marked heterogeneity and frequent mixed infection of TT virus demonstrated by PCR with primers from coding and noncoding regions. Virology 259:428–436
    [Google Scholar]
18. Okamoto H., Nishizawa T., Ukita M., Takahashi M., Fukuda M., Iizuka H., Miyakawa Y., Mayumi M. 1999b; The entire nucleotide sequence of a TT virus isolate from the United States (TUS01): comparison with reported isolates and phylogenetic analysis. Virology 259:437–448
    [Google Scholar]
19. Page R. D. M. 1996; Treeview: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12:357–358
    [Google Scholar]
20. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, USA 85:2444–2448
    [Google Scholar]
21. Pringle C. L. 1999; Virus taxonomy at the XIth International Congress of Virology, Sydney, Australia, 1999. Archives of Virology 144:2065–2068
    [Google Scholar]
22. Takahashi K., Ohta Y., Mishiro S. 1998a; Partial ∼2·4-kb sequences of TT virus (TTV) genome from eight Japanese isolates: diagnostic and phylogenetic implications. Hepatology Research 12:111–120
    [Google Scholar]
23. Takahashi K., Hoshino H., Ohta Y., Yoshida N., Mishiro S. 1998b; Very high prevalence of TT virus (TTV) infection in general population of Japan revealed by a new set of PCR primers. Hepatology Research 12:233–239
    [Google Scholar]
24. Takahashi K., Iwasa Y., Hijikata M., Mishiro S. 2000; Identification of a new human DNA virus (TTV-like mini virus: TLMV) intermediately related to TT virus and chicken anaemia virus. Archives of Virology (in press
    [Google Scholar]
25. Tanaka Y., Mizokami M., Orito E., Ohno T., Nakano T., Kato T., Kato H., Mukaide M., Park Y.-M., Kim B.-S., Ueda R. 1998; New genotypes of TT virus (TTV) and a genotyping assay based on restriction fragment length polymorphism. FEBS Letters 437:201–206
    [Google Scholar]
26. 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 Research 22:4673–4680
    [Google Scholar]