TT Virus (TTV) Genotyping Tool

 
Introduction

In 1997, a novel unenveloped human virus was isolated from the serum of a patient of transfusion hepatitis of unknown etiology, and it was named TT virus (TTV) after the initials of the index patient (Nishizawa et al., 1997). TTV has a circular single-stranded DNA genome of approximately 3.8 kilobases with negative polarity (Mushahwar et al., 1999; Okamoto et al., 1999b).

TTV has a wide range of sequence divergence, allowing the classification into more than 30 genotypes separated by pairwise sequence differences of more than 30 percent (Okamoto et al., 1999a; Peng et al., 2002). These genotypes are classified into five groups or phylogenetic clusters (Table 1).
 

Method for TTV Genotype Identification

The DNA sequence of a 222- to 231-nucleotide long PCR-amplified fragment (the N22 region) from the central portion of ORF1 is commonly used to identify the genotype of a TTV isolate or amplicon. This fragment exhibits considerable genetic variability, apparent at both protein and DNA levels.

Phylogenetic analysis is by far the most reliable method to determine the genotype of a TTV sequence. However, the observed level of genetic heterogeneity in the N22 region allowed us to develop a rapid method for genotyping TTV amplicons based on the sequence of the N22 region (Takács et al., 2002).

We apply the fasty3 program of the FASTA3 package (Pearson, 1999) to search against a database of translated reference TTV DNA sequences (see Table 1) and find those most similar to the DNA sequence query. The most probable genotype of the query sequence is then reported. This method is tolerant to sequencing errors, even frameshifts, allowing raw sequences to be rapidly checked for their genotype. This analysis is much faster than constructing phylogenetic trees and gives a reasonably accurate result when the full N22 sequence is used as a query. Reliability of the result is estimated based on Smith-Waterman scores of the protein alignments. Phylogenetic analysis is recommended where support for the given genotype is too low. The latter mostly occurs if the query contains only a portion of the N22 region.
 

The web site

The web-based TTV genotyping tool can be accessed from here.
 

How to cite?

Please, cite the following paper if you use this tool:
Takács, M., Balog, K., Tóth, G., Balogh, Z., N. Szomor, K., Brojnás, J., Rusvai, E., Minárovits, J. & Berencsi, G. (2003) TT virus in Hungary: sequence heterogeneity and mixed infections. FEMS Immunol. Med. Microbiol. 35: 153-157.

 

References

  1. Hallett, R.L., Clewley, J.P., Bobet, F., McKiernan, P.J. & Teo, C.G. (2000) Characterization of a highly divergent TT virus genome. J. Gen. Virol. 81: 2273-2279.
  2. 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. Biochem. Biophys. Res. Commun. 241: 92-97.
  3. Muljono, D.H., Nishozawa, T., Tsuda, T., Takahashi, M. & Okamoto, H. (2001) Molecular epidemiology of TT virus (TTV) and characterixation of two novel TTV genotypes in Indonesia. Arch. Virol. 146: 1249-1266.
  4. Mushahwar, I.K., Erker, J.C., Muerhoff, A.S. et al. (1999) Molecular and biophysical characterization of TT virus: evidence for a new virus family infecting humans. Proc. Natl. Acad. Sci. USA 96: 3177-3182.
  5. Okamoto, H., Takahashi, M., Nishizawa, T. et al. (1999a) Marked genomic heterogeneity and frequent mixed infection of TT virus demonstrated by PCR with primers fromcoding and noncoding regions. Virology 259: 428-436.
  6. Okamoto, H., Nishizawa, T., Ukita, M. et al. (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.
  7. Pearson, W.R. (1999) Flexible similarity searching with the FASTA3 program package. In: Bioinformatics Methods and Protocols, S. Misener and S. A. Krawetz, ed. (Totowa, NJ: Humana Press), pp. 185-219.
  8. Peng, Y.H., Nishizawa, T., Takahashi, M., Ishikawa, T., Yoshikawa, A. & Okamoto, H. (2002) Analysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants. Arch. Virol. 147: 21-41.
  9. Takács, M., Balog, K., Tóth, G., Balogh, Z., N. Szomor, K., Brojnás, J., Rusvai, E., Minárovits, J. & Berencsi, G. (2003) TT virus in Hungary: sequence heterogeneity and mixed infections. FEMS Immunol. Med. Microbiol. 35: 153-157.