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.