Isolation of multiple TT virus genotypes from spleen biopsy tissue from a Hodgkin's disease patient: genome reorganization and diversity in the hypervariable region

Abstract

We report the isolation of 24 novel genotypes of TT viruses from a surgically removed spleen of a patient with Hodgkin's disease. The sequence analysis of our 24 isolates revealed the remarkable heterogeneity of TT virus isolates not only from the same patient but also from the same biopsy material. These isolates belong to four phylogenetic groups of TT viruses. Nucleotide sequence analyses revealed five distinct genotypes (tth3, tth4, tth5, tth6, and tth7). The limited variation in sequence identity of the other isolates defines the latter as variants of four of these genotypes. A group of 6 isolates (the tth7 group) revealed a reorganization of open reading frame 1 (ORF1) leading to one larger and a varying number of smaller ORFs. The nucleotide difference of the full-length genomes was less than 1%. A variation of 69 to 97% in amino acids of a second group of 8 isolates (the tth3 group) was restricted to the hypervariable region of ORF1, indicating the existence of a quasi-species. These isolates differed by less than 2% in the remainder of their nucleotide sequences. An alignment of these isolates with 79 previously reported TT virus genotypes permits the proposal of TT virus genera and species within the family Anelloviridae in analogy to a previous proposal for the papillomaviruses (family Papillomaviridae).

FIG. 1.

Nucleotide and amino acid sequences of the HVRs (HVR1, HVR2, and HVR3) of the variants of tth3. Dashes indicate nucleotides or amino acids identical to those of the consensus sequence.

FIG. 2.

Additional ORFs within ORF1 amplified from the spleen of a patient with Hodgkin's disease. The number of amino acids in each of the respective ORFs is indicated.

FIG. 3.

Putative ORFs for TTV ta278 (a) and tth7 (b).

FIG. 4.

Frequency distribution of pairwise identity percentages from nucleotide sequence comparisons (3,200 nt) of 103 TTV isolates.

FIG. 5.

Phylogenetic tree containing sequences of 103 TTV. The outermost semicircular symbols identify TTV genera, and the number at each inner semicircular symbol refers to the TTV species.