Marked Genomic Heterogeneity and Frequent Mixed Infection of TT Virus Demonstrated by PCR with Primers from Coding and Noncoding Regions

Abstract

A nonenveloped, single-stranded, and circular DNA virus designated TT virus (TTV) has been reported in association with hepatitis of unknown etiology. TTV has a wide sequence divergence (approximately 52%), by which it is classified into at least 16 genotypes separated by an evolutionary distance of >0.30. Therefore, the detection of TTV DNA by polymerase chain reaction would be influenced by primers deduced from conserved or divergent regions of the genome. Of the 30 sera from healthy individuals, up to 17% tested positive with primers deduced from coding region, much less frequently than up to 93% testing positive with primers from noncoding region. These differences were not attributable to the sensitivity of detection, because a cloned TTV DNA of genotype 1a was detected sensitively (up to 1 copy per test) with primers deduced from either the coding or the noncoding region of the same genotype. Sera testing positive only with noncoding region primers, or those showing higher titers with noncoding than coding region primers, contained TTV DNA strains with sequence divergence of 47-53% from the TA278 isolate of genotype 1a within the N22 region spanning 222-231 nucleotides. Some of the sera contained two or three TTV DNA strains of distinct genotypes. These results indicate TTV strains with extremely high sequence divergence prevailing in healthy individuals and frequent mixed infection with TTV strains of distinct genotypes.

Extensive Homologous Recombination among Widely Divergent TT Viruses

“…While the role played by mutation has long been considered, it is becoming increasingly apparent that recombination also plays a key role in the evolution of many virus groups (19,24). The recent availability of several full-length TTV sequences (3,6,10,11,16), along with evidence for mixed infection by multiple genetic types (2,4,17,21), prompted this investigation into whether recombination might also play a role in the evolution of TTV.A total of 15 full-length or near-full-length TTV genomes with the following isolate names (accession numbers) were collected from GenBank: TA278 (AB017610) (16); GH1 (AF122913) (11); TUS01 (AB017613) (16); SAN-BAN (AB025946) (6); JA20 (AF122914), JA9 (AF122915), JA10 (AF122919), JA4 (AF122917), JA1 (AF122916), JA2B (AF122918), US32 (AF122921), and US35 (AF122920) (3); and BDH1 (AF116842), TTVCHN1 (AF079173), and TTVCHN2 (AF129887). The sequences were aligned using CLUSTAL W (23) and adjusted by hand.…”

“…While the role played by mutation has long been considered, it is becoming increasingly apparent that recombination also plays a key role in the evolution of many virus groups (19,24). The recent availability of several full-length TTV sequences (3,6,10,11,16), along with evidence for mixed infection by multiple genetic types (2,4,17,21), prompted this investigation into whether recombination might also play a role in the evolution of TTV.…”

A multiplex PCR assay able to simultaneously detect Torque teno virus isolates from phylogenetic groups 1 to 5

“…Much progress in TTV detection has been done since then, with the use of primers located in a short, highly conserved genomic region (15,21,22).…”

TT virus infection in children and adults who visited a general hospital in the south of Brazil for routine procedure

“…Very high seroprevalences (30-93%) of TTV have been found in normal healthy populations from different parts of the world, including developed and developing countries (Prescott & Simmonds 1998, Tanaka et al 1998, Okamoto et al 1999, Handa et al 2000. In several other studies, however, the true TTV prevalence has been greatly underestimated due to the use of PCR primers and/or protocols that did not allow the successfull amplification of DNAs from all the isolates.…”

“…Indeed, TTV is a virus with a great genetic heterogeneity. The existence of at least 16 genotypes (1 to 16) has been demonstrated by Okamoto et al (1999) and a recent study has proposed the classification of TTV into five different virus species (TTV I to V), due to the considerable evolutionary distance separating the strains (Khudyakov et al 2000). Depending on the PCR assay used, the different TTV genotypes (or species) may or may not be detected.…”