Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population

Abstract

Torque teno virus (TTV) is one of the most common human viruses and can infect an individual with multiple genotypes chronically and persistently. TTV group 6 is a recently discovered phylogenetic group first isolated from eastern Taiwan indigenes, but whether the TTV group 6 was also prevalent in the general population still unknown. One hundred and three randomly collected blood samples from general population and 66 TTV positive DNA samples extracted from Taiwan indigenes were included. A group-6-specific PCR was developed for re-screen over TTV positive samples. Two TTV group 6 positive samples from general population were cloned and sequenced for identifying mix-infected TTVs and confirming their classification by maximum-likelihood and Bayesian inference phylogeny. TTV group 6 can be detected in 4.5% (4/89) and 7.6% (5/66) of TTV positive samples from Taiwanese general population and eastern Taiwan indigenes, respectively. Sample VC09 was mix-infected with TTV groups 3 and 6. Sample VC99 was mix-infected with TTV groups 3, 4 and 6. A highly diverse triple overlapping region was observed, which may represent a unique phenomenon of TTV. The group-6-specific PCR can successfully detect TTV group 6. TTV group 6 may be prevalent worldwide regardless of the geographic region and/or ethnic groups.

Keywords: TTV; Taiwan; anellovirus; group 6; phylogenetic analysis.

Figure 1.

Bayesian tree of TTV ORF1 well-aligned region. A Bayesian inferred maximum clade credibility tree that reconstructed on the basis of TTV ORF1 well-aligned region. Grey square indicates group 1. Dark tan square indicates group 2. Light blue indicates group 3 and green, blue and yellow indicate subgroups 3a, 3b and 3c respectively. Orange square indicates group 4. Red square indicates group 5. Purple square indicates group 6. Dark blue indicates group 7. Posterior probabilities are labelled beside stems of each TTV phylogenetic groups. Branches with a * indicate posterior probabilities above 0.95 and are considered as strongly supported. Only major branches were labelled, check electronic supplementary material, Tree S1 for detail. Sequences from this study are labelled by colour bar labels. Pink labels beside taxa names indicate sequences from sample VC09; yellow labels beside taxa names indicate sequences from VC99. The scale bar at the left bottom indicates the evolutionary distance in units of substitutions per site per year.

Figure 2.

The splicing diagram and ORF map of TTV group 6 based on representative sequence TW53A26. Reading frames are indicated at left for both the splicing diagram and ORF map. (a) In the splicing diagram, arrow boxes indicate the three distinct reading frames. Putative splicing donor and acceptor sites are linked by dash lines. (b) In the ORF map, potential start codons (AUG) are indicated with a half-height line and stop codons (UGA, UAA, UAG) are indicated by full-height lines. (c) In the substitutions map, the vertical lines represent nucleotide substitutions compare with representative sequence TW53A26. Sequences that aligned to gaps of TW53A26 were removed and gaps that aligned to TW53A26 were counted as substitutions. * A C → T premature mutation at 523 bp was ignored here.

Figure 3.

A close-up of TTV Group 6 clade of Bayesian tree. Posterior probabilities are labelled beside well-supported branches (greater than 0.95). Sequences from this study are labelled in bold. The scale bar at the bottom indicates evolutionary distance in units of substitutions per site per year. Both sequences from VC09 and VC99 were closely related to TW53A26 clade. In addition, P13-1 and P14-1 (labelled in italic) were submitted by an independent human virome study [40], and also belong to TTV group 6.