Molecular and biophysical characterization of TT virus: Evidence for a new virus family infecting humans

Abstract

The recent isolation of a novel DNA virus from the serum of a Japanese patient (T.T.) has provided the latest possible candidate virus associated with cryptogenic hepatitis. In the present study, we report the complete nucleotide sequence of this virus (TTV) isolated from the serum of a West African. Based on PCR studies designed to amplify overlapping regions of the viral genome and sensitivity to digestion with mung bean nuclease, the viral genome is circular and negative stranded, and comprises 3,852 nt, which is 113 nt longer than the prototype isolate from Japan. Cesium chloride density gradient centrifugation demonstrated banding of the virus at 1.31–1.34 g/ml; filtration studies indicated that TTV had a particle size of 30–50 nm. These results suggest that the virus is similar to the Circoviridae, viruses known to infect plants and vertebrates (e.g., birds and swine); however, sequence similarity searches of available databases did not reveal identity between TTV and other viruses. Phylogenetic analyses of a 260-nt region from 151 globally distributed isolates demonstrated the existence of three major TTV genotypes. Several individuals at high risk for infection with parenterally transmitted viruses were infected with more than one genotype. There was no correlation between genotype and geographic origin. Finally, intravenous inoculation of TTV-positive human serum into chimpanzees demonstrated that TTV can be transmitted to primates; no biochemical or histological evidence for hepatitis was obtained. The distinct biophysical and molecular characteristics of TTV suggest that it is a member of a new family of viruses, which we have tentatively named the Circinoviridae.

Analyses of TT virus full-length genomic sequences.

“…The 260 nucleotide regions of several TT virus isolates (Table 1 ; Mushahwar et al, 1999) were extended to genome length by inverse PCR (Fig. 1).…”

Sequence diversity of TT virus in geographically dispersed human populations.

“…There is presently no agreement about the classification of TTV, although it has been suggested that TTV may be a parvovirus (Okamoto et al, 1998 b), a circovirus (Takahashi et al, 1998 b) or correspond to a member of a new virus family (Mushahwar et al, 1999).…”

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.…”

“…Subsequent studies, however, have shown it to be very widespread and to occur at an extremely high prevalence even in healthy populations (1,9,18,20), casting doubt on its causal role in human disease. Its circular, single-stranded, negative-sense DNA genome, approximately 3,850 nucleotides in length (10,11), bears little or no identifiable similarity to other known viruses, and TTV appears to represent a new virus family, tentatively designated Circinoviridae (11).…”

“…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.…”