The entire nucleotide sequence of a TT virus isolate from the United States (TUS01): comparison with reported isolates and phylogenetic analysis

Identification and whole genome characterization of novel anelloviruses in masked palm civets (Paguma larvata): Segregation into four distinct clades

The members of the family Anelloviridae are small and single-stranded DNA viruses with marked diversity in sequence and length, which ubiquitously infect many vertebrates, including mammals, birds and reptiles. The anelloviruses isolated from mammals are currently classified into 11 assigned and four proposed genera; some anelloviruses remain unassigned. The present study was conducted to identify anelloviruses in wild-caught masked palm civets (Paguma larvata) in Japan using a rolling-circle amplification method. Thirteen novel anellovirus strains were identified from 8 of 10 masked palm civets and their entire genomic sequences (2039-2535 nucleotides) were determined; they were classifiable into four distinct clades. Comparative analyses of all reported anelloviruses for which the entire or near-entire genomic sequences have been determined, including the 13 strains obtained in the present study, revealed that anelloviruses can provisionally be classified into 20 clades, which may correspond to 20 genera (including 11 assigned and four proposed genera) by a >70% amino acid sequence difference in open reading frame 1 (ORF1). This study suggested that novel anelloviruses of marked diversity are circulating in animals worldwide, and that the rolling-circle amplification method would be useful for identifying novel anelloviruses and other viruses with a circular DNA genome.

Viruses with Circular Single-Stranded DNA Genomes Are Everywhere!

Circular single-stranded DNA viruses infect archaea, bacteria, and eukaryotic organisms. The relatively recent emergence of single-stranded DNA viruses, such as chicken anemia virus (CAV) and porcine circovirus 2 (PCV2), as serious pathogens of eukaryotes is due more to growing awareness than to the appearance of new pathogens or alteration of existing pathogens. In the case of the ubiquitous human circular single-stranded DNA virus family Anelloviridae, there is still no convincing direct causal relation to any specific disease. However, infections may play a role in autoimmunity by changing the homeostatic balance of proinflammatory cytokines and the human immune system, indirectly affecting the severity of diseases caused by other pathogens. Infections with CAV (family Anelloviridae, genus Gyrovirus) and PCV2 (family Circoviridae, genus Circovirus) are presented here because they are immunosuppressive and affect health in domesticated animals. CAV shares genomic organization, genomic orientation, and common features of major proteins with human anelloviruses, and PCV2 DNA may be present in human food and vaccines.

Rapid detection of human torque teno viruses using high-resolution melting analysis

Torque teno viruses (TTVs) are recently discovered DNA viruses, with heterogeneous genomes, highly prevalent in populations worldwide. The species that infect humans are Torque teno virus (TTV), Torque teno midi virus (TTMDV) and Torque teno mini virus (TTMV). High-resolution melting analysis (HRMA) is a sensitive and effective method for genotyping and mutation scanning. Up to now, HRMA has not been utilized for detection of TTVs. The aim of this study was to asses if HRMA is suitable for detecting TTVs variants. DNA was extracted from the blood and saliva of 13 healthy subjects for method optimization. Additionally, saliva samples from 100 healthy individuals were collected for estimating the TTVs' prevalence. Viral DNA was amplified by heminested polymerase chain reaction (PCR). Second round amplicons were used for the HRMA. The samples were analyzed using two fluorescent dyes, SYBR (®) Green I and EvaGreen®. The prevalence values for TTV, TTMDV and TTMV were 71.0, 31.0 and 54.0%, respectively. The three major melting curve patterns corresponding to TTV, TTMDV and TTMV on HRMA can be easily distinguished regardless of kit used. Our results showed that HRMA is a rapid and efficient method of detecting human TTVs.

Molecular characterization of human Torque Teno virus

The present study analyzed the presence of human Torque Teno virus (TTV) in hospitalized patients from different departments. In total, 378 serum specimens were collected from the patients (171 with cardiovascular disease, 192 with tumor and 15 with gastroenteritis) and analyzed by ELISA and nest-polymerase chain reaction (PCR) to detect the presence of TTV. The results showed that 64 specimens (17%) were TTV positive from detection with the human ELISA kit, and the patients aged <30 years have a higher prevalence. TTV in males was more common than in female patients. In addition, nest-PCR was used to detect TTV within different phylogenetic groups among the 64 specimens, and the results showed that groups 1 (TA278 strain), 4 (KC009) and 5 (CT39) were much more prevalent than groups 2 (PMV isolate) and 3 (11 genotypes) in the different departmental patients.

Development of a Serological Assay for the Sea Lion (Zalophus californianus) Anellovirus, ZcAV

New diseases in marine animals are emerging at an increasing rate, yet methodological limitations hinder characterization of viral infections. Viral metagenomics is an effective method for identifying novel viruses in diseased animals; however, determining virus pathogenesis remains a challenge. A novel anellovirus (Zalophus californianus anellovirus, ZcAV) was recently reported in the lungs of captive California sea lions involved in a mortality event. ZcAV was not detected by PCR in the blood of these animals, creating the inability to assess the prevalence of ZcAV in live sea lions. This study developed an enzyme-linked immunosorbent assay (ELISA) to detect antibodies to ZcAV in sea lion serum. To assess ZcAV prevalence, paired serum and lung samples (n = 96) from wild sea lions that stranded along the California coast were tested through ELISA and PCR, respectively. Over 50% of the samples tested positive for ZcAV by ELISA (34%), PCR (29%), or both (11%) assays. ZcAV is prevalent in stranded wild sea lion populations and results suggest that PCR assays alone may grossly underestimate ZcAV exposure. This ELISA provides a tool for testing live sea lions for ZcAV exposure and is valuable for subsequent studies evaluating the potential pathogenicity of this anellovirus.

Detection and genotyping of torque teno virus (TTV) in healthy blood donors and patients infected with HBV or HCV in Qatar

Torque Teno virus (TTV) has been associated with non A-G hepatitis. The goal of this study was to estimate the infection rates and genotypic characteristics of TTV in the State of Qatar. A total of 644 blood samples representing different nationalities: (i) Qatari (118) and (ii) non-Qatari (526) nationals (mostly from Arab and South Eeast Asia countries) were tested for the presence of TTV DNA by nested PCR. The majority (573) of the blood samples belonged to healthy blood donors, whereas 54 and 53 of the blood samples belonged to patients infected with hepatitis B virus (HBV) and hepatitis C virus (HCV), respectively. The results obtained showed that the TTV infection rates in the healthy blood donors, and those infected with HBV or HCV patients were 81.4, 90.75 and 84.9%, respectively. Significant association between TTV viremia and age, or nationality was observed. Sequence analysis of PCR fragments amplified from the 5'-untranslated region (5'-UTR) of all (531) TTV positive samples showed that 65.5% (348/531) of the PCR fragment sequences were classified into main genogroup 3, followed by main genogroups 5 (24%), 2 (5.8%), and 1 (4.7%). Genogroup 4 was not detected among the our studied subjects. Phylogenetic and pairwise analyses using sequences from TTV viremic samples also showed an overall close similarity to the main genogroup 3. In conclusion, there was no significant difference in the rates of TTV detection among Qataris and non-Qataris and several genotypes, mainly genotype 3, were isolated.

Validation of SYBR Green based quantification assay for the detection of human Torque Teno virus titers from plasma

Background

Quantification of titers of ubiquitous viruses such as Torque teno virus (TTV) that do not cause clinical symptoms might be helpful in assessing the immune status of an individual. We hereby describe the validation of a SYBR Green-based TTV quantification method for plasma samples.

Methods

Plasmids with TTV specific inserts were used for preparing standards and absolute quantification of TTV was performed using SYBR Green methodology. The method was assessed for its accuracy and precision (intra and inter-day) on four non-consecutive days. TTV was also quantified from plasma samples of 20 healthy volunteers and from 30 hematopoietic stem cell transplant (HSCT) recipients.

Results

The assay was specific and showed satisfactory efficiency (82.2%, R²=0.99) with the limit of quantification defined as 100 copies per reaction. The assay had good precision (inter and intra-day coefficient of variation in cycle threshold (C_T) < 4%) and accuracy (100 ± 10%) in the range of 100 to 10¹⁰ copies/reaction. We found TTV loads ranging from 2.5 – 4.07 log copies/mL of plasma with C_T (mean ± SD) of 33.8 ± 1.77 in healthy individuals and 2.06 – 8.49 log copies/mL of plasma with C_T (mean ± SD) of 24.3 ± 1.04 in HSCT recipients.

Conclusion

SYBR Green-based q-PCR assay combines simplicity with satisfactory sensitivity and may be suitable for monitoring the immune status of transplant recipients, where TTV loads over time may serve as a marker for immune reconstitution in human plasma samples.

Phylogenetic analysis of Torque Teno Virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients

BACKGROUND

Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world.

METHODS

TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0.

RESULTS

Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2).

CONCLUSION

The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5'-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.

Rescue of a porcine anellovirus (torque teno sus virus 2) from cloned genomic DNA in pigs

Anelloviruses are a group of single-stranded circular DNA viruses infecting humans and other animal species. Animal models combined with reverse genetic systems of anellovirus have not been developed. We report here the construction and initial characterization of full-length DNA clones of a porcine anellovirus, torque teno sus virus 2 (TTSuV2), in vitro and in vivo. We first demonstrated that five cell lines, including PK-15 cells, are free of TTSuV1 or TTSuV2 contamination, as determined by a real-time PCR and an immunofluorescence assay (IFA) using anti-TTSuV antibodies. Recombinant plasmids harboring monomeric or tandem-dimerized genomic DNA of TTSuV2 from the United States and Germany were constructed. Circular TTSuV2 genomic DNA with or without introduced genetic markers and tandem-dimerized TTSuV2 plasmids were transfected into PK-15 cells, respectively. Splicing of viral mRNAs was identified in transfected cells. Expression of TTSuV2-specific open reading frame 1 (ORF1) in cell nuclei, especially in nucleoli, was detected by IFA. However, evidence of productive TTSuV2 infection was not observed in 12 different cell lines transfected with the TTSuV2 DNA clones. Transfection with circular DNA from a TTSuV2 deletion mutant did not produce ORF1 protein, suggesting that the observed ORF1 expression is driven by TTSuV2 DNA replication in cells. Pigs inoculated with either the tandem-dimerized clones or circular genomic DNA of U.S. TTSuV2 developed viremia, and the introduced genetic markers were retained in viral DNA recovered from the sera of infected pigs. The availability of an infectious DNA clone of TTSuV2 will facilitate future study of porcine anellovirus pathogenesis and biology.

Metagenomic analysis of the viral flora of pine marten and European badger feces

A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families Paramyxo- and Picornaviridae were detected.

Viral infection and aging as cofactors for the development of pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a disease of unknown origin and progression that primarily affects older adults. Accumulating clinical and experimental evidence suggests that viral infections may play a role, either as agents that predispose the lung to fibrosis or exacerbate existing fibrosis. In particular, herpesviruses have been linked with IPF. This article summarizes the evidence for and against viral cofactors in IPF pathogenesis. In addition, we review mechanistic studies in animal models that highlight the fibrotic potential of viral infection, and explore the different mechanisms that might be responsible. We also review early evidence to suggest that the aged lung may be particularly susceptible to viral-induced fibrosis and make recommendations for future research directions.

Prevalence and genotyping of group 3 torque teno viruses detected in health care workers in Hungary

Torque teno viruses (TTVs) are classified into the Anellovirus genus of the Circoviridae family. In addition to TTV isolates, TTV genogroup 3 also includes the 8 virus strains known as SENV-A to H. In this study, the prevalence of TTV group 3 viruses and that of SENV-D and H in particular were determined among the staff of a hospital in Budapest. Viruses were genotyped using type-specific PCR primers and by cloning and sequencing of PCR products. Frequency of infection with TTV group 3 was high among both the hospital staff and the control group. Prevalence of SENV-H was similar in the two groups, but SENV-D infection was significantly more common in the study group than in controls. Sequencing of PCR products showed that viruses closely related to isolate TUS01 are common in Hungary. Several sequences could not be genotyped and may represent a previously undescribed genotype within the genogroup. TTV group 3 sequences detected in the serum samples of a symptomless health care worker were followed-up for 15 years. Some strains persisted for up to 10 years, while others caused transient infections and could be detected in only one of the samples. Results showed that TTV infection, superinfection, and viral clearance often occur over the years without apparent symptoms.

Classification of TTV and related viruses (anelloviruses)

Ten years after the identification of the first partial sequences of Torque teno virus (TTV), more than 200 full-length related genomes have been characterized in humans and in several animal species. As suspected in the earlier stages of their description, a considerable genetic variability characterizes TTV and related viruses, the current members of the floating genus Anellovirous. Since information related to anelloviruses diversity is in constant evolution, the challenge in their taxonomic classification is to take into account all pertinent parameters, along with the taxonomic situation of other viruses having circular single-stranded DNA genomes. Past, present and future phylogenetic and taxonomic considerations are exposed.

History of discoveries and pathogenicity of TT viruses

Since 1997, groups of novel nonenveloped DNA viruses with a circular, single-stranded (negative sense) DNA genome of 3.6-3.9 kb, 3.2 kb, or 2.8-2.9 kb in size have been discovered and designated Torque teno virus (TTV), Torque teno midi virus (TTMDV), and Torque teno mini virus (TTMV), respectively, in the floating genus Anellovirus. These three anelloviruses frequently and ubiquitously infect humans, and the infections are characterized by lifelong viremia and great genetic variability. Although TTV infection has been epidemiologically suggested to be associated with many diseases including liver diseases, respiratory disorders, hematological disorders, and cancer, there is no direct causal evidence for links between TTV infection and specific clinical diseases. The pathogenetic role of TTMV and TTMDV infections remains unknown. The changing ratio of the three anelloviruses to each other over time, relative viral load, or combination of different genotype(s) of each anellovirus may be associated with the pathogenicity or the disease-inducing potential of these three human anelloviruses. To clarify their disease association, polymerase chain reaction (PCR) systems for accurately detecting, differentiating, and quantitating all of the genotypes and/or genogroups of TTV, TTMDV, and TTMV should be established and standardized, as should methods to detect past infections and immunological responses to anellovirus infections.

TT viruses in animals

Infection with TT virus (Torque teno virus, TTV), a small, nonenveloped virus with a circular, single-stranded DNA genome classified in the floating genus Anellovirus, is not restricted to humans. Using highly conserved primers derived from the untranslated region of the human TTV genome, a variety of TTV-like viruses have been found circulating in nonhuman primates such as chimpanzees, macaques, and tamarins. TTV variants in nonhuman primates are species-specific, although some genetic groups of human and chimpanzee TTVs cluster to make human/chimpanzee clades. TTVs from macaques and tamarins are increasingly divergent from TTV variants infecting humans and chimpanzees. TTV-like mini virus (TTMV) infections have also been detected in chimpanzees, with genotypes distinct but interspersed with human TTMV genotypes. Pets are also naturally infected with species-specific TTVs, and several isolates have been found in cats and dogs. In addition, other mammals such as tupaias and pigs have species-specific TTVs: swine TTVs are found among pigs worldwide. The genomic organization and proposed transcriptional profiles of TTVs infecting nonhuman primate and other mammalian species are similar to those of human TTVs, and co-evolution of TTVs with their hosts has been suggested. To date, TTVs infecting nonhuman primates and other mammalian species have been under-examined. It is likely that essentially all animals are naturally infected with species-specific TTVs.

Immunobiology of the Torque teno viruses and other anelloviruses

Many features of the Torque teno virus and the other anelloviruses (AVs) that have been identified after this virus was discovered in 1997 remain elusive. The immunobiology of the AVs is no exception. However, evidence is progressively accumulating that at least some AVs have an interesting interplay with cells and soluble factors known to contribute to the homeostasis of innate and adaptive immunity. Evidence is also accumulating that this interplay can have a significant impact on how effectively an infected host can deal with superimposed infectious and non-infectious noxae. This review article discusses the scanty information available on these aspects and highlights the ones that would be more urgent to precisely understand in order to get an adequate assessment of how important for human health these extremely ubiquitous and pervasive viruses really are.

First description of swine Torque teno virus (TTV) and detection of a new genogroup in Hungary: short communication

Torque teno virus (TTV) belongs to the floating genus of Anellovirus. It was discovered in a human patient, and later it was also found in animals including pigs. The aim of this study was to investigate the presence and estimate the prevalence of swine TTV in Hungarian pig herds for the first time, and to characterise the viruses found. Serum samples of 82 adult swine from 13 piggeries and 44 weaned pigs from one large herd were tested by PCR for the presence of TTV DNA. Viral DNA was found in 30% of the adult swine and 73% of the weaned pigs tested. Liver and intestine of weaned pigs were also tested and found to be infected at a lower rate. The TTV sequences found in sera and intestines were similar and could be clustered as swine genogroup 1. However, the sequences derived from one liver were remarkably different from all other known genogroups and seemed to represent a new genogroup.

[Distribution of TT virus genotypes and genogroups in 69 healthy and 59 hepatitis B virus infected Korean individuals]

BACKGROUND

TT virus (TTV) infection is highly prevalent in general population and patients with hepatitis B virus (HBV) infection. The aim of the present study was to determine the distribution of the genotypes and genogroups of TTV in healthy and HBV-infected individuals in Korea.

METHODS

Distribution of TTV genotypes and genogroups was investigated in the serum samples of 69 healthy and 59 HBV-infected individuals. PCR products of N22 region were genotyped by sequence analysis. TTV genogroups were determined by 5 different genogroup-specific PCR assays.

RESULTS

Among the 20 sequenced isolates, 9 (45%) were genotype 2, 8 (40%) were genotype 1, 2 (10%) were genotype 3, and 1 (5%) was genotype 4. TTV genogroup 4 was found most frequently (52/128), followed by genogroup 3 (42/128), genogroup 1 (35/128), genogroup 5 (32/128), and genogroup 2 (1/128). Mixed infections with different genogroups were frequent.

CONCLUSIONS

TTV genotype 2 and 1 are predominant genotypes. TTV genotype 3 was detected for the first time in Korea. TTV genogroups 4 and 3 were predominant genogroups. No significant difference was observed in the distribution of TTV genogroups between healthy and HBV-infected individuals.

Torque teno virus: Its prevalence and isotypes in North India

AIM: To investigate the prevalence and genotype distribution of Torque teno virus (TTV) in patients with different liver diseases and chronic renal failure treated at a referral hospital in North India.

METHODS: Whereas prevalence of TTV was based on amplification of conserved region of ORF2 of TTV genome, the genotyping of TTV was carried out using restriction fragment length polymorphism (RFLP) procedure on the N22 region of ORF1.

RESULTS: TTV-DNA was detected in 137 of 513 (26.7%) patients with liver diseases and 38 of 65 (58.5%) patients with chronic renal failure. TTV was also detected in 27% of healthy controls. The sequence analysis of the PCR product from 10 randomly selected cases failed to show a significant sequence divergence when compared with that of the TRM1 isolate of TTV genotype 1. The results of genotyping in 55 randomly selected patients showed the presence of genotype 1 (G1) in 53 (96.4%) and genotype 2 (G2) in 2 cases (3.6%), respectively. Other genotypes were not identified in this patient subgroup, suggesting that G1 is predominant in this area. The results of genotyping by RFLP were also supported by phylogenetic tree analysis, where G1 was found to be the major genotype.

CONCLUSION: These results indicate that TTV is moderately present in Indian patients, with G1 to be the major genotype in North India. The pathogenicity and etiological role of TTV in different diseases is still a question mark and warrant further studies.

Gene expression of the human Torque Teno Virus isolate P/1C1

Torque Teno Virus (TTV) has been assigned to the floating genus Anellovirus. TTV ssDNA genomes have a size of 3.6 to 3.8 kb and display up to 30% nucleotide diversity. The pathogenic potential of TTV is under investigation. To address a putative link of pathogenicity with the observed sequence variations, the transcription profile of P/1C1 (genogroup 1) isolated from a patient diseased with a non A-G hepatitis was analysed. Four mRNAs were identified, which encoded the seven proteins ORF1, ORF1/1, ORF1/2, ORF2, ORF2/2, ORF3 and ORF4. Expression of the ORF1 protein and its splice variant ORF1/1 in cell culture was detected by an ORF1-specific antiserum. Analysis of N-terminal tagged P/1C1-encoded proteins revealed that ORF1, ORF1/1 and ORF1/2 were localised in the nucleoli, ORF3 and ORF4 resided in the nucleoplasm, ORF2/2 appeared either in the nucleoli or the whole nucleus while ORF2 was the only protein seen in the cytoplasm.

Clinical outcome of frequent exposure to Torque Teno virus (TTV) through blood transfusion in thalassemia patients with or without hepatitis C virus (HCV) infection

As a consequence of the high prevalence of TorqueTeno virus (TTV) in blood donors, thalassemia patients frequently acquire various genotypes of this virus through therapeutic blood transfusions. At present, the clinical consequences of TTV infection remain indeterminate for these patients. Here, several hundred thalassemia patients were tested for the presence of TTV and its genotypes using a combination of PCR and clone-based DNA sequencing. Approximately 10% (12/118) of the patients aged 2-20 years remained negative for TTV including eight genotypes of SENV. Ferritin, aspartate-aminotransferase (AST) and alanine-aminotransferase (ALT) levels were invariably lower in TTV-negative patients (P = 0.02, <0.01, and 0.06, respectively) than in TTV-positive patients. Patients with TTV-HCV co-infection showed elevated ferritin and ALT levels compared with patients with TTV infection alone (P < 0.02 and P < 0.01). AST and ALT levels were within the normal range for all TTV-negative patients, whereas abnormal levels of AST and ALT were seen in a significant proportion of TTV-positive patients (30.7% and 33.6%, respectively) and patients with TTV-HCV co-infections (70.0% and 56.6%, respectively). Only TTV-positive patients (28.0%) and patients with TTV-HCV co-infections (36.3%) had hyper-ferritin levels (> or =3,000 ng/ml). The genotype(s) of TTV responsible for the liver dysfunction could not be determined. However, high levels of AST and ALT were found to be correlated with detection of a higher number of TTV genotypes in the patients. The data suggests that frequent and persistent TTV infection through blood transfusion is associated with hepatic dysfunction and/or damage in transfusion dependent thalassemia patients.

Development of PCR assays with nested primers specific for differential detection of three human anelloviruses and early acquisition of dual or triple infection during infancy

We recently identified a novel human virus classifiable into a third group in the genus Anellovirus, tentatively designated torque teno midi virus (TTMDV), with a circular DNA genome of 3.2 kb and genomic organization resembling those of torque teno virus (TTV) (3.8 to 3.9 kb) and torque teno mini virus (TTMV) (2.8 to 2.9 kb). TTMDV was characterized by extreme genetic diversity similar to the TTV and TTMV genomes. Taking advantage of universal and virus species-specific primers derived from a highly conserved area located just downstream of the TATA box of the TTV, TTMDV, and TTMV genomes, a PCR method with simultaneous amplification of the genomic DNAs of these three anelloviruses in the first round and subsequent differential amplifications of these viruses in the second round was developed. High prevalence of TTMDV viremia was seen in adults (75/100 [75%]), comparable with the prevalences of TTV viremia (100%) and TTMV viremia (82%). Although none of 10 cord blood samples had detectable TTV, TTMDV, and TTMV DNAs, the prevalences of these three anelloviruses increased with the number of months after birth of the individual and reached 100% for individuals at one year of age. Dual or triple infection of TTV, TTMDV, and/or TTMV was seen in 10 (47.6%) of 21 infants 9 to 180 days of age and more frequently among infants 181 to 364 days of age (20/23 [86.9%]), comparable with the 93.1% (243/261) prevalence among subjects 1 to 81 years of age, indicating early acquisition of dual or triple anellovirus infection during infancy.

Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus

Recently, we identified a novel human virus with a circular DNA genome of 3.2 kb, tentatively designated as torque teno midi virus (TTMDV), with a genomic organization resembling those of torque teno virus (TTV) of 3.8-3.9 kb and torque teno mini virus (TTMV) of 2.8-2.9 kb. To investigate the extent of genomic variability of TTMDV genomes, the full-length sequence was determined for 15 TTMDV isolates obtained from viremic individuals in Japan. The 15 TTMDV isolates comprised 3175-3230 bases and shared 67.0-90.3% identities with each other, and were only 68.4-73.0% identical to the 3 reported TTMDV isolates over the entire genome. TTMDV possessed a genomic organization with four open reading frames (ORF1-ORF4) with characteristic sequence motifs and stem and loop structures with high GC content, similar to TTV and TTMV. The total of 18 TTMDV genomes differed by up to 60.7% from each other in the amino acid sequence of ORF1 (658-677 amino acids), but segregated phylogenetically into the same cluster, which was distantly related to the TTVs and TTMVs. These results indicate that TTMDV with a circular DNA genome of 3.2 kb, has an extremely high degree of genomic variability, and is classifiable into a third group in the genus Anellovirus.

Construction and biological activity of a full-length molecular clone of human Torque teno virus (TTV) genotype 6

Torque teno virus (TTV) is a non-enveloped human virus with a circular negative-sense (approximately 3800 nucleotides) ssDNA genome. TTV resembles in genome organization the chicken anemia virus, the animal pathogen of the Circoviridae family, and is currently classified as a member of a new, floating genus, Anellovirus. Molecular and cell biological research on TTV has been restricted by the lack of permissive cell lines and functional, replication-competent plasmid clones. In order to examine the key biological activities (i.e. RNA transcription and DNA replication) of this still poorly characterized ssDNA virus, we cloned the full-length genome of TTV genotype 6 and transfected it into cells of several types. TTV mRNA transcription was detected by RT-PCR in all the cell types: KU812Ep6, Cos-1, 293, 293T, Chang liver, Huh7 and UT7/Epo-S1. Replicating TTV DNA was detected in the latter five cell types by a DpnI-based restriction enzyme method coupled with Southern analysis, a novel approach to assess TTV DNA replication. The replicating full-length clone, the cell lines found to support TTV replication, and the methods presented here will facilitate the elucidation of the molecular biology and the life cycle of this recently identified human virus.

Identification and genomic characterization of a novel human torque teno virus of 3.2 kb

In the process of searching for the recently described small anelloviruses 1 and 2 (SAVs) with the genomic DNA length of 2.2 or 2.6 kb in human sera, we isolated a novel virus with its genomic organization resembling those of torque teno virus (TTV) of 3.8-3.9 kb and torque teno mini virus (TTMV) of 2.8-2.9 kb. The entire genomic sequence of three isolates (MD1-032, MD1-073 and MD2-013), which comprised 3242-3253 bases and exhibited 76-99 % identities with the SAVs within the overlapping sequence, was determined. Although the MD1-032, MD1-073 and MD2-013 isolates differed by 10-28 % from each other over the entire genome, they segregated into the same cluster and were phylogenetically distinguishable from all reported TTVs and TTMVs. These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus.

Genetic relationship of Torque Teno virus (TTV) between humans and camels in United Arab Emirates (UAE)

Torque Teno Virus (TTV) species-cross infection has been documented. However, the genetic relationship between human and animal TTV remains uncertain. In this study, genotypic characterization of TTV in different Camel specimens from the United Arab Emirates (UAE) was undertaken for comparison with human UAE TTV. A total of 56 specimens: 34 sera, 14 raw, and 8 pasteurized milk samples were tested for TTV. The results showed that the rate of infection was, 38.2% (13/34), 35.7% (5/14), and 100% (8/8), for the samples of sera, raw, and pasteurized milk respectively. The 5'untranslated region (5'UTR) of 23 clones that were generated from PCR products amplified from Camel samples (three sera, three raw, and two pasteurized milk samples) were subjected to sequence analysis. The camel TTV clones were classified as genotype 11 (47.8%), group 5 (43.5%), and SENV-H or genotype 16 (8.7%) which are among the predominant genotypes found in humans in the UAE. Phylogenetic analysis of representative sequences revealed that the similarity between isolates from camels and humans is 92%-97% for the same genotypes. The data lead to the conclusion that camels and humans share a common source of TTV infection in the UAE.

Molecular epidemiology and genotyping of TT virus isolated from Saudi blood donors and hepatitis patients

BACKGROUND

In Saudi Arabia, the epidemiology and clinical significance of Torque Teno virus (TTV) infection alone and in patients with hepatitis virus infections have not been determined in a single study. In this paper, we molecularly investigated the rate and genotypes of TTV infection among Saudi Arabian blood donors and patients with viral hepatitis. The effect of TTV coinfection on viral hepatitis was also examined.

SUBJECTS AND METHODS

DNA was extracted from the sera of 200 healthy blood volunteers, 45 hepatitis B virus patients, 100 hepatitis C virus patients, 19 hepatitis G virus patients, and 56 non-A-G hepatitis patients. TTV DNA was amplified using primers derived from the ORF1 and 5'UTR regions. The alanine aminotransferase (ALT) level was determined for each specimen. Sequencing of ORF1 amplicons was carried out to investigate TTV genotypes.

RESULTS

Using primers derived from ORF1 and 5'UTR, TTV DNA was detected in 5.5% and 50.5%, respectively, of healthy blood donors, in 2.2% and 88.8% in hepatitis B patients, in 2.0% and 70% of hepatitis C patients, in 15.8% and 100% of hepatitis G patients, in 5.4% and 12.5% of non-A-G hepatitis patients and in 4.8% and 56.4% overall. No detrimental effect of TTV coinfection in viral hepatitis patients was noted. An overall prevalence of 4.8% and 56.4% was established. Phylogenetic analysis indicated that the most common genotype of TTV among Saudis is 2c.

CONCLUSION

The rate of TTV infection among Saudi Arabians seems to be lower than that stated in previous reports on Saudi Arabia and in some other countries. The virus does not seem to worsen the status of those who are suffering from viral hepatitis infection.

[Transfusion-transmitted virus (TTV) and renal failure]

In 1997, a new DNA virus, designated TTV "Transfusion Transmitted Virus", was isolated and seemed to be associated with non A-G post-transfusion hepatitis. The virus infects mainly patients at risk for parenteral exposure and hence, prone to develop chronic liver disease, as well as healthy populations worldwide. Few reports, however, have been published on the epidemiology and potential significance of TTV infection in patients with renal disease. This paper reviews, characterization of the virus, the history of its discovery, taxonomy and identification. Current status of TTV infection in patients with renal diseases are also summarised.

Transfusion transmitted virus: A review on its molecular characteristics and role in medicine

The present review gives an updated overview of transfusion transmitted virus (TTV), a novel agent, in relation to its molecular characteristics, epidemiological features, modes of transmission, tissue tropism, pathogenesis, role in various diseases and its eradication from the body. TTV, a DNA virus, is a single stranded, non-enveloped, 3.8 kb long DNA virus with a small and covalently closed circular genome comprising 3852 bases. It was tentatively designated Circinoviridae virus. TTV genome sequence is heterogeneous and reveals the existence of six different genotypes and several subtypes. TTV has been reported to transmit not only via parenteral routes, but also via alternate routes. This virus has been detected in different non-human primates as well. At present, TTV is detected by polymerase chain reaction (PCR) with no other available diagnostic assays. It shows its presence globally and was detected in high percent populations of healthy persons as well as in various disease groups. Initially it was supposed to have strong association with liver disease; however, there is little evidence to show its liver tropism and contribution in causing liver diseases. It shows high prevalence in hemodialysis patients, pointing towards its significance in renal diseases. In addition, TTV is associated with several infectious and non-infectious diseases. Although its exact pathogenesis is not yet clear, TTV virus possibly resides and multiplies in bone marrow cells and peripheral blood mononuclear cells (PBMCs). Recently, attempts have been made to eradicate this virus with interferon treatment. More information is still needed to extricate various mysteries related to TTV.

Human circovirus TT virus genotype 6 expresses six proteins following transfection of a full-length clone

The expression profile of the circovirus TTV has not yet been fully characterized. In this paper, we show that following transfection of a full-length viral clone of TTV genotype 6, each of the three virally encoded mRNAs is translated from two initiating AUGs, and therefore, the TTV genome generates at least six proteins. Localization studies of hemagglutinin-tagged versions of these proteins in fixed cells, and green fluorescent protein-tagged versions of these proteins in living cells, expressed following transfection, demonstrated that two were primarily nuclear, two were primarily cytoplasmic, and two were found throughout the cell.

Molecular characterization of porcine TT virus, an orphan virus, in pigs from six different countries

Human TT virus (TTV), originally isolated from a patient with post-transfusion hepatitis in 1997, is ubiquitous and non-pathogenic. Viruses related to human TTV have since been identified in non-human primates, bovine, ovine, porcine, feline, and canine. The objective of this study was to genetically characterize porcine TTV from pigs in different geographic regions. PCR primers based on the non-coding region of the only available porcine TTV isolate were designed to amplify porcine TTV DNA from sera of pigs in six different countries. Porcine TTV DNA was detected in 66.2% (102/154) of the swine sera. The percentages of positive pigs varied greatly from country to country and even within the same country: 33% in Iowa, USA; 40% in Thailand; 46% in Ontario, Canada; 80% in China; 85% in Korea; 90% in Spain; 100% in Quebec and Saskatchewan, Canada. A total of 40 porcine TTV isolates (five from each geographic region) were sequenced for a 218 bp fragment within the non-coding region. Sequence analyses revealed that porcine TTV isolates from different geographic regions shared 86-100% nucleotide sequence identity to each other. The prototype Japanese isolate of porcine TTV, Sd-TTV31, shared 90-97% nucleotide sequence identity with porcine TTV isolates reported in this study. Phylogenetic analysis showed that the clustering of the porcine TTV isolates is not associated with geographic origins. Although porcine TTV is not known to be associated with any swine disease, co-infection of pigs with TTV and other known swine pathogens may result in enhanced disease. There are also concerns for risk of potential human infection during xenotransplantation.

Genomic characterization of a Brazilian TT virus isolate closely related to SEN virus-F

SEN virus (SENV) is a circular, single stranded DNA virus that has been first characterized in the serum of a human immunodeficiency virus type 1 (HIV-1)-infected patient. Eight genotypes of SENV (A-H) have been identified and further recognized as variants of TT virus (TTV) in the family Circoviridae. Here we describe the first genomic characterization of a SENV isolate (5-A) from South America. Using 'universal' primers, able to amplify most, if not all, TTV/SENV genotypes, a segment of > 3 kb was amplified by polymerase chain reaction from the serum of an HIV-1 infected patient. The amplicon was cloned and a 3087-nucleotide sequence was determined, that showed a high (85%) homology with the sequence of the Italian isolate SENV-F. Proteins encoded by open reading frames (ORFs) 1 to 4 consisted of 758, 129, 276, and 267 amino acids, respectively. By phylogenetic analysis, isolate 5-A was classified into TTV genotype 19 (phylogenetic group 3), together with SENV-F and TTV isolate SAa-38.

Transcriptional regulation of TT virus: promoter and enhancer regions in the 1.2-kb noncoding region

Since the discovery of TT virus (TTV) in 1997, its mechanism of transcriptional control has remained unsolved. Molecular analysis points at the 1.2-kb noncoding region (NCR) as being responsible for transcriptional control. The 5' terminus of TTV mRNA was located at nt 114 using the primer extension method (nt 114 will be referred to as position +1). This employed the PE1 primer, designed to start approximately 100 nt downstream of the predicted initiation site. Overall promoter and enhancer activity of the NCR was analyzed using dual luciferase assays in K562, Jurkat, U937, A549, HepG2, Huh7, and HeLaS3 cells. Of those tested, K562 showed the highest relative luciferase activity of 31.1, and activity in HepG2 (14.6) was significantly higher than that in Huh7 (2.8). Fragments of <250 nt length, spanning the NCR, were inserted into a luciferase vector possessing an SV40 promoter. Fragments F5(-542/-311) and F6(-310/-197) showed promoter-enhancing activities of >6.0 by insertion not only in the sense orientation, but also both in the antisense orientation and downstream of the luciferase gene. The 5' deletion of NCR from -1201 to -370 resulted in no significant decrease in the level of luciferase activity. A gradual decrease in the activity of the 5'-deletion mutants from position -370 through -155 was consistent with the loss of enhancer binding sites detected during fragment analysis. A further deletion at position -76 completely abolished luciferase expression, indicating that region -154/-76 contains the critical regulatory element for functioning of the TTV promoter.

Detection and genotyping of TT virus in healthy and subjects with HBV or HCV in different populations in the United Arab Emirates

TT virus (TTV) and TTV-like viruses (TTVLs) have been reported to be associated with non-A-E hepatitis. To determine the rate of infection and genotypic characteristics of TTV in the United Arab Emirates (UAE), a total of 449 serum samples representing different populations in the UAE and comprising healthy as well as patients positive for HBsAg and HCV were screened. National subjects (n = 200) and non-nationals residing in the UAE (n = 249) were tested by PCR. The results obtained showed that the rate of TTV infection in healthy nationals, and those with HBsAg or antibody to HCV were 34.9, 97.9, and 95.7, respectively, compared to 89.1% (115/129), 89.2% (66/74), and 84.8% (39/46), respectively, in non-nationals. Sequence analysis of the untranslated region (UTR) using 71 clones generated from the PCR products of eight serum samples from healthy individuals (four nationals and four non-nationals) showed that 83.1% of the TTV clones were classified into groups 1-4, whereas 16.9% into possibly new genotype(s). The analysis also revealed that healthy national subjects carried multiple viruses. Phylogenetic analysis of representative sequences revealed clustering of clones into at least five major groups. Also, when compared to reference genotypes (from GenBank), two of our clones belonged to two previously identified genotypes. Non-significant gender differences were seen in all ethnic groups studied (P > 0.05). In conclusion, the rate of TTV infection in the UAE nationals is significantly lower (P < 0.05) than that of the non-nationals and several genotypes were isolated with common multi-infections.

TT virus in Hungary: sequence heterogeneity and mixed infections

The majority of the viral hepatitis cases is caused by five hepatitis viruses (A,B,C,D,E). In 1997, TT virus was discovered. It was supposed that a number of the unknown hepatitis cases was caused by the TT virus. The aim of this study was to characterize TT viruses carried by healthy individuals and patients suffering from hepatitis of unknown origin in Hungary. TTV DNA was detected by seminested PCR with the commonly used N22 primers. Twenty of the 108 sera (18.5%) taken from healthy persons and 115 of the 228 sera (50.4%) of patients with hepatitis of unknown origin were found to be positive. The nucleotide sequences of 26 clones derived from 17 hepatitis patients and 15 clones from nine healthy persons were determined and a phylogenetic tree was constructed. Genotype 2 (group 1) was found to be the most frequent, but other group 1 genotypes (1, 6) and genotypes 8 and 17 of group 2 were also detected. Mixed TTV infections were found in eight cases (two healthy persons and six hepatitis patients). Variants belonging to the same group were carried in seven cases, and the presence of group 1 (genotype 2) and group 2 (genotype 8) TTV sequences were found in one single hepatitis patient.

TT virus has a ubiquitous diffusion in human body tissues: analyses of paired serum and tissue samples

The tissue tropism and possible correlation with liver disease of the TT virus (TTV) as well as its prevalence and genotype distribution remain undefined. TTV-DNA was investigated in paired sera and tissue samples from 144 patients, and sera and cerebrospinal fluids (CSF) from additional six subjects. Of the 144 tissue samples, 128 were liver biopsy specimens from subjects with hepatic disease while 16 were surgically obtained nonliver specimens from patients with extrahepatic disease. TTV cloning, sequencing and genotype analyses were performed on isolates from sera, tissue specimens and peripheral blood mononuclear cells of two patients with hepatic and four patients with extrahepatic pathologies, as well as from sera and CSFs of two subjects. TTV was found in 100% of the examined tissues and in 60.1 and 50% of sera from patients with hepatic and extrahepatic pathologies, respectively. Moreover, TTV was detected in four of the six CSFs analysed but only in two correspondent sera. Genotyping revealed the coexistence of multiple TTV genotypes and genetic variants in each infected individual, and the analysis of TTV mRNA showed the presence of transcripts in all the six different tissues studied. These results indicate that the entire adult population in our area is more likely infected by TTV, although several subjects are not viraemic and that TTV infects many different human tissues and is able to invade the central nervous system.

Distribution of TT virus genomic groups 1-5 in Brazilian blood donors, HBV carriers, and HIV-1-infected patients

Human isolates of the highly prevalent TT virus (TTV) have been classified into five major genomic groups (1-5). The geographical distribution of the groups throughout the world is not well known. Five different PCR assays were developed in an attempt to amplify specifically TTV DNAs of each genomic group. Serum samples collected from 72 Brazilian adults (24 voluntary blood donors, 24 hepatitis B virus (HBV) carriers, and 24 human immunodeficiency virus type 1 (HIV-1)-infected patients) were tested. TTV DNA from at least one genomic group was detected in 11 (46%) blood donors, 13 (54%) HBV carriers, and 24 (100%) HIV-1 patients. All five genomic groups were detected in the three populations, with the exception of group 2 in blood donors. Some samples, negative with all five specific assays, were positive with the commonly used untranslated region (UTR) PCR system. On the other hand, TTV DNA was detected in some samples by using specific assays but not with the UTR PCR. Mixed infections with 2-5 TTV isolates from different groups were detected in 21% blood donors, 29% HBV carriers, and 71% HIV-1 patients. Fifteen PCR products (three obtained with each assay) were sequenced. Most sequences showed high (>86%) homology with those of TTV isolates belonging to their presumed groups. However, three sequences had low homology with all TTV sequences available from the DNA databanks. In conclusion, TTV isolates belonging to all five known genomic groups circulate in Brazil, and the results suggest the existence of new and as yet uncharacterised major genomic groups.

High TT virus load as an independent factor associated with the occurrence of hepatocellular carcinoma among patients with hepatitis C virus-related chronic liver disease

The TT virus (TTV) load was estimated in sera obtained from 237 patients with hepatitis C virus (HCV)-related chronic liver disease including 42 patients with hepatocellular carcinoma (HCC), by real-time detection PCR using primers and a probe derived from the well-conserved untranslated region of the TTV genome, which can detect all known TTV genotypes. Of the 237 patients studied, 18 (8%) were negative for TTV DNA, 87 (37%) had low TTV viremia (1.3 x 10(2)-9.9 x 10(3) copies/ml), and 132 (56%) had high TTV viremia (1.0 x 10(4)-2.1 x 10(6) copies/ml). Various features were compared between the patients with high TTV load (n = 132) and those with no TTV viremia or low viral load (n = 105). High TTV viremia (> or =10(4) copies/ml) was significantly associated with higher age (P < 0.05), past history of blood transfusion (P < 0.001), complication of cirrhosis (P < 0.05) or HCC (P < 0.0005), lower HCV RNA titer (P < 0.05), and lower platelet count (P < 0.01). On multivariate logistic regression analysis, high TTV viral load was a significant risk factor for HCC (P < 0.05), independent from known risk factors such as complication of liver cirrhosis (P < 0.0001) and high age (> or =65 years, P < 0.05), among all 237 patients. Furthermore, high TTV viral load was an independent risk factor for HCC among the 90 cirrhotic patients (P < 0.05). These results suggest that a high TTV viral load is associated independently with the complication of HCC and may have prognostic significance in patients with HCV-related chronic liver disease, although whether high TTV viremia mediates the progression of HCV-related chronic liver disease remains to be defined.

Nucleic acid testing for emerging viral infections

The development of new technologies leads to the discovery of new viruses. For each of these new infectious agents, relevance to transfusion, including transmissibility by transfusion, pathogenicity, prevalence in blood donors, persistence and the availability of screening assays needs to be assessed. Since 1995, one virus and a new family of viruses have been identified. GB virus-C/hepatitis G virus (GBV-C/HGV), a flavi virus with some homology with and epidemiological features of HCV, is not related to post-transfusion hepatitis but seems to positively interfere with human immunodeficiency virus replication. Human circoviruses include TT virus (TTV) and SEN-V. Both are highly variable, constituting a large family of distantly related viruses. They appear ubiquitous, infecting humans very early in life and are largely persistent. No clinical symptoms or pathogenicity is associated with TTV, but SEN-V might be associated with some non-A-E post-transfusion hepatitis. Parvovirus B19 has been known for many years, but its transmission to recipients of plasma derivatives despite viral inactivation raised the issue of screening plasma pools by nucleic acid testing. Most fractionators quantify B19 DNA in plasma pools to ensure a viral load of <10(4) IU mL-1.

Prevalence and genomic variability of transfusion transmitted virus in Italian cryptogenic chronic liver disease and healthy blood donors

BACKGROUND

Infection with transfusion transmitted virus, a new member of the Parvoviridae family, has been found in patients both with chronic and fulminant post-transfusion cryptogenic hepatitis.

AIM

To evaluate the prevalence and clinical impact of transfusion transmitted virus infection in Italy.

PATIENTS AND METHODS

Studies were carried out on 256 patients and control subjects from three centres from Northern, Central and Southern Italy (92 nonA-nonC chronic hepatitis, 10 acute non fulminant cryptogenic hepatitis, 41 hepatitis C virus-related chronic hepatitis and 113 blood donors). Serum transfusion transmitted virus was detected by nested polymerase chain reaction using two overlapping sets of primers.

RESULTS

A total of 52 of the 92 patients (54.3%) with chronic cryptogenic liver disease and 17 of the 41 hepatitis C virus chronic hepatitis patients (41.4%) were transfusion transmitted virus-DNA positive. Transfusion transmitted virus co-infection in hepatitis C virus patients was not associated with either a higher severity of liver histology or higher alanine transaminase levels or signs of cholestasis, transfusion transmitted virus was found in 48 out of 113 (42.4%) blood donors. In the majority of samples, transfusion transmitted virus DNA was detected with only one of the two sets of primers used. Genotyping and phylogenetic analysis performed on 21 randomly selected viral isolates showed the presence of both type 1 and type 2 transfusion transmitted virus and allowed identification of two isolates with high homology to genotype 6, described, so far, mostly in Japan.

CONCLUSIONS

Transfusion transmitted virus type 1 and 2 infection is common among blood donors and patients with liver disease in Italy. The pathogenic potential of transfusion transmitted virus type 1 and 2 in nonA-nonC hepatitis patients is unlikely but further studies are needed to evaluate the epidemiological and clinical impact of other transfusion transmitted virus subtypes.

Genomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias

Using PCR with primers derived from a non-coding region of the human TT virus (TTV) genome, the TTV sequence in serum samples obtained from pigs (Sus domesticus), dogs (Canis familiaris) and cats (Felis catus) was identified and the entire genomic sequence was determined for each representative isolate. Three TTV isolates (Sd-TTV31 from a pig, Cf-TTV10 from a dog and Fc-TTV4 from a cat) comprising 2878, 2797 and 2064 nucleotides, respectively, each had three open reading frames (ORFs) encoding 436-635 (ORF1), 73-105 (ORF2) and 224-243 (ORF3) aa but lacked ORF4, similar to tupaia TTV. ORF3 was presumed to arise from a splicing of TTV mRNA, similar to human prototype TTV. Although the nucleotide sequence of Sd-TTV31, Cf-TTV10 and Fc-TTV4 differed by more than 50% from each other and from previously reported TTVs of 3.4-3.9 kb and TTV-like mini viruses (TLMVs) of 2.8-3.0 kb isolated from humans and non-human primates as well as tupaia TTVs of 2.2 kb, they resembled known TTVs and TLMVs with regard to genomic organization and presumed transcriptional profile rather than animal circoviruses of 1.7-2.3 kb. Phylogenetic analysis revealed that Sd-TTV31, Cf-TTV10 and Fc-TTV4 were closer to TTVs from lower-order primates and tupaias than to TTVs from higher-order primates and TLMVs. These results indicate that domestic pigs, cats and dogs are naturally infected with species-specific TTVs with small genomic size and suggest a wide distribution of TTVs with extremely divergent genomic sequence and length in animals.

Novel variants related to TT virus distributed widely in China

TTV is a DNA virus with high genetic heterogeneity. To investigate the novel isolates of the virus, blood samples were collected from subjects who lived in various parts of China and suffered from hepatitis or were asymptomatic carriers. Nested PCR was carried out to amplify a 3.2-kb fragment using primers deduced from the prototype TTV (TA278). The ten entire 3.2-kb nt sequences were aligned with isolate TA278, SANBAN, TUS01, and SENV retrieved from GenBank, and a phylogenetic tree was constructed by Neighbor-Joining method. The analysis indicated that five novel variants of the present study have not been described before, and all TTV-related isolates could be classified into three groups. The isolate TCHN-A, B and TUS01 were included in a group, and the remaining novel isolates together with SANBAN and TA278 clustered into another group, while SEN virus formed a distinct group. The genetic distances of the five novel variants were 0.5507-0.8476 to TA278, 0.4635-0.7877 to SANBAN, 0.6064-0.7834 to TUS01 and 0.6936-0.8236 to SENV. Of these novel variants, the ORF1 consisted of 426-772 aa and ORF2 of 141-156 aa. The nt identities of ORF1 and ORF2 between those variants and TA278, SANBAN, and TUS01 were 46.1-60.8 and 48.7-63.6%, and those of aa sequences were only 27.1-52.4 and 28.9-45.5%, respectively. The first 65 aa of ORF1 were rich in arginine and most conserved with homology of 56.5-70.0%. There was a hypervariable region from aa 286 to 403 with merely 17.7-27.0% of identity. Despite a low aa identity between TA278 and the variants, they have similar hydrophilicity profiles of ORF1. There were 2-10 N-glycosylation motifs found in these variants. In conclusion, despite the high divergence, sequences of all these isolates shared common genome organisation, ORF structure, hydrophilicity patterns, and some potential motifs with TTV prototype. It is suggested that various TTV and TTV-related isolates belong to a very large and complex family, which remains to be studied.

Cloning and sequencing of TT virus genotype 6 and expression of antigenic open reading frame 2 proteins

The near-full-length genome of a TT virus (TTV) (HEL32), closely related to the previously uncharacterized genotype 6, was cloned and sequenced. The genomic organization of HEL32 was compared to 41 published near-full-length TTV sequences representing 17 genotypes. In the majority of genomes, the open reading frame (ORF) 2 region was divided into two separate ORFs, 2a and 2b. The ORF2a sequence was conserved among all genotypes, while the ORF2b region showed more variability. The two corresponding putative proteins of HEL32 were expressed in prokaryotes and their antigenic potential was studied. IgM and IgG antibodies to the respective ORF2-encoded proteins, fp2a and fp2b, and the presence of TTV DNA were studied in the sera of 89 constitutionally healthy adults. By immunoblot using the small TTV proteins as antigens, strong IgM and IgG reactivities were found in 9 and 10% of subjects, respectively. Follow-up studies for 12-15 years of three subjects showed either a persistent coexistence of IgM and TTV DNA or the appearance of viral DNA regardless of pre-existing antibodies. The low prevalence of IgG could be due to the weak immunogenicity of these probably non-structural proteins or to a genotype-specific antibody response. By nested PCR of the conserved ORF2a region, the prevalence of TTV DNA was 85%. TTV genotype 6 sequences were found by specific PCR in 3 of 35 (8.6%) subjects. The low prevalence of TTV IgG compared to the high TTV DNA prevalence, the coexistence of antibodies and viral DNA and the appearance of TTV DNA regardless of pre-existing antibodies suggest that the B-cell immunity against these minor TTV proteins would not be cross protective.

Phylogenetic classification of TT virus groups based on the N22 region is unreliable

Evolutionary studies on the recently discovered TT virus (TTV) are currently focused on approximately 220 nts of the N22 region, since this is the region for which most sequence information is available. Regarding the extensive sequence heterogeneity in this region, within group classification can be sufficiently reliable, however, between group classification becomes problematic. We observed high divergence at the nucleotide level between distant related strains (TTV groups) preventing unambiguous alignments, saturation in transitions within TTV groups and considerable phylogenetic noise due to conflicting signals within distinct genotypes. Consequently, analysing all TTV groups in one tree, using this 220 nt region provides unreliable results. Also within genotype analysis can produce conflicting results. On the other hand, this region is still suitable to some extent for within TTV group phylogenetic analysis. We suggest that care should be taken in future TTV phylogenetic analysis, in particular, larger and more conserved regions should be sequenced to allow between group comparisons.

Frequent detection of the replicative form of TT virus DNA in peripheral blood mononuclear cells and bone marrow cells in cancer patients

The TT virus (TTV), a member of a family of human viruses related to the circoviridae viruses, was associated initially with acute and chronic liver diseases. TTV consists of a single-stranded, circular DNA genome of 3.8 kilobases (kb) and at least three open reading frames (ORFs). The objective of the present study was to determine whether or not TTV replicated in peripheral blood mononuclear cells (PBMCs) and bone marrow cells (BMCs). DNA was extracted from the PBMCs or BMCs of 153 cancer patients and from the PBMCs of 50 healthy blood donors (the controls). By using a single round of polymerase chain reaction (PCR), TTV was detected in 98.6% (141 of 143) of the PBMCs and in 90% (9 of 10) of the BMCs from cancer patients. TTV DNA was detected in significantly fewer control subjects at 86% (43 of 50; P < 0.05). Strand-specific PCR (SSPCR) targeting the ORF2 of the common genotypes of TTV was developed specifically to detect TTV positive or negative strand DNA and to examine TTV replication. TTV positive strand DNA, which may be an intermediate of viral replication, was detected in 55.3% (78 of 141) of the TTV-infected PBMCs of the cancer patients and in 7% (3 of 43) of the controls (P < 0.001). The replicative form of TTV was also detectable in 55.6% (5 of 9) of the TTV-infected BMCs. The existence of double-strand (positive and negative strands) TTV DNA in PBMCs and BMCs of the cancer patients was also supported by the finding that TTV DNA extracted from these cells was resistant to S1 nuclease. Using in situ hybridization, TTV DNA was also demonstrated to be present in the nucleus of PBMCs. It is concluded that replicative intermediate forms of TTV DNA are present in both PBMCs and BMCs, indicating that blood cells may be a site of TTV replication.