Comprehensive profiling of antibody responses to the human anellome using programmable phage display.

Anelloviruses represent a major constituent of the commensal human virome; however, little is known about their immunobiology. Here, we present "AnelloScan," a T7 phage library representing the open reading frame 1 (ORF1), ORF2, ORF3, and torque teno virus (TTV)-derived apoptosis-inducing protein (TAIP) sequences of more than 800 human anelloviruses and profile the antibody reactivities of serum samples from a cross-sectional cohort of 156 subjects by using phage-immunoprecipitation sequencing (PhIP-Seq). A majority of anellovirus peptides are not reactive in any of the subjects tested (n = ∼28,000; ∼85% of the library). Antibody-reactive peptides are largely restricted to the C-terminal region of the capsid protein ORF1. Moreover, using a longitudinal cohort of matched blood-transfusion donors and recipients, we find that most transmitted anelloviruses do not elicit a detectable antibody reactivity in the recipient and that the remainder elicit delayed responses appearing ∼100-150 days after transfusion.

Molecular validation of pathogen-reduction technologies using rolling-circle amplification coupled with real-time PCR for torquetenovirus DNA quantification.

BACKGROUND: Pathogen reduction technologies (PRT) based on nucleic-acid damaging chemicals and/or irradiation are increasingly being used to increase safety of blood components against emerging pathogens, such as convalescent plasma in the ongoing COVID-19 pandemic. Current methods for PRT validation are limited by the resources available to the blood component manufacturer, and quality control rely over pathogen spiking and hence invariably require sacrifice of the tested blood units: quantitative real-time PCR is the current pathogen detection method but, due to the high likelihood of detecting nonviable fragments, requires downstream pathogen culture. We propose here a new molecular validation of PRT based on the highly prevalent human symbiont torquetenovirus (TTV) and rolling circle amplification (RCA). MATERIALS AND METHODS: Serial apheresis plasma donations were tested for TTV before and after inactivation with Intercept® PRT using real-time quantitative PCR (conventional validation), RCA followed by real-time PCR (our validation), and reverse PCR (for cross-validation). RESULTS: While only 20% of inactivated units showed significant decrease in TTV viral load using real-time qPCR, all donations tested with RCA followed by real-time PCR showed TTV reductions. As further validation, 2 units were additionally tested with reverse PCR, which confirmed absence of entire circular genomes. DISCUSSION: We have described and validated a conservative and easy-to-setup protocol for molecular validation of PRT based on RCA and real-time PCR for TTV.

Identification of heterologous Torque Teno Viruses in humans and swine.

Torque Teno Viruses (TTVs) are ubiquitous viruses which are highly prevalent in several mammalian species. Human TTV's are epidemiologically associated with several human disease conditions such as respiratory illnesses, auto-immune disorders and hepatitis. Recently it was found that swine TTV's (TTSuVs) can act as primary pathogens. The common occurrence of TTVs as environmental contaminants and the increasing interest in the use of swine organs for xenotransplantation lend importance to the question of whether TTV's can cross-infect across species. In this study, we examined human and swine sera by swine or human TTV-specific PCRs, to determine whether swine TTVs (TTSuV) DNA can be detected in humans and vice versa. Surprisingly, both human and TTSuV DNA were present in a majority of the samples tested. Transfection of human PBMC's with TTSuV1 genomic DNA resulted in productive viral infection which was sustained for the three serial passages tested. Lymphoproliferative responses in infected human PBMCs were diminished when compared to the controls. Furthermore, mild to moderate antibody responses against the TTSuV1 ORF2 protein was detected in 16 of the 40 human sera by ELISA. Therefore, these study findings provide initial and fundamental evidence for possible cross-species transmission of TTVs.

Serological profile of torque teno sus virus species 1 (TTSuV1) in pigs and antigenic relationships between two TTSuV1 genotypes (1a and 1b), between two species (TTSuV1 and -2), and between porcine and human anelloviruses.

The family Anelloviridae includes human and animal torque teno viruses (TTVs) with extensive genetic diversity. The antigenic diversity among anelloviruses has never been assessed. Using torque teno sus virus (TTSuV) as a model, we describe here the first investigation of the antigenic relationships among different anelloviruses. Using a TTSuV genotype 1a (TTSuV1a) or TTSuV1b enzyme-linked immunosorbent assay (ELISA) based on the respective putative ORF1 capsid antigen and TTSuV1-specific real-time PCR, the combined serological and virological profile of TTSuV1 infection in pigs was determined and compared with that of TTSuV2. TTSuV1 is likely not associated with porcine circovirus-associated disease (PCVAD), because both the viral loads and antibody levels were not different between affected and unaffected pigs and because there was no synergistic effect of concurrent PCV2/TTSuV1 infections. We did observe a higher correlation of IgG antibody levels between anti-TTSuV1a and -TTSuV1b than between anti-TTSuV1a or -1b and anti-TTSuV2 antibodies in these sera, implying potential antigenic cross-reactivity. To confirm this, rabbit antisera against the putative capsid proteins of TTSuV1a, TTSuV1b, or TTSuV2 were generated, and the antigenic relationships among these TTSuVs were analyzed by an ELISA and by an immunofluorescence assay (IFA) using PK-15 cells transfected with one of the three TTSuV ORF1 constructs. The results demonstrate antigenic cross-reactivity between the two genotypes TTSuV1a and TTSuV1b but not between the two species TTSuV1a or -1b and TTSuV2. Furthermore, an anti-genogroup 1 human TTV antiserum did not react with any of the three TTSuV antigens. These results have important implications for an understanding of the diversity of anelloviruses as well as for the classification and vaccine development of TTSuVs.

Epstein-Barr virus stimulates torque teno virus replication: a possible relationship to multiple sclerosis.

Viral infections have been implicated in the pathogenesis of multiple sclerosis. Epstein-Barr virus (EBV) has frequently been investigated as a possible candidate and torque teno virus (TTV) has also been discussed in this context. Nevertheless, mechanistic aspects remain unresolved. We report viral replication, as measured by genome amplification, as well as quantitative PCR of two TTV-HD14 isolates isolated from multiple sclerosis brain in a series of EBV-positive and -negative lymphoblastoid and Burkitt's lymphoma cell lines. Our results demonstrate the replication of both transfected TTV genomes up to day 21 post transfection in all the evaluated cell lines. Quantitative amplification indicates statistically significant enhanced TTV replication in the EBV-positive cell lines, including the EBV-converted BJAB line, in comparison to the EBV-negative Burkitt's lymphoma cell line BJAB. This suggests a helper effect of EBV infections in the replication of TTV. The present study provides information on a possible interaction of EBV and TTV in the etiology and progression of multiple sclerosis.

Replication of and protein synthesis by TT viruses.

The host cells and the events in the cells during Torque teno (TT) virus infection are at present unknown. Replicating TT virus DNA has been detected in liver, in peripheral blood mononuclear cells (PBMC), and in bone marrow. By alternative splicing this small virus generates three mRNA species, from which by alternative translation initiation at least six proteins are produced. The functions of the proteins are not yet fully understood. However, functions associated with, e.g., DNA replication, immunomodulation, and apoptosis have been suggested to reside in the multifunctional proteins of anelloviruses.

Replication of chicken anemia virus (CAV) requires apoptin and is complemented by VP3 of human torque teno virus (TTV).

To test requirement for apoptin in the replication of chicken anemia virus (CAV), an apoptin-knockout clone, pCAV/Ap(-), was constructed. DNA replication was completely abolished in cells transfected with replicative form of CAV/Ap(-). A reverse mutant competent in apoptin production regained the full level of DNA replication. DNA replication and virus-like particle (VLP) production of CAV/Ap(-) was fully complemented by supplementation of the wild-type apoptin. The virus yield of a point mutant, CAV/ApT(108)I, was 1/40 that of the wild type, even though its DNA replication level was full. The infectious titer of CAV was fully complemented by supplementing apoptin. Progeny virus was free from reverse mutation for T(108)I. To localize the domain within apoptin molecule inevitable for CAV replication, apoptin-mutant expressing plasmids, pAp1, pAp2, pAp3, and pAp4, were constructed by deleting amino acids 10-36, 31-59, 59-88 and 80-112, respectively. While Ap1 and Ap2 were preferentially localized in nuclei, Ap3 and Ap4 were mainly present in cytoplasm. Although complementation capacity of Ap3 and Ap4 was 1/10 of the wild type, neither of them completely lost its activity. VP3 of TTV did fully complement the DNA replication and VLP of CAV/Ap(-). These data suggest that apoptin is inevitable not only for DNA replication but also VLP of CAV. The common feature of apoptin and TTV-VP3 presented another evidence for close relatedness of CAV and TTV.

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.

Detection of Torque teno virus in Epstein-Barr virus positive and negative lymph nodes of patients with Hodgkin lymphoma.

The age-specific incidence of Hodgkin lymphoma (HL) is bimodal with peaks occurring among young adults (15 - 34 years old) and people older than 45 years. Epstein-Barr virus (EBV) is associated with only one-third of HL cases. This study sought to determine if Torque teno virus (TTV) might be independently associated with HL. The presence of EBV was appraised by in situ hybridization and immunohistochemistry in lymph node biopsies from 46 patients (3 - 81 years old) with HL. TTV DNA was assessed by PCR amplification. EBV was detected in 22 (48%) patients. TTV DNA was detected in 24/46 (52%) patients, as well as in 12/20 (60%) control patients with lymphoid unspecific hyperplasia. TTV DNA was not significantly more frequent in EBV negative (54%) than in EBV positive (50%) nodes. However, it was observed that the group of young adults (15 - 34 years, n = 19) showed the lowest EBV frequency (21%) but the highest TTV occurrence (60%). This may suggest an involvement of TTV infection in the pathogenesis of HL in young adults. Further large population-based studies are required to confirm our findings.

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. Though, 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.

Detection of TT virus in lymph node biopsies of B-cell lymphoma and Hodgkin's disease, and its association with EBV infection.

Human TT virus (TTV) recently isolated from the serum of a patient with post-transfusion hepatitis does seem to have only hepatopathic effect. The virus can also infect the serum, peripheral blood mononuclear cells (PBMC) and bone marrow cells (BMC ). Additional evidence has indicated that TTV is also present in the serum of people with hematopoietic malignancies. A significant increase in the incidence of lymphoma has recently been observed worldwide. We have investigated the presence of TTV DNA in lymph node biopsies of Italian patients affected with the most common lymphoma types in Western Countries: follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL) and nodular sclerosis Hodgkin's disease (NS-HD). The possible role of a co-infection with Epstein-Barr virus (EBV) has also been investigated. DNA was extracted from 73 paraffin-embedded and 38 snap-frozen tissue specimens. From these, only 67 samples (29 paraffin-embedded and 38 snap-frozen tissues) from a total of 56 patients, were suitable for PCR analysis. TTV and EBV were detected by PCR using primers from two different conserved region in TTV and EBV genomes respectively. TTV DNA was detected in 30.0-50.0% of FL, 30.8% of DLBCL and 30.0-50.0% of NS-HD cases, depending on the primers used. All cases of non-specific reactive lymphoid hyperplasia (RLH), used as a putative control, were negative. The two major TTV genotypes circulating in Italy (G1 and G2) were detected in the analysed lymphoid neoplasms. EBV DNA was detected in 40.0% of FL, in 72.7%of DLBCL, in 80.0% of SN-HD and in 40.0% of RLH cases. EBV co-infection was found in 90% of TTV positive cases. The in situ hybridization assay was performed in TTV positive frozen samples. The significant prevalence of TTV DNA in lymphocytes circulating in the lymph nodes of both B-cell lymphomas and HD reported herewith suggests an implication of TTV infection in the development of these lymphoproliferative disorders.

Detection of TT virus (TTV) in children and youth with chronic viral hepatitis B and C.

BACKGROUND: TTV is a newly discovered virus and little is known about the frequency of TTV infection in children in Poland. The aim of our study was to investigate the frequency of TTV infection in children with chronic viral hepatitis B and C. MATERIAL/METHODS: Two patient groups were tested: 74 patients with chronic hepatitis B aged 4 to 20 years, and 13 patients with chronic hepatitis C aged 10 to 18 years. Nucleic acids were extracted from serum using the spin column technique (QIAGEN(r), Hilden, Germany), and TTV DNA sequences were amplified by nested PCR. RESULTS: TTV DNA was found in 47.3% of patients with chronic hepatitis B and in 53.8% of patients with hepatitis C. Among those patients with chronic B hepatitis there was no statistical difference between the frequency of coinfection with TTV and clinical-histopathological diagnosis, activity of aminotransaminases, frequency of seroconversion of HBeAg to antiHBe, or interferon alpha therapy. CONCLUSIONS: In Poland, TTV viremia is frequent in patients with chronic viral hepatitis B and C. TTV coinfection did not modify the course and activity of chronic hepatitis B or influence the outcome of interferon therapy.

TT virus is distributed in various leukocyte subpopulations at distinct levels, with the highest viral load in granulocytes.

When TT virus (TTV) DNA was quantitated in whole blood and plasma aliquots from 27 viremic individuals by real-time detection PCR that can detect essentially all TTV genotypes, the TTV load was 6.9 +/- 3.5 (mean +/- standard deviation)-fold higher in the whole blood than in the plasma samples [P < 0.002 (paired t test)]. To clarify the reason for this difference, peripheral blood cells of various types including red blood cells, granulocytes (CD15+), B cells (CD19+), T cells (CD3+), monocytes (CD14+), and NK cells (CD3-/CD56+) were separated at a purity of 95.4-99.5% from each of three infected individuals with relatively high TTV viremia, and their TTV viral loads were determined. Red blood cells were uniformly negative, but the other cell types were positive for TTV DNA at various titers. In all three patients, the highest TTV load was found in granulocytes (4.2 x 10(4)-3.1 x 10(5) copies/10(6) cells), followed by monocytes (1.4-2.2 x 10(4) copies/10(6) cells) and NK cells (5.4-6.5 x 10(3) copies/10(6) cells); B and T cells were positive, with a low viral load (6.7 x 10(1)-2.7 x 10(3) copies/10(6) cells). These results indicate that TTV is distributed in various peripheral blood cell types at distinct levels, with the highest viral load in granulocytes, and that a significant proportion of the TTV DNA in peripheral blood is not identified by the standard plasma/serum DNA detection methods.

Heterogeneous distribution of TT virus of distinct genotypes in multiple tissues from infected humans.

TT virus (TTV) DNA was quantitated in the serum and nine autopsy tissues (bone marrow, lymph node, muscle, thyroid gland, lung, liver, spleen, pancreas, and kidney) obtained from each of three TTV-infected subjects by real-time polymerase chain reaction (PCR), which can detect all TTV genotypes. TTV DNA was detected in all examined tissues, with the viral load being equal to or up to 300 times higher than that in the corresponding serum (2.1 x 10(5) to 5.3 x 10(7) copies/g vs 1.2-3.9 x 10(5) copies/ml). Generally, the TTV viral load was higher in the bone marrow, lung, spleen, and liver than in the other tissues, although it varied by individual. Restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified TTV DNA of 3.3 kilobases (kb) revealed considerable differences among the TTVs in the serum and tissue specimens from each subject. Further, the 3.3-kb amplicons from the serum and tissue specimens from one subject were molecularly cloned, and 30 clones each from the serum and each tissue specimen were subjected to RFLP and sequence analysis (total, 300 clones): the TTV clones were classified into six genotypes including four novel genotypes. The genotypic variability was remarkable: each specimen had one to five TTV genotypes at different frequencies. TTV DNA in replicative intermediate forms and TTV mRNA were detectable in all tissues tested. These results indicate the broad, uneven distribution of TTV genotypes in tissues and suggest that viral replication takes place in multiple tissues at distinct levels in infected individuals.

Phosphorylation of serine-rich protein encoded by open reading frame 3 of the TT virus genome.

TT virus (TTV) is a newly discovered human virus with a single-stranded, circular DNA genome. The TTV DNA sequence includes two major open reading frames (ORFs), ORF1 and ORF2. Recently, spliced TTV mRNAs were detected and revealed two additional coding regions, ORF3 and ORF4. We found sequence similarity between the TTV ORF3 protein and hepatitis C virus (HCV) nonstructural 5A (NS5A) protein, which is a phosphoprotein and is thought to associate with various cellular proteins. To test whether the TTV ORF3 protein is phosphorylated, the state of phosphorylation was analyzed with a transient protein production system. The TTV ORF3 protein was phosphorylated at the serine residues in its C-terminal portion. Furthermore, the TTV ORF3 gene generated two forms of proteins with a different phosphorylation state, similar to the HCV NS5A region, suggesting that TTV ORF3 protein has function(s) similar to phosphorylated viral proteins such as the HCV NS5A protein.

Three spliced mRNAs of TT virus transcribed from a plasmid containing the entire genome in COS1 cells.

A permuted whole-genome construct of a TT virus (TTV), named VT416, had 3,852 nucleotides (nt) 98.2% similar to the prototype TA278 genome. To allow the transcription of TTV from the internal promoter, pBK*VT416(1.3G), carrying 1.3 units of VT416, was constructed. The poly(A)(+) RNAs expressed in COS1 cells 48 h posttransfection contained three TTV mRNA species 3.0, 1.2, and 1.0 kb in length, which were recovered in the 13 DNA clones from a lambda phage cDNA library. These mRNAs in the antigenomic orientation possessed in common the 3' terminus downstream of a poly(A) signal (A(3073)ATAAA) and the 5' terminus downstream of a cap site (C(98)ACTTC). A common splicing to join nt 185 with nt 277 was detected in all mRNAs. The coding region of the largest open reading frame (ORF) was maintained in 3.0-kb mRNA, because this splicing was located upstream of its initiation codon (A(589)TG). The second splicing was detected in 1.2-kb mRNA to join nt 711 with nt 2374 and in 1.0-kb mRNA to bind nt 711 to nt 2567. They linked a proposed ORF2 to another ORF for creating new ORFs over nt 2374 to 2872 in frame 2 and nt 2567 to 3074 in frame 3. The donor and acceptor sites of all three splicings matched the consensus sequence and were conserved in most of the 16 TTVs of distinct genotypes retrieved from the database. The observed transcription profile is unique to TTV among known members in the family Circoviridae.