Genomic and Molecular Evolutionary Analysis of a Newly Identified Infectious Agent (SEN Virus) and Its Relationship to the TT Virus Family

Tanaka, Yasuhito; Primi, Daniélé; Wang, Richard Y.-H.; Umemura, Takeji; Yeo, Anthony E. T.; Mizokami, Masashi; Alter, Harvey J.; Shih, Jennifer

doi:10.1086/318091

Cited by 159 publications

(147 citation statements)

References 32 publications

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Section: Discussionmentioning

confidence: 99%

“…The justification for different genera and species has, in addition, been suggested (45,55). The use of different regions of the genome for establishing phylogeny has frequently been questioned and debated (3,39,45,55). Recombination between TT isolates has been discussed (28,59), although according to our experience this may represent PCR artifacts (generating genomes or partial genomes by PCR amplification on DNA templates harboring several closely related TTV genomes) (unpublished data).…”

Section: Discussionmentioning

confidence: 99%

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Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

Jelčić¹,

Hotz‐Wagenblatt

Hunziker³

et al. 2004

J Virol

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We report the isolation of 24 novel genotypes of TT viruses from a surgically removed spleen of a patient with Hodgkin's disease. The sequence analysis of our 24 isolates revealed the remarkable heterogeneity of TT virus isolates not only from the same patient but also from the same biopsy material. These isolates belong to four phylogenetic groups of TT viruses. Nucleotide sequence analyses revealed five distinct genotypes (tth3, tth4, tth5, tth6, and tth7). The limited variation in sequence identity of the other isolates defines the latter as variants of four of these genotypes. A group of 6 isolates (the tth7 group) revealed a reorganization of open reading frame 1 (ORF1) leading to one larger and a varying number of smaller ORFs. The nucleotide difference of the full-length genomes was less than 1%. A variation of 69 to 97% in amino acids of a second group of 8 isolates (the tth3 group) was restricted to the hypervariable region of ORF1, indicating the existence of a quasi-species. These isolates differed by less than 2% in the remainder of their nucleotide sequences. An alignment of these isolates with 79 previously reported TT virus genotypes permits the proposal of TT virus genera and species within the family Anelloviridae in analogy to a previous proposal for the papillomaviruses (family Papillomaviridae).TT viruses (TTV) are ubiquitous in nature and have been demonstrated in more than 90% of serum samples from healthy individuals where they persist over time (14,16,27,41). Viral particles have been purified from feces (17, 34) and, in addition, are excreted in saliva, breast milk, and bile juice (9,38,47,49). Transplacental transmission from mother to child has been controversial, but postnatal transmission has been confirmed repeatedly (15,20,24,30,33,37,48,51,52,57 (39,44). Peripheral blood mononuclear cells act as a reservoir for TTV (41), but the highest viral load is found in the granulocytes (54). Viral transcription naturally occurs in bone marrow cells and not in peripheral blood mononuclear cells (40), although transcription in vitro has been achieved by DNA transfection into stimulated peripheral blood monocytes (29) and in a monkey cell line (19).A large number of full-length or near full-length genomes of TTV has been isolated from humans and primates. They have also been identified in farm animals (23), although the genomes of recent isolates from pigs, dogs, and cats proved to be considerably smaller in size than the TTV found in humans and primates (43). The highly conserved noncoding region constitutes about one-third of the genome. The coding region consists of a large open reading frame (ORF), ORF1, coding for the viral capsid protein as well as the smaller ORF2, ORF3, and ORF4. Additional mRNAs result from splicing events (19,40). Many different genotypes have been isolated, and an extremely wide range of DNA sequence divergence has been demonstrated (45). The steadily increasing number of new genotypes and the high sequence variability point to the need for a uniform and defined cla...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

Jelčić¹,

Hotz‐Wagenblatt

Hunziker³

et al. 2004

J Virol

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“…Here, patients carrying genotype 1 or non-genotype 1 TTV or having different pretreatment TTV loads showed no differences in their ability to clear TTV in response to IFN, but further studies involving larger series of patients will be needed to draw conclusions on this matter. Being targeted to a highly conserved domain of the viral UTR, the real-time PCR we used to measure TTV loads detects a wide range of diverse TTV genomes, some of which have recently been proposed to represent distinct viral species (16,32). Thus, it is most likely that among the large variety of viral genomes currently labeled as TTV, there are definite subtypes or species with different IFN sensitivities.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Persistent TT Virus Infection, as Determined in Patients Treated with Alpha Interferon for Concomitant Hepatitis C Virus Infection

Maggi¹,

Pistello²,

Vatteroni³

et al. 2001

J Virol

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TT virus (TTV) is a recently identified widespread DNA virus of humans that produces persistent viremia in the absence of overt clinical manifestations. In an attempt to shed light on the dynamics of chronic infection, we measured the levels of TTV in the plasma of 25 persistently infected patients during the first 3 months of alpha interferon (IFN-␣) treatment for concomitant hepatitis C virus (HCV) infection. The first significant decline of TTV loads was observed at day 3 versus day 1 for HCV. Subsequently, the loads of TTV became progressively lower in most patients, but some initial responders relapsed before the end of the follow-up, suggesting that at least in some subjects the effects of IFN on TTV can be very short-lived. No correlation between the responses of TTV and HCV to therapy was found. Fitting the viremia data obtained during the first week of treatment into previously developed mathematical models showed that TTV sustains very active chronic infections, with over 90% of the virions in plasma cleared and replenished daily and a minimum of approximately 3.8 ؋ 10 10 virions generated per day. Low levels of TTV were occasionally detected in the peripheral blood mononuclear cells of patients who had cleared plasma viremia, thus corroborating previous results showing that these cells may support TTV replication and/or persistence.

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“…However, several cases of acute hepatitis E have been reported in persons with no recent history of travel outside the United States 23,24 and HEV infection should be considered in patients with non-ABC hepatitis. Additional candidate hepatitis viruses that have been isolated from patients with posttransfusion hepatitis include hepatitis G virus (also called GB virus C), TTV, and SENV 25,26,27,28 ; however, none of these viruses has been demonstrated to be a cause of acute or chronic hepatitis 27,29 .…”

Section: Non-abc Hepatitismentioning

confidence: 99%

Selected Infectious Diseases

Elson¹

2017

Obstetric Care

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Genomic and Molecular Evolutionary Analysis of a Newly Identified Infectious Agent (SEN Virus) and Its Relationship to the TT Virus Family

Cited by 159 publications

References 32 publications

Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

Dynamics of Persistent TT Virus Infection, as Determined in Patients Treated with Alpha Interferon for Concomitant Hepatitis C Virus Infection

Selected Infectious Diseases

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