Genomic Diversity of Torque Teno Virus in Blood Samples from Febrile Paediatric Outpatients in Tanzania: A Descriptive Cohort Study

Laubscher, Florian; Hartley, Mary-Anne; Kaiser, Laurent; Cordey, Samuel

doi:10.3390/v14081612

Cited by 6 publications

(7 citation statements)

References 25 publications

(35 reference statements)

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“…Overall, there were no false positives ( Table S1 ). Furthermore, SCANellome was evaluated on 10 blood samples of which we had previously analyzed and published the genomic diversity of TTV [ 17 ]. This comparative analysis shows the robustness of SCANellome, which successfully detected all of the TTV species reported in our previous study.…”

Section: Methodsmentioning

confidence: 99%

“…It is known (and seems to be the rule) that a single individual (a child or adult) can be co-infected by a large number of different human anellovirus species and genotypes of the same genus [ 14 , 15 , 16 , 17 ]. We recently reported a significant trend toward an increase in TTV genomic diversity with age in a cohort of children under five years of age [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

Laubscher

Kaiser

Cordey

2023

Viruses

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Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

Laubscher

Kaiser

Cordey

2023

Viruses

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“…Bile [11,12] Liver [13] Cervical [2] Bone marrow [12,13] Gut [14] Nasal [15] Fetal [16] Gastric [17] Placenta [16] Cervical lymph nodes [18] Blood [19] Saliva [20] Urine [21] Fecal [22] Sweat [23] Semen [20] Plasma [24] Breast milk [5] Amniotic fluid [25] Torque teno mini virus (TTMV) Bile [12] Liver [26] Cervical [2,27] Bone marrow [12] Brain [28,29] Gingival [30] Cervical lymph nodes [18] Blood [24] Saliva [24] Torque teno midi virus (TTMDV) Cervical [31] Nasopharyngeal [32] Blood [33] Urine [32] Stool [32] Kb, and the TTMV genome is 2.7 to 2.9 Kb [1,47]. TTV has diverse tissue tropism, and the virus genome has the ability to replicate simultaneously in several different tissues and organs, such as the liver, spleen, pancreas, bone marrow, muscle, lung, kidney, peripheral blood mononuclear cells (PBMC), etc [21,48].…”

Section: Torque Teno Virus (Ttv)mentioning

confidence: 99%

“…Torque teno virus (TTV) belongs to alphatorquevirus, torque teno mini virus (TTMV) belongs to betatorquevirus and torque teno midi virus (TTMDV) belongs to gammatorquevirus. The genome of these viruses is circular single-stranded, negative-sense DNA ranging from ∼2.0 to 3.9 kilobases (kb); the capsid of these viruses has icosahedron symmetry, and their total particle diameter is about 18 to 30 nm, and their nucleocapsid does not have a lipid envelope [1][2][3][4][5][6]. Human anelloviruses (AVs) are among the most common human viruses and are considered part of the human virome.…”

Section: Introductionmentioning

confidence: 99%

The mysterious anelloviruses: investigating its role in human diseases

Sabbaghian,

Gheitasi,

Shekarchi

et al. 2024

BMC Microbiol

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Anelloviruses (AVs) that infect the human population are members of the Anelloviridae family. They are widely distributed in human populations worldwide. Torque teno virus (TTV) was the first virus of this family to be identified and is estimated to be found in the serum of 80–90% of the human population. Sometime after the identification of TTV, Torque teno mini virus (TTMV) and Torque teno midi virus (TTMDV) were also identified and classified in this family. Since identifying these viruses, have been detected in various types of biological fluids of the human body, including blood and urine, as well as vital organs such as the liver and kidney. They can be transmitted from person to person through blood transfusions, fecal-oral contact, and possibly sexual intercourse. Recent studies on these newly introduced viruses show that although they are not directly related to human disease, they may be indirectly involved in initiating or exacerbating some human population-related diseases and viral infections. Among these diseases, we can mention various types of cancers, immune system diseases, viral infections, hepatitis, and AIDS. Also, they likely use the microRNAs (miRNAs) they encode to fulfill this cooperative role. Also, in recent years, the role of proliferation and their viral load, especially TTV, has been highlighted to indicate the immune system status of immunocompromised people or people who undergo organ transplants. Here, we review the possible role of these viruses in diseases that target humans and highlight them as important viruses that require further study. This review can provide new insights to researchers.

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“…Advances in next-generation sequencing (NGS) have deepened our knowledge on the microbial world. The combination of molecular biology technics like rolling circle amplification (RCA) with NGS on different human samples (both fluid and tissues) demonstrated that anelloviruses are one of the major components of the human virome, with TTV being one of the most prevalent viruses detected [ 24 , 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

Torque Teno Virus (TTV) in Renal Transplant Recipients: Species Diversity and Variability

Reyes,

Spezia,

Jara

et al. 2024

Viruses

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Torque Teno Virus (TTV) is a nonpathogenic and ubiquitous ssDNA virus, a member of the Anelloviridae family. TTV has been postulated as a biomarker in transplant patients. This study aimed to determine the TTV species diversity and variability in renal transplant recipients and to associate species diversity with the corresponding TTV viral load. From 27 recipients, 30 plasma samples were selected. Viral load was determined using two real-time PCR assays, followed by RCA-NGS and ORF1 phylogenetic analysis. The TTV diversity was determined in all samples. Variability was determined in three patients with two sequential samples (pre- and post-transplantation). Most of the samples presented multiple TTV species, up to 15 different species were detected. In the pre-transplant samples (n = 12), the most prevalent species were TTV3 (75%) and TTV13 (75%), and the median number of species per sample was 5 (IQR: 4–7.5). TTV3 was also the most prevalent (56%) in the post-transplant samples (n = 18), and the median number of species was 2 (IQR: 1.8–5.5). No significant correlation between the number of species and viral load was found. The number and type of TTV species showed total variability over time. We report high TTV species diversity in Argentinian recipients, especially in pre-transplant period, with total intra-host variability. However, we found no significant correlation between this high diversity and TTV viral load.

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Genomic Diversity of Torque Teno Virus in Blood Samples from Febrile Paediatric Outpatients in Tanzania: A Descriptive Cohort Study

Cited by 6 publications

References 25 publications

SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

The mysterious anelloviruses: investigating its role in human diseases

Torque Teno Virus (TTV) in Renal Transplant Recipients: Species Diversity and Variability

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