High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever

Detection and Genomic Characterization of Torque Teno Virus in Pneumoconiosis Patients in China

Pneumoconiosis is a common occupational disease that can worsen with accompanying infection. Torque teno virus (TTV) is a prevalent human virus with multiple genotypes that can chronically and persistently infect individuals. However, the prevalence of TTV in pneumoconiosis patients is still unclear. This research aims to detect the presence and prevalence of TTV in the alveolar lavage fluid of pneumoconiosis patients in the Hunan Province of China using PCR. As a result, a 65.5% positive rate (19 out of 29) of TTV was detected. The TTV detection rate varies among different stages of silicosis and different pneumoconiosis patient ages. Nine novel TTV genomes ranging in size from 3719 to 3908 nt, named TTV HNPP1, HNPP2, HNPP3, HNPP4, HNPP5, HNPP6-1, HNPP6-2, HNPP7-1 and HNPP7-2, were identified. A genomic comparison and phylogenetic analysis indicated that these nine TTVs represent five different species with high genetic diversity which belong to the genus Alphatorquevirus. HNPP6-1 and HNPP6-2 belong to TTV3, HNPP5 belongs to TTV13, HNPP1 belongs to TTV24, HNPP4 belongs to TTV20, and the others belong to TTV19. The genomes of TTV HNPP1, HNPP6-1, and HNPP6-2 contain three putative open reading frames (ORFs) coding for proteins, ORF1, ORF2, and ORF3, while the other six TTV genomes contain two ORFs coding for proteins, ORF1 and ORF2. These results provide the first description of TTV epidemiology in pneumoconiosis patients in China. The newly identified TTV genome sequences reveal the high genetic diversity of TTV in pneumoconiosis patients and could contribute to a deeper understanding of TTV retention and infection in humans.

Nocardia farcinica brain abscess with torque teno virus co-infection: A case report

Background

Brain abscesses caused by Nocardia are rare and difficult to diagnose. Nocardia farcinica is among the most common species; however, the conventional diagnosis of N. farcinica infection consists of cerebrospinal fluid (CSF) and blood culture and Gram staining. These procedures prolong the time to diagnosis and initiating treatment.

Case presentation

A 69-year-old woman with diabetes mellitus presented with headaches and dizziness persisting for 2 weeks, which was initially diagnosed as a brain abscess. Due to the unusual presentation and rapid progression of symptoms, she underwent surgical resection of the brain abscess. No pathogens were detected in blood or CSF cultures. However, metagenomic next-generation sequencing (mNGS) identified N. farcinica and Torque teno virus in pus extracted from the abscesses. The patient received appropriate antibiotic therapy and recovered fully without any residual neurological deficits.

Conclusion

mNGS useful for prompt diagnosis and selection of antibiotic therapy for brain abscesses caused by Nocardia. Surgical intervention is necessary in some cases.

Phylogenetic analysis of torque teno virus in Romania: possible evidence of distinct geographical distribution

Torque teno virus (TTV) is highly prevalent, but little is known about its circulation in humans. Here, we investigated the geographical distribution and phylogeny of TTV in Romania. A fragment of TTV untranslated region B was sequenced in samples from volunteers across the country. Additional sequences from dialyzed patients were also included in the study. Phylogenetic analysis showed that more than 80% of Romanian sequences clustered with isolates assigned to the species Torque teno virus 1 and Torque teno virus 3 (former genogroup 1), and this analysis discriminated between isolates from the North-East and West regions. Further studies assessing the pathogenic potential of TTV isolates should employ analysis based on genomic regions with phylogenetic resolution below the species level.

The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin

Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.

Torque teno virus from Korean domestic swine farms, 2017-2018

Background

Torque teno viruses (TTVs) have been detected worldwide, from a wide range of animals. Up to date, few studies focused on the prevalence of TTVs in general and swine torque teno viruses (TTSuVs) in particular in Korean swine farms.

Objective

This study aimed to investigate the appearance of TTSuVs and TTVs in sick pigs during the 2017–2018 period.

Materials and Methods

Molecular‐based method using TTSuV1‐, TTSuV2‐ and TTV3‐specific primers was used to screen for the viruses from either sera or pooled internal organs of sick pigs. For genetic characterization, genomic sequences of TTVs were sequenced by a primer walking method. Several bioinformatic tools have been utilized to investigate the genomic organization and genetic relationship of TTVs.

Results

Two years of prevalence survey reveal that the prevalence of TTSuV2 is about twice that of TTSuV1. Furthermore, we identified TTV of genogroup 3 in swine pooled organ samples. The genome of two strains, M265_Korea_2017 and N119_Korea_2018, are 3,817 bp in size; M265_2017 has three open reading frames (ORFs); and N119_2018 strain has four ORFs. The complete genome nucleotide sequencing of the two strains shows 98.4% homology, and the phylogenetic analysis of Open reading frame (ORF)1 indicates that the strains are located close to TUPB strain subgroup C of genogroup 3.

Conclusion

Our study provided the information of TTSuVs prevalence in swine farms in Korea and highlighted the presence of TTV genogroup 3 strains in pigs.

Torque teno virus microRNA detection in cerebrospinal fluids of patients with neurological pathologies

BACKGROUND

Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host.

OBJECTIVE

To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases.

STUDY DESIGN

Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses.

RESULTS

TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region.

CONCLUSIONS

These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.

The Molecular Epidemiology and Phylogeny of Torque Teno Virus (TTV) in Jordan

Torque teno virus (TTV) is the most common component of the human blood virobiota. Little is known, however, about the prevalence of TTV in humans and the most common farm domesticates in Jordan, or the history and modality of TTV transmission across species lines. We therefore tested sera from 396 Jordanians and 171 farm animals for the presence of TTV DNA using nested 5'-UTR-PCR. We then performed phylogenetic, ordination and evolutionary diversity analyses on detected DNA sequences. We detected a very high prevalence of TTV in Jordanians (~96%); much higher than in farm animal domesticates (~29% pooled over species). TTV prevalence in the human participants is not associated with geography, demography or physical attributes. Phylogenetic, ordination and evolutionary diversity analyses indicated that TTV is transmitted readily between humans across the geography of the country and between various species of animal domesticates. However, the majority of animal TTV isolates seem to derive from a single human-to-animal transmission event in the past, and current human-animal transmission in either direction is relatively rare. In conclusion, animal TTV in Jordan is historically derived from human variants; however, ongoing human-animal TTV exchange is minimal and zoonotic infection seems to be of limited importance.

The Role of Emerging and Neglected Viruses in the Etiology of Hepatitis

PURPOSE OF REVIEW

In this review, we present the overview of emerging and neglected viruses associated with liver involvement.

RECENT FINDINGS

Hepatitis E virus (HEV) emerged in the last two decades, causing hepatitis in many parts of the world. Moreover, liver involvement was also described in some emerging arboviral infections. Many reports showed dengue-associated liver injury; however, chikungunya, West Nile, tick-borne encephalitis, and Zika virus are rarely associated with clinically manifest liver disease. In addition, some neglected highly prevalent viruses such as adenoviruses and parvovirus B19 are capable of causing hepatitis in specific population groups. Anelloviruses (torque teno virus/torque teno mini virus/torque teno midi virus, SEN virus), human bocavirus, pegiviruses, and lymphocytic choriomeningitis virus have shown a little potential for causing hepatitis, but their role in the etiology of liver disease remains to be determined. In addition to the well-known hepatotropic viruses, many emerging and neglected viruses have been associated with liver diseases. The number of emerging zoonotic viruses has been increasingly recognized. While zoonotic potential of HEV is well documented, the recent identification of new hepatitis-related animal viruses such as HEV strains from rabbits and camels, non-primate hepaciviruses in domestic dogs and horses, as well as equine and porcine pegivirus highlights the possible zoonotic transmission in the context of "One Health." However, zoonotic potential and hepatotropism of animal hepatitis viruses remain to be determined.

Identification of a novel torque teno mini virus in cerebrospinal fluid from a child with encephalitis

Anelloviruses are single-strand circular DNA viruses and ubiquitous within the human population. Although there is no direct evidence, many studies have suggested the anelloviruses may be associated with a variety of diseases. In this study, a novel torque teno mini virus (TTMV) was detected in a child with unexplained encephalitis. The detected virus had a circular genome of 2943 nt in length and 3 open reading frames. It shared 45.4% - 35.9% nucleotide identities with known TTMV species and < 35% with the other species of anellovirus, which suggested it might belong to a new species within the genus Betatorquevirus. Phylogenetic analysis based on the amino acid sequences of ORF1 showed that this virus represented a distinct branch within the diversity of anellovirus. Whether this novel anellovirus strain is associated with encephalitis requires further study.

Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology

Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients with hepatitis without identified aetiological agents were evaluated. Additionally, one pool of patients with hepatitis E (HEV) and pools of healthy volunteers were included as controls. A high diversity of anelloviruses, including novel sequences, was found in pools from patients with hepatitis of unknown aetiology. Moreover, viruses recently associated with gastroenteritis as sapovirus GV.2 and astrovirus VA3 were also detected only in those pools. Besides, most of the HEV genome was recovered from the HEV pool. Finally, GB virus C and human endogenous retrovirus were found in the HEV and healthy pools. Our study provides an overview of the virome in serum from hepatitis patients suggesting a potential role of these viruses not previously described in cases of hepatitis. However, further epidemiologic studies are necessary to confirm their contribution to the development of hepatitis.

Exploring the virome of diseased horses

Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.

Human anelloviruses: an update of molecular, epidemiological and clinical aspects

Human torque teno viruses (TTVs) are new, emerging infectious agents, recently assigned to the family Anelloviridae. The first representative of the genus, torque teno virus (TTV), was discovered in 1997, followed by torque teno mini virus (TTMV) in 2000, and torque teno midi virus (TTMDV) in 2007. These viruses are characterized by an extremely high prevalence, with relatively uniform distribution worldwide and a high level of genomic heterogeneity, as well as an apparent pan-tropism at the host level. Although these viruses have a very high prevalence in the general population across the globe, neither their interaction with their hosts nor their direct involvement in the etiology of specific diseases are fully understood. Since their discovery, human anelloviruses, and especially TTV, have been suggested to be associated with various diseases, such as hepatitis, respiratory diseases, cancer, hematological and autoimmune disorders, with few arguments for their direct involvement. Recent studies have started to reveal interactions between TTVs and the host's immune system, leading to new hypotheses for potential pathological mechanisms of these viruses. In this review article, we discuss the most important aspects and current status of human TTVs in order to guide future studies.