Search Results (10)

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. Full article

The spatial distribution of Dendroctonus frontalis Zimmermann, 1868, and Dendroctonus mexicanus Hopkins, 1905, was determined from 2020 to 2021 in the Tixtlancingo ejido. The information came from two surveys because, despite the abundant forested areas in this geographical area of the state of Guerrero, Mexico, economic resources for pest biomonitoring are limited. However, it was possible to identify the presence of 76 outbreaks affecting 1117.697 hectares and 95,078 trees, totaling 14,223.8 ${\mathrm{m}}^3$ of standing timber volume. In 2020, 28 outbreaks were reported, with the eastern spatial distribution showing the most damage from bark beetles, particularly in outbreaks 7 and 14 of the surveyed area. The most affected conifers were Pinus maximinoi H. E. Moore (44.71%), Pinus oocarpa Schiede ex Schltdl. (39.93%), and Pinus pseudostrobus Lindl. (15.36%). The affected timber volume was observed in diameter categories of 30 cm for the three pine species, with infestation of 90,549 trees (13,497.6 ${\mathrm{m}}^3$ t.t.v. (total tree volume)) across 1057.64 hectares. In 2021, 48 outbreaks were recorded, with the northeastern and southern parts of the surveyed area showing the most damage from the bark beetle. The trees most affected by the bark beetle were P. oocarpa (59.17%), P. maximinoi (33.94%), and P. pseudostrobus (6.89%). It was observed that the affected volume occurred in trees with diameter categories of 50 cm for the three pine species, affecting 4529 trees (726.214 ${\mathrm{m}}^3$ t.t.v.) distributed over 60.06 hectares. The contribution of this work lies in establishing a baseline for monitoring damage caused by this beetle, which affects forest resources and diminishes the possibility of maintaining carbon capture areas in the medium and long term, thus impacting the Sustainable Development Goals (SDGs) of the 2030 agenda, specifically Goals 11, 13, and 15. Full article

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. Full article

The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC. Full article

A next-generation sequencing (NGS) study identified a very high viral load of Torquetenovirus (TTV) in KD patients. We aimed to evaluate the feasibility of a newly developed quantitative species-specific TTV-PCR (ssTTV-PCR) method to identify the etiology of KD. We applied ssTTV-PCR to samples collected from 11 KD patients and 22 matched control subjects who participated in our previous prospective study. We used the NGS dataset from the previous study to validate ssTTV-PCR. The TTV loads in whole blood and nasopharyngeal aspirates correlated highly (Spearman’s R = 0.8931, p < 0.0001, n = 33), supporting the validity of ssTTV-PCR. The ssTTV-PCR and NGS results were largely consistent. However, inconsistencies occurred when ssTTV-PCR was more sensitive than NGS, when the PCR primer sequences mismatched the viral sequences in the participants, and when the NGS quality score was low. Interpretation of NGS requires complex procedures. ssTTV-PCR is more sensitive than NGS but may fail to detect a fast-evolving TTV species. It would be prudent to update primer sets using NGS data. With this precaution, ssTTV-PCR can be used reliably in a future large-scale etiological study for KD. Full article

Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients’ plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26–36%). TTV (median 3.29 × 10⁵ copies/mL) and HPgV-1 (median 1.18 × 10⁶ copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes. Full article

Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related. Full article

Torque teno virus (TTV) is considered to be an ubiquitous member of the commensal human blood virome commonly reported in mixed genotype co-infections. This study investigates the genomic diversity of TTV in blood samples from 816 febrile Tanzanian children. Metagenomic next-generation sequencing was used to screen for TTV in individual blood samples from a cohort of 816 febrile Tanzanian paediatric outpatients. For positive samples, the number of TTV species and genotypes present were evaluated. We investigate the linear relationship between individual TTV diversity and the patient age by linear regression. TTV was detected in 97.2% of sera. ORF1 analysis revealed the presence of 149 genotypes from 38 species, suggesting the presence of 13 new species. These genotypes were mostly present as co-infections with a median of 11 genotypes/subject (range: 1–71). In terms of species, we found a median of nine species/subject (range: 1–29). We further show a significant association between the diversity of co-detected TTV and the age of the subjects (p value < 0.0001). This study shows that significant TTV genomic diversity is acquired by the age of five and that this diversity tends to increase with age, which indicates a repetitive TTV acquisition during the first months/years of life. Full article

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. Full article

A two-temperature CFD (computational fluid dynamics) solver is a prerequisite to any spacecraft re-entry numerical study that aims at producing results with a satisfactory level of accuracy within realistic timescales. In this respect, a new two-temperature CFD solver, hy2Foam, has been developed within the framework of the open-source CFD platform OpenFOAM for the prediction of hypersonic reacting flows. This solver makes the distinct juncture between the trans-rotational and multiple vibrational-electronic temperatures. hy2Foam has the capability to model vibrational-translational and vibrational-vibrational energy exchanges in an eleven-species air mixture. It makes use of either the Park TTv model or the coupled vibration-dissociation-vibration (CVDV) model to handle chemistry-vibration coupling and it can simulate flows with or without electronic energy. Verification of the code for various zero-dimensional adiabatic heat baths of progressive complexity has been carried out. hy2Foam has been shown to produce results in good agreement with those given by the CFD code LeMANS (The Michigan Aerothermodynamic Navier-Stokes solver) and previously published data. A comparison is also performed with the open-source DSMC (direct simulation Monte Carlo) code dsmcFoam. It has been demonstrated that the use of the CVDV model and rates derived from Quantum-Kinetic theory promote a satisfactory consistency between the CFD and DSMC chemistry modules. Full article