AIM： To investigate the prevalence and genotype distribution of Torque teno virus （TTV） in patients with different liver diseases and chronic renal failure treated at a referral hospital in North India. METHODS： W...AIM： To investigate the prevalence and genotype distribution of Torque teno virus （TTV） in patients with different liver diseases and chronic renal failure treated at a referral hospital in North India. METHODS： Whereas prevalence of TFV was based on amplification of conserved region of ORF2 of TTV genome, the genotyping of TFV was carried out using restriction fragment length polymorphism （RFLP） procedure on the N22 region of ORFI. RESULTS： TTV-DNA was detected in 137 of 513 （26.7%） patients with liver diseases and 38 of 65 （58.5%） patients with chronic renal failure. Trv was also detected in 2/7% of healthy controls. The sequence analysis of the PCR product from 10 randomly selected cases failed to show a significant sequence divergence when compared with that of the TRM1 isolate of TTV genotype 1. The results of genotyping in 55 randomly selected patients showed the presence of genotype 1 （G1） in 53 （96.4%） and genotype 2 （G2） in 2 cases （3.6%）, respectively. Other genotypes were not identified in this patient subgroup, suggesting that G1 is predominant in this area. The results of genotyping by RFLP were also supported by phylogenetic tree analysis, where G1 was found to be the major genotype. CONCLUSION： These results indicate that TTV is moderately present in Indian patients, with G1 to be the major genotype in North India. The pathogenicity and etiological role of TTV in different diseases is still a question mark and warrant further studies.展开更多
Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased seque...Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.展开更多
The review presents the data accumulated for more than 20 years of research of torque teno virus(TTV).Its molecular genetic structure,immunobiology,epidemiology,diagnostic methods,possible replication sites,and pathog...The review presents the data accumulated for more than 20 years of research of torque teno virus(TTV).Its molecular genetic structure,immunobiology,epidemiology,diagnostic methods,possible replication sites,and pathogenicity factors are described.TTV is a virus that is frequently detectable in patients with different viral hepatitides,in cases of hepatitis without an obvious viral agent,as well as in a healthy population.There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection.There are sufficient histological signs of liver damage,which confirm that the virus can undergo a replicative cycle in hepatocytes.Along with this,cytological hybridization in TTV-infected cells has shown no substantial cytopathic(cell-damaging)effects that are characteristic of pathogenic hepatotropic viruses.Studying TTV has led to the evolution of views on its role in the development of human pathology.The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses,including the viruses of the known types of hepatitides.The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a nonpathogenic virus.It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status.The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses.Fortunately,the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties.The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.展开更多
Torque teno virus(TTV) is a nonenveloped virus containing a single-stranded,circular DNA genome of approximately 3.8kb.We completely synthesized the 3 808 nucleotides of the TTV(SANBAN isolate) genome,which contains a...Torque teno virus(TTV) is a nonenveloped virus containing a single-stranded,circular DNA genome of approximately 3.8kb.We completely synthesized the 3 808 nucleotides of the TTV(SANBAN isolate) genome,which contains a hairpin structure and a GC-rich region.More than 100 overlapping oligonucleotides were chemically synthesized and assembled by polymerase chain assembly reaction(PCA),and the synthesis was completed with splicing by overlap extension(SOEing).This study establishes the methodological basis of the chemical synthesis of a viral genome for use as a live attenuated vaccine or gene therapy vector.展开更多
Carotenoids are secondary metabolite responsible for colored pigments in plants and microbes(Li et al.,2022).They are a class of C40 tetraterpenoids consisting of eight isoprenoid units,and can be classified into caro...Carotenoids are secondary metabolite responsible for colored pigments in plants and microbes(Li et al.,2022).They are a class of C40 tetraterpenoids consisting of eight isoprenoid units,and can be classified into carotenes and xanthophylls on the basis of their functional groups(Saini et al.,2015).Carotenes can be lin‐ear(phytoene,phytofluene,andζ-carotene)or branched(β-carotene andα-carotene).Xanthophylls compriseβ,β-xanthophylls(β-cryptoxanthin,zeaxanthin,violaxanthins,and neoxanthin)andβ,ε-xanthophylls(α-cryptoxanthin,α-carotene,and lutein).展开更多
Numerical simulation methods for unsteady vortex field of helicopter rotor with high resolution and low dissipation TENO8-AA primitive variables reconstruction schemes are established based on moving-embedded grid and...Numerical simulation methods for unsteady vortex field of helicopter rotor with high resolution and low dissipation TENO8-AA primitive variables reconstruction schemes are established based on moving-embedded grid and Navier-Stokes equations.Firstly,the Targeted Essentially Non-Oscillatory(TENO)scheme are developed by employing ENO-like candidate stencil selection strategy,and the candidate stencil is adopted with optimal weight in smooth region while it is discarded completely in discontinuous region,which reduces the dissipation and dispersion errors and approaches better spectral properties.Then,the aerodynamic characteristics of Helishape-7A model rotor in Blade Vortex Interaction(BVI)state and the flowfield of Lynx rotor in hover are simulated,which validates that the blade tip vortex trajectory with larger wake age and more details of vortex can be captured by TENO8-AA scheme with only a quarter of grid points and half time comparing to WENO-JS scheme.Moreover,the simulation accuracy of thrust coefficient is improved by up to 36%.Finally,the analyses for BVI and aeroacoustic characteristics of Operational Loads Survey(OLS)rotor are conducted,and the different forms of interaction mechanism are explored,such as oblique and parallel interactions.The results indicate that TENO scheme not only ensures the resolution of simulation in discontinuous region,but also minimizes the numerical dissipation in smooth region dominated by blade tip vortex.Therefore,the acoustic pressure peak prediction error of rotor in BVI state is significantly reduced to 5.6%and 0.8%at two microphone locations,respectively.展开更多
Dear Editor, Anelloviruses, which are all single-strand circular DNA viruses, have extremely heterogeneous genetic features. To date, the family Anelloviridae is divided into 1 l genus, and the most dominated species ...Dear Editor, Anelloviruses, which are all single-strand circular DNA viruses, have extremely heterogeneous genetic features. To date, the family Anelloviridae is divided into 1 l genus, and the most dominated species include torque teno virus （TTV）, torque teno mini virus （TTMV） and torque teno midi virus （TTMDV）, belonging to the genus Alphatorquevirus, Betatorquevirus and Gammatorquevirus, respectively. Most of these viruses are detected in the body fluid from the majority of human populations, although their disease associations are still elusive （de Oliveira, 2015; Focosi et al., 2016）.展开更多
[Objective] Torque teno virus （TIT） is a novel virus with negative single-strand DNA discovered in recent years, which is ubiquitous and nonpatho- genie. Torque teno sus virus （TrsuV） is widely prevalent in swine ...[Objective] Torque teno virus （TIT） is a novel virus with negative single-strand DNA discovered in recent years, which is ubiquitous and nonpatho- genie. Torque teno sus virus （TrsuV） is widely prevalent in swine populations, which is considered to be associated with some diseases such as post-weaning multi- systemic wasting syndrome （PMWS）. This study aimed to provided data for epidemiology of Tl＇suV in Guangdong Province. [Method] PCR primers were synthe- sized based on untranslated region （UTR） segment of TYsuV genome, to conduct PCR detection of 14 swine serum samples from two swine farms in Guangdong Province. A total of four PCR products of TrsuV1 and TrsuV2 from two swine farms were selected for cloning, sequencing and analysis. [ Result] Ten TrsuVl pos- itive samples （71% ） and eight TrsuV2 positive samples （57%） were obtained by PCR, including five double-positive samples （36%）. Sequence analysis of PCR products and reference strains showed that the UTR segments of samples GDTI-1 and GDT1-2 were both 305 bp, sharing 90.2% -95.1% similarity with Tl＇suVl reference strain, and the UTR segments of samples GDT2-1 and GDT2-2 were respectively 259 bp and 248 bp, sharing 67.3% - 100% similarity with TrsuV2 refer- ence strain. [ Conclusion] These results conformed that there are at least two types of Tl＇suV in Guangdong Province, with relatively high detection rates in some swine farms. Despite the putative harmlessness of Tl＇suV, the public health significance of TTsuV is noticeable due to its potential pathogenicity.展开更多
Torque teno virus(TTV)has been proposed as a surrogate biomarker for immune monitoring in different patient cohorts.Historically,TTV has been associated with different liver diseases such as post-transfusion hepatitis...Torque teno virus(TTV)has been proposed as a surrogate biomarker for immune monitoring in different patient cohorts.Historically,TTV has been associated with different liver diseases such as post-transfusion hepatitis,hepatitis B,and hepatitis C,but the virus's pathogenicity is controversial.TTV is a ubiquitous DNA virus,highly prevalent and mostly indolent in the general population.Thus,TTV viral load is more relevant than prevalence to understand TTV infection.In the context of liver transplantation,TTV viral load is modulated by the immune,viral,and inflammatory status.After liver transplantation,the TTV viral load positively correlates with the intensity of immunosuppression(IS),and low TTV viral burden is a predictor of acute rejection episodes,making it an attractive marker for the efficacy of IS.However,the TTV role as a single or a panel biomarker needs to be evaluated in further independent prospective trails.展开更多
Objective:To perform whole-genome sequencing and phylogenetic analysis of the local endemic strain of Rodent Torque teno virus (RoTTV), RoTTV3-HMU1, found in Rattus norvegicus, Haikou City, Hainan Province, and establ...Objective:To perform whole-genome sequencing and phylogenetic analysis of the local endemic strain of Rodent Torque teno virus (RoTTV), RoTTV3-HMU1, found in Rattus norvegicus, Haikou City, Hainan Province, and establish a SYBR Green I based real-time PCR detection assay for RoTTV3.Methods: Based on the high-throughput genome sequencing analysis, specific primers were designed and the whole genome sequence was amplified by PCR and Sanger sequencing. Specific detection primers were designed based on the conserved sequences of RoTTV3. The recombinant plasmid contained the whole genome of RoTTV3-HMU1 was constructed as a standard control. The experimental conditions were optimized and the real-time PCR detection assay of RoTTV3 was established.Results: The genomic sequence of RoTTV carried by Rattus norvegicus in Haikou City was successfully sequenced. Phylogenetic analysis indicated that the virus belongs to the RoTTV3 genotype. In this experiment, the real-time PCR detection method of RoTTV3 was established. The standard curve generated had a wide dynamic range from 1×(102-108) copies/μL, with a linear correlation (R2=1.000). The melting curve analysis using SYBR Green showed only one specific melting peak and no primer-dimmers represented. The detection limit was 100 copies/reaction.Discussion: This study was the first report of the RoTTV in Hainan Islands, and its phylogenetic analysis was of great significance to the origin and evolution of RoTTV. The RoTTV3 real-time PCR detection method established in this experiment has a high sensitivity and good specificity, which lays a technical foundation for the epidemiological investigation of RoTTV3.展开更多
In this paper,a new five-point targeted essentially non-oscillatory(TENO)scheme with adaptive dissipation is proposed.With the standard TENO weighting strategy,the cut-off parameter C_(T) determines the nonlinear nume...In this paper,a new five-point targeted essentially non-oscillatory(TENO)scheme with adaptive dissipation is proposed.With the standard TENO weighting strategy,the cut-off parameter C_(T) determines the nonlinear numerical dissipation of the resultant TENO scheme.Moreover,according to the dissipation-adaptive TENO5-A scheme,the choice of the cut-off parameter C_(T) highly depends on the effective scale sensor.However,the scale sensor in TENO5-A can only roughly detect the discontinuity locations instead of evaluating the local flow wavenumber as desired.In this work,a new five-point scale sensor,which can estimate the local flow wavenumber accurately,is proposed to further improve the performance of TENO5-A.In combination with a hyperbolic tangent function,the new scale sensor is deployed to the TENO5-A framework for adapting the cut-off parameter C_(T),i.e.,the local nonlinear dissipation,according to the local flow wavenumber.Overall,sufficient numerical dissipation is generated to capture discontinuities,whereas a minimum amount of dissipation is delivered for better resolving the smooth flows.A set of benchmark cases is simulated to demonstrate the performance of the new TENO5-A scheme.展开更多
While the recently proposed TENO(targeted essentially non-oscillatory)schemes[Fu et al.,Journal of Computational Physics 305(2016):333-359]exhibit better performance than the classical WENO(weighted essentially non-os...While the recently proposed TENO(targeted essentially non-oscillatory)schemes[Fu et al.,Journal of Computational Physics 305(2016):333-359]exhibit better performance than the classical WENO(weighted essentially non-oscillatory)schemes with the same accuracy order,there is still a room for further improvement,e.g.,the physical discontinuities may be significantly smeared by the excessive numerical dissipation due to the enforcement of the ENO property after a long-time advection.More recently,a new fifth-order TENO5-THINC scheme is proposed by coupling the TENO5 scheme with a non-polynomial THINC(tangent of hyperbola for interface capturing)scheme based on a parameter-free discontinuity indicator.The novelty originates from the fact that the new strategy locates the discontinuities accurately and deploys the jump-like THINC reconstruction scheme for resolving the discontinuities with a sub-cell resolution,instead of enforcing the ENO property.The new scheme successfully leverages the excellent wave-resolution property of standard TENO schemes for smooth and under-resolved continuous scales and the discontinuity-resolving capability of THINC for reconstructing genuine discontinuities.In this work,we further develop the low-dissipation discontinuity-resolving very-high-order TENO-THINC reconstruction schemes for hyperbolic conservation laws by proposing tailored coupling strategies.Without loss of generality,the six-and eight-point TENO-THINC schemes are developed,and the explicit formulas are given as well as the built-in parameters.Based on a set of critical benchmark simulations,the newly proposed schemes show S.Takagi,H.Wakimura,L.Fu and F.Xiao/Commun.Comput.Phys.,34(2023),pp.1043-1078 significantly lower numerical dissipation when compared to the counterpart TENO schemes without sacrificing numerical robustness.The presented numerical results represent the state-of-the-art in the literature and can serve as references for future algorithm development.展开更多
基金Indian Council of Medical Research (ICMR),New Delhi-110049 for financial grant
文摘AIM： To investigate the prevalence and genotype distribution of Torque teno virus （TTV） in patients with different liver diseases and chronic renal failure treated at a referral hospital in North India. METHODS： Whereas prevalence of TFV was based on amplification of conserved region of ORF2 of TTV genome, the genotyping of TFV was carried out using restriction fragment length polymorphism （RFLP） procedure on the N22 region of ORFI. RESULTS： TTV-DNA was detected in 137 of 513 （26.7%） patients with liver diseases and 38 of 65 （58.5%） patients with chronic renal failure. Trv was also detected in 2/7% of healthy controls. The sequence analysis of the PCR product from 10 randomly selected cases failed to show a significant sequence divergence when compared with that of the TRM1 isolate of TTV genotype 1. The results of genotyping in 55 randomly selected patients showed the presence of genotype 1 （G1） in 53 （96.4%） and genotype 2 （G2） in 2 cases （3.6%）, respectively. Other genotypes were not identified in this patient subgroup, suggesting that G1 is predominant in this area. The results of genotyping by RFLP were also supported by phylogenetic tree analysis, where G1 was found to be the major genotype. CONCLUSION： These results indicate that TTV is moderately present in Indian patients, with G1 to be the major genotype in North India. The pathogenicity and etiological role of TTV in different diseases is still a question mark and warrant further studies.
基金supported by a grant from the National Natural Science Foundation of China (No. 81072350)the National Hi-Tech Research and Development (863) Program of China (No. 2012AA022-003)+2 种基金the China Mega-Project on Major Drug Development (No. 2011ZX09401-023)the China Mega-Project on Infectious Disease Prevention (No. 2013ZX10004-605, No. 2013ZX10004-607, No. 2013ZX10004-217, and No. 2011ZX10004-001) the State Key Laboratory of Pathogen and BioSecurity Program (No. SKLPBS1113)
文摘Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.
文摘The review presents the data accumulated for more than 20 years of research of torque teno virus(TTV).Its molecular genetic structure,immunobiology,epidemiology,diagnostic methods,possible replication sites,and pathogenicity factors are described.TTV is a virus that is frequently detectable in patients with different viral hepatitides,in cases of hepatitis without an obvious viral agent,as well as in a healthy population.There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection.There are sufficient histological signs of liver damage,which confirm that the virus can undergo a replicative cycle in hepatocytes.Along with this,cytological hybridization in TTV-infected cells has shown no substantial cytopathic(cell-damaging)effects that are characteristic of pathogenic hepatotropic viruses.Studying TTV has led to the evolution of views on its role in the development of human pathology.The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses,including the viruses of the known types of hepatitides.The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a nonpathogenic virus.It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status.The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses.Fortunately,the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties.The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.
基金The Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-Z-3)
文摘Torque teno virus(TTV) is a nonenveloped virus containing a single-stranded,circular DNA genome of approximately 3.8kb.We completely synthesized the 3 808 nucleotides of the TTV(SANBAN isolate) genome,which contains a hairpin structure and a GC-rich region.More than 100 overlapping oligonucleotides were chemically synthesized and assembled by polymerase chain assembly reaction(PCA),and the synthesis was completed with splicing by overlap extension(SOEing).This study establishes the methodological basis of the chemical synthesis of a viral genome for use as a live attenuated vaccine or gene therapy vector.
基金This work was supported by the National Key Research and Development Program of China(No.2021YFD1600802-02)。
文摘Carotenoids are secondary metabolite responsible for colored pigments in plants and microbes(Li et al.,2022).They are a class of C40 tetraterpenoids consisting of eight isoprenoid units,and can be classified into carotenes and xanthophylls on the basis of their functional groups(Saini et al.,2015).Carotenes can be lin‐ear(phytoene,phytofluene,andζ-carotene)or branched(β-carotene andα-carotene).Xanthophylls compriseβ,β-xanthophylls(β-cryptoxanthin,zeaxanthin,violaxanthins,and neoxanthin)andβ,ε-xanthophylls(α-cryptoxanthin,α-carotene,and lutein).
基金the National Natural Science Foundation of China(Nos.12032012,12072156)the National Key Laboratory Foundation of China(No.61422202103)the Priority Academic Program Development of Jiangsu Higher Education Institutions,China(PAPD).
文摘Numerical simulation methods for unsteady vortex field of helicopter rotor with high resolution and low dissipation TENO8-AA primitive variables reconstruction schemes are established based on moving-embedded grid and Navier-Stokes equations.Firstly,the Targeted Essentially Non-Oscillatory(TENO)scheme are developed by employing ENO-like candidate stencil selection strategy,and the candidate stencil is adopted with optimal weight in smooth region while it is discarded completely in discontinuous region,which reduces the dissipation and dispersion errors and approaches better spectral properties.Then,the aerodynamic characteristics of Helishape-7A model rotor in Blade Vortex Interaction(BVI)state and the flowfield of Lynx rotor in hover are simulated,which validates that the blade tip vortex trajectory with larger wake age and more details of vortex can be captured by TENO8-AA scheme with only a quarter of grid points and half time comparing to WENO-JS scheme.Moreover,the simulation accuracy of thrust coefficient is improved by up to 36%.Finally,the analyses for BVI and aeroacoustic characteristics of Operational Loads Survey(OLS)rotor are conducted,and the different forms of interaction mechanism are explored,such as oblique and parallel interactions.The results indicate that TENO scheme not only ensures the resolution of simulation in discontinuous region,but also minimizes the numerical dissipation in smooth region dominated by blade tip vortex.Therefore,the acoustic pressure peak prediction error of rotor in BVI state is significantly reduced to 5.6%and 0.8%at two microphone locations,respectively.
文摘Dear Editor, Anelloviruses, which are all single-strand circular DNA viruses, have extremely heterogeneous genetic features. To date, the family Anelloviridae is divided into 1 l genus, and the most dominated species include torque teno virus （TTV）, torque teno mini virus （TTMV） and torque teno midi virus （TTMDV）, belonging to the genus Alphatorquevirus, Betatorquevirus and Gammatorquevirus, respectively. Most of these viruses are detected in the body fluid from the majority of human populations, although their disease associations are still elusive （de Oliveira, 2015; Focosi et al., 2016）.
基金Supported by Funding Project of Guangdong Science and Technology Department(No.2011B010500023)Funding Project of Guangzhou Science and Information Technology Department(No.12A64071507)
文摘[Objective] Torque teno virus （TIT） is a novel virus with negative single-strand DNA discovered in recent years, which is ubiquitous and nonpatho- genie. Torque teno sus virus （TrsuV） is widely prevalent in swine populations, which is considered to be associated with some diseases such as post-weaning multi- systemic wasting syndrome （PMWS）. This study aimed to provided data for epidemiology of Tl＇suV in Guangdong Province. [Method] PCR primers were synthe- sized based on untranslated region （UTR） segment of TYsuV genome, to conduct PCR detection of 14 swine serum samples from two swine farms in Guangdong Province. A total of four PCR products of TrsuV1 and TrsuV2 from two swine farms were selected for cloning, sequencing and analysis. [ Result] Ten TrsuVl pos- itive samples （71% ） and eight TrsuV2 positive samples （57%） were obtained by PCR, including five double-positive samples （36%）. Sequence analysis of PCR products and reference strains showed that the UTR segments of samples GDTI-1 and GDT1-2 were both 305 bp, sharing 90.2% -95.1% similarity with Tl＇suVl reference strain, and the UTR segments of samples GDT2-1 and GDT2-2 were respectively 259 bp and 248 bp, sharing 67.3% - 100% similarity with TrsuV2 refer- ence strain. [ Conclusion] These results conformed that there are at least two types of Tl＇suV in Guangdong Province, with relatively high detection rates in some swine farms. Despite the putative harmlessness of Tl＇suV, the public health significance of TTsuV is noticeable due to its potential pathogenicity.
文摘Torque teno virus(TTV)has been proposed as a surrogate biomarker for immune monitoring in different patient cohorts.Historically,TTV has been associated with different liver diseases such as post-transfusion hepatitis,hepatitis B,and hepatitis C,but the virus's pathogenicity is controversial.TTV is a ubiquitous DNA virus,highly prevalent and mostly indolent in the general population.Thus,TTV viral load is more relevant than prevalence to understand TTV infection.In the context of liver transplantation,TTV viral load is modulated by the immune,viral,and inflammatory status.After liver transplantation,the TTV viral load positively correlates with the intensity of immunosuppression(IS),and low TTV viral burden is a predictor of acute rejection episodes,making it an attractive marker for the efficacy of IS.However,the TTV role as a single or a panel biomarker needs to be evaluated in further independent prospective trails.
基金National natural science foundation of China,No.81860367,31460017,81672072Key Research and Development Program of Hainan Province,No.ZDYF2017091+1 种基金Special Project for Scientific Research of Institutions of Higher Learning in Hainan Province,No.Hnky2017ZD-16,Hnkyzx2014-08Open Fund Project of State key Laboratory of Virology in 2018.Project,No.2018IOV002.
文摘Objective:To perform whole-genome sequencing and phylogenetic analysis of the local endemic strain of Rodent Torque teno virus (RoTTV), RoTTV3-HMU1, found in Rattus norvegicus, Haikou City, Hainan Province, and establish a SYBR Green I based real-time PCR detection assay for RoTTV3.Methods: Based on the high-throughput genome sequencing analysis, specific primers were designed and the whole genome sequence was amplified by PCR and Sanger sequencing. Specific detection primers were designed based on the conserved sequences of RoTTV3. The recombinant plasmid contained the whole genome of RoTTV3-HMU1 was constructed as a standard control. The experimental conditions were optimized and the real-time PCR detection assay of RoTTV3 was established.Results: The genomic sequence of RoTTV carried by Rattus norvegicus in Haikou City was successfully sequenced. Phylogenetic analysis indicated that the virus belongs to the RoTTV3 genotype. In this experiment, the real-time PCR detection method of RoTTV3 was established. The standard curve generated had a wide dynamic range from 1×(102-108) copies/μL, with a linear correlation (R2=1.000). The melting curve analysis using SYBR Green showed only one specific melting peak and no primer-dimmers represented. The detection limit was 100 copies/reaction.Discussion: This study was the first report of the RoTTV in Hainan Islands, and its phylogenetic analysis was of great significance to the origin and evolution of RoTTV. The RoTTV3 real-time PCR detection method established in this experiment has a high sensitivity and good specificity, which lays a technical foundation for the epidemiological investigation of RoTTV3.
基金the fund from National Key R&D Program of China(No.2022YFA1004500)the fund from Research Grants Council(RGC)of the Government of Hong Kong Special Administrative Region(HKSAR)with RGC/ECS Project(No.26200222)+2 种基金the fund from Guangdong Basic and Applied Basic Research Foundation(No.2022A1515011779)the fund from the Project of Hetao Shenzhen-Hong Kong Science and Technology Innovation Cooperation Zone(No.HZQB-KCZYB-2020083)the fund from Key Laboratory of Computational Aerodynamics,AVIC Aerodynamics Research Institute.
文摘In this paper,a new five-point targeted essentially non-oscillatory(TENO)scheme with adaptive dissipation is proposed.With the standard TENO weighting strategy,the cut-off parameter C_(T) determines the nonlinear numerical dissipation of the resultant TENO scheme.Moreover,according to the dissipation-adaptive TENO5-A scheme,the choice of the cut-off parameter C_(T) highly depends on the effective scale sensor.However,the scale sensor in TENO5-A can only roughly detect the discontinuity locations instead of evaluating the local flow wavenumber as desired.In this work,a new five-point scale sensor,which can estimate the local flow wavenumber accurately,is proposed to further improve the performance of TENO5-A.In combination with a hyperbolic tangent function,the new scale sensor is deployed to the TENO5-A framework for adapting the cut-off parameter C_(T),i.e.,the local nonlinear dissipation,according to the local flow wavenumber.Overall,sufficient numerical dissipation is generated to capture discontinuities,whereas a minimum amount of dissipation is delivered for better resolving the smooth flows.A set of benchmark cases is simulated to demonstrate the performance of the new TENO5-A scheme.
基金supported by National Key R&D Program of China(No.2022YFA1004500)Lin Fu acknowledges the fund from the Research Grants Council(RGC)of the Government of Hong Kong Special Administrative Region(HKSAR)with RGC/ECS Project(No.26200222)+3 种基金the fund from Guangdong Basic and Applied Basic Research Foundation(No.2022A1515011779)the fund from Key Laboratory of Computational Aerodynamics,AVIC Aerodynamics Research Institute,and the fund from the Project of Hetao Shenzhen-Hong Kong Science and Technology Innovation Cooperation Zone(No.HZQB-KCZYB-2020083)Feng Xiao acknowledges the fund from JSPS(Japan Society for the Promotion of Science)under Grant Nos.18H01366 and 19H05613Hiro Wakimura acknowledges the fund from JSPS under Grant No.22KJ1331.
文摘While the recently proposed TENO(targeted essentially non-oscillatory)schemes[Fu et al.,Journal of Computational Physics 305(2016):333-359]exhibit better performance than the classical WENO(weighted essentially non-oscillatory)schemes with the same accuracy order,there is still a room for further improvement,e.g.,the physical discontinuities may be significantly smeared by the excessive numerical dissipation due to the enforcement of the ENO property after a long-time advection.More recently,a new fifth-order TENO5-THINC scheme is proposed by coupling the TENO5 scheme with a non-polynomial THINC(tangent of hyperbola for interface capturing)scheme based on a parameter-free discontinuity indicator.The novelty originates from the fact that the new strategy locates the discontinuities accurately and deploys the jump-like THINC reconstruction scheme for resolving the discontinuities with a sub-cell resolution,instead of enforcing the ENO property.The new scheme successfully leverages the excellent wave-resolution property of standard TENO schemes for smooth and under-resolved continuous scales and the discontinuity-resolving capability of THINC for reconstructing genuine discontinuities.In this work,we further develop the low-dissipation discontinuity-resolving very-high-order TENO-THINC reconstruction schemes for hyperbolic conservation laws by proposing tailored coupling strategies.Without loss of generality,the six-and eight-point TENO-THINC schemes are developed,and the explicit formulas are given as well as the built-in parameters.Based on a set of critical benchmark simulations,the newly proposed schemes show S.Takagi,H.Wakimura,L.Fu and F.Xiao/Commun.Comput.Phys.,34(2023),pp.1043-1078 significantly lower numerical dissipation when compared to the counterpart TENO schemes without sacrificing numerical robustness.The presented numerical results represent the state-of-the-art in the literature and can serve as references for future algorithm development.
