A retrospective study revealing complex viral diversity and a substantial burden of HPV infection in SARS-CoV-2 positive individuals, Sierra Leone.

BACKGROUND: The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments. METHODS: We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV. RESULTS: The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections. CONCLUSIONS: The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.

An endogenous oxygen self-supplied nanoplatform with GSH-depleted and NIR-II triggered electron-hole separation for enhanced photocatalytic anti-tumor therapy.

The use of artificial enzymes and light energy in photocatalytic therapy, a developing drug-free therapeutic approach, can treat malignant tumors in vivo. However, the relatively deficient oxygen concentration in the tumor microenvironment (TME) restrains their further tumor treatment capability. Herein, a novel nanoplatform with Cu7S4@Au nanocatalyst coated by MnO2 was successfully designed. After 1064 nm light irradiation, the designed nanocatalyst can promote the separation of light generated electron-hole pairs, resulting in ROS generation and tumor cell apoptosis. The MnO2 shelled nanoplatform can function as a TME-responsive oxygen self-supplied producer to improve photocatalyst treatment and GSH depletion. In summary, the designed novel nanoplatform shows efficient inhibition of tumor growth via GSH depletion and synergistic photocatalytic therapy, which is of great significance for improving the clinical tumor treatment effect.

A Multiplex Recombinase-Aided qPCR Assay for Highly Sensitive and Rapid Detection of khe, blaKPC -2, and blaNDM -1 Genes in Klebsiella pneumoniae.

OBJECTIVE: This study aimed to establish a highly sensitive and rapid single-tube, two-stage, multiplex recombinase-aided qPCR (mRAP) assay to specifically detect the khe, blaKPC-2, and blaNDM-1 genes in Klebsiella pneumoniae. METHODS: mRAP was carried out in a qPCR instrument within 1 h. The analytical sensitivities of mRAP for khe, blaKPC-2, and blaNDM-1 genes were tested using recombinant plasmids and dilutions of reference strains. A total of 137 clinical isolates and 86 sputum samples were used to validate the clinical performance of mRAP. RESULTS: mRAP achieved the sensitivities of 10, 8, and 14 copies/reaction for khe, blaKPC-2, and blaNDM-1 genes, respectively, superior to qPCR. The Kappa value of qPCR and mRAP for detecting khe, blaKPC-2, and blaNDM-1 genes was 1, 0.855, and 1, respectively (p < 0.05). CONCLUSION: mRAP is a rapid and highly sensitive assay for potential clinical identification of khe, blaKPC-2, and blaNDM-1 genes in K. pneumoniae.

A rapid and highly sensitive multiple detection of human adenovirus type 3, type 7 and respiratory syncytial virus by recombinase-aided reverse transcription PCR.

BACKGROUND: Polymerase chain reaction (PCR) has been widely used for many pathogen detection. However, PCR technology still suffers from long detection time and insufficient sensitivity. Recombinase-aided amplification (RAA) is a powerful nucleic acid detection tool with high sensitivity and amplification efficiency, but its complex probes and inability of multiplex detection hinder the further application of this technology. METHODS: In this study, we developed and validated the multiplex reverse transcription recombinase-aided PCR (multiplex RT-RAP) assay for human adenovirus 3 (HADV3), human adenovirus 7 (HADV7), and human respiratory syncytial virus (HRSV) within 1 h with Human RNaseP protein as a reference gene to monitor the whole process. RESULTS: Using recombinant plasmids, the sensitivity of multiplex RT-RAP for the detection of HADV3, HADV7, and HRSV was 18, 3, and 18 copies per reaction, respectively. The multiplex RT-RAP showed no cross-reactivity with other respiratory viruses, demonstrating its good specificity. A total of 252 clinical specimens were tested by multiplex RT-RAP and the results were found to be consistent with those of corresponding RT-qPCR assays. After testing serial dilutions of selected positive specimens, the detection sensitivity of multiplex RT-RAP was two to eightfold higher than that of corresponding RT-qPCR. CONCLUSION: We conclude the multiplex RT-RAP is a robust, rapid, highly sensitive, and specific assay with the potential to be used in the screening of clinical samples with low viral load.

HYAL-1-induced autophagy facilitates pancreatic fistula for patients who underwent pancreaticoduodenectomy.

The main mechanism of hyaluronidase 1(HYAL-1) in the development of postoperative pancreatic fistula (POPF) after pancreatoduodenectomy (PD) was unknown. In this study, a comprehensive inventory of pre-, intra-, and postoperative clinical and biological data of two cohorts (62 pancreatic cancer [PCa] and 111 pancreatic ductal adenocarcinoma [PDAC]) which could induce POPF were retrospectively analyzed. Then, a total of 7644 genes correlated with HYAL-1 was predicted in PDAC tissues and the enriched pathway, kinase targets and biological process of those correlated genes were evaluated. Finally, a mouse pancreatic fistula (PF) model was first built and in vitro studies were performed to investigate the effects of HYAL-1 on PF progression. Our data indicated that preoperative serum HYAL-1 level, pancreatic fibrosis score, and pancreatic duct size were valuable factors for detecting POPF of Grade B and C. The serum HYAL-1 level of 2.07 mg/ml and pancreatic fibrosis score of 2.5 were proposed as the cutoff values for indicating POPF. The bioinformatic analysis and in vitro and in vivo studies demonstrated that HYAL-1 facilitates pancreatic acinar cell autophagy via the dephosphorylation of adenosine 5'-monophosphate-activated protein kinase (AMPK) and signal transducers and activators of transcription 3 (STAT3) signaling pathways, which exacerbate pancreatic secretion and inflammation. In summary, the preoperative serum HYAL-1 was a significant predictor for POPF in patients who underwent PD. Tumor-induced HYAL-1 is one of core risk in accelerating PF and then promoting pancreatic secretion and acute inflammation response through the AMPK and STAT3-induced autophagy.

Differentiation of low- and high-grade pediatric gliomas with amide proton transfer imaging: added value beyond quantitative relaxation times.

OBJECTIVES: To evaluate whether amide proton transfer (APT) MRI can be used to characterize gliomas in pediatric patients and whether it provides added value beyond relaxation times. METHODS: In this prospective study, APT imaging and relaxation time mapping were performed in 203 pediatric patients suspected of gliomas from February 2018 to December 2019. The region of interest (ROI) in the tumor was automatically generated with artifact detection and ROI-shrinking algorithms. Several APT-related metrics (CESTR, CESTRnr, MTRRex, AREX, and APT#) and quantitative T1 and T2 were compared between low-grade and high-grade gliomas using the student's t-test or Mann-Whitney U-test. The performance of these parameters was assessed using the receiver operating characteristic (ROC) analysis. A stepwise multivariate logistic regression model was used to combine the imaging parameters. RESULTS: Forty-eight patients (mean age: 6 ± 4 years; 23 males and 25 females) were included in the final analysis. All the APT-related metrics except APT# had significantly (p < 0.05) higher values in the high-grade group than the low-grade group. Under different ROI-shrinking cutoffs, the quantitative T1 (p = 0.045-0.200) and T2 (p = 0.037-0.171) values of high-grade gliomas were typically lower than those of low-grade ones. The stepwise multivariate logistic regression revealed that CESTRnr and APT# were combined significant predictors of glioma grades (p < 0.05), with an area under the ROC curve (AUC) of 0.86 substantially larger than those of T1 (AUC = 0.69) and T2 (AUC = 0.68). CONCLUSIONS: APT imaging can be used to differentiate high-grade and low-grade gliomas in pediatric patients and provide added value beyond quantitative relaxation times. KEY POINTS: • Amide proton transfer (APT) MRI showed significantly (p < 0.05) higher values in pediatric patients with high-grade gliomas than those with low-grade ones. • The area under the curve was 0.86 for APT MRI to differentiate low-grade and high-grade gliomas in pediatric patients, which was substantially higher than that for quantitative T1 (0.69) and T2 (0.68). • APT MRI demonstrated added value beyond quantitative T1 and T2 mapping in characterizing pediatric gliomas.

Alkaline phosphatase determination via regulation of enzymatically generated poly(thymine) as a template for fluorescent copper nanoparticle formation.

We propose a new fluorometric method for alkaline phosphatase (ALP) determination. This method is based on the regulation of enzymatically generated poly(thymine) for the preparation of copper nanoparticles (CuNPs). 2'-Deoxythymidine 5'-triphosphate (dTTP) serves as the source for polymerization mediated by terminal deoxynucleotidyl transferase (TdT). This process generates poly(thymine), which acts as the template for synthesis of fluorescent CuNPs. However, if ALP catalyzes the hydrolysis of dTTP, the TdT-mediated polymerization will be disabled. This prevents the formation of CuNPs and causes a drop in fluorescence. The findings were used to design a sensitive and selective fluorometric method for ALP determination. A linear response in the activity range from 0.1 to 20 U L-1 and a limit of quantification of 0.3 U L-1 were obtained. The results indicate that the proposed method can be successfully applied to ALP assay in spiked diluted serum. This demonstrates the method's reliability and practicability. Graphical abstract A fluoromoetric method for alkaline phosphatase assay has been developed based on regulation of enzymatically generated poly(thymine) as template for the formation of fluorescent CuNPs.

Plasma D-Dimer Level Is an Early Predictor of Severity of Acute Pancreatitis Based on 2012 Atlanta Classification.

BACKGROUND Acute pancreatitis (AP) is a common digestive disorder. Its management depends on the severity; therefore, it is essential to stratify AP patients early. D-dimer, a coagulation indicator, appears to be associated with the pathogenesis of AP. The aim of this study was to evaluate D-dimer as an early predictor of the severity of AP. MATERIAL AND METHODS This was a single-center retrospective study of 1260 patients diagnosed based on the revised Atlanta classification. Only patients hospitalized within 24 h of onset were included, and 334 patients were enrolled. Blood was collected at admission and 3 times within 48 h of admission. Values at admission and average of the 3 blood samples were evaluated by univariate and multivariate analyses. Furthermore, the area under the receiver-operating characteristic curve (AUC) was used to estimate the validity of the predictor and to define optimal cut-off points for prediction. RESULTS We found that 53.3% of the patients had mild AP (MAP), 24.3% had moderately severe AP (MSAP), and 22.4% had severe AP (SAP). D-dimer at admission and the average D-dimer could distinguish MAP patients from MSAP and SAP patients, with cut-off values of 3.355 mg/L and 4.868 mg/L, respectively. No difference in the parameters at admission was observed in multivariate analysis in distinguishing SAP from MSAP, but the average D-dimer level was significantly different with a cut-off value of 7.268 mg/L by comparing Ranson score, APACHE II score, and D-dimer level. CONCLUSIONS The average value of D-dimer levels could be used as a predictor of severity of AP. In general, patients with an average D-dimer level <4.868 could be diagnosed with MAP, >7.268 would develop into SAP, and between 4.868 and 7.268 would be MSAP.

A fluorescent aptasensor for ochratoxin A detection based on enzymatically generated copper nanoparticles with a polythymine scaffold.

A fluorescence enhancement method is presented for the determination of ochratoxin A (OTA). The interaction of OTA with its aptamer causes structural changes which, in turn, change fluorescence of enzymatically generated polythymine-coated copper nanoparticles (CuNPs) (with excitation/emission maxima at 340/625 nm). The OTA-binding aptamer was immobilized on magnetic beads. When it binds OTA, it is partially released and exposes a region with a partly complimentary DNA strand (cDNA). After magnetic separation, the cDNA was employed as a primer to trigger the terminal deoxynucleotidyl transferase-mediated polymerization. This process generates polythymine which act as a template for synthesis of the CuNPs. The method is sensitive in having a 2.0 nM detection limit for OTA. It was successfully applied to the determination of OTA in spiked diluted red wine. Graphical abstract Schematic presentation of a fluorometric enhancement method for ochratoxin A assay based on ochratoxin A inducing structure switching of its aptamer and enzymatically generated polythymine for copper nanoparticles formation.

MnO2 nanosheets as oxidase mimics for colorimetric detection of alkaline phosphatase activity.

A sensitive colorimetric method is described for the determination of the activity of alkaline phosphatase (ALP). It is based on the regulation of the oxidase-mimicking activity of MnO2 nanosheets. In the absence of ALP, MnO2 nanosheets are capable of catalyzing the oxidation of the colorless substrate 3,3',5,5'-tetramethylbenzidine (TMB) by oxygen to form a blue oxidized product (TMB Ox) with an absorption peak at 652 nm. In the presence of ALP and its substrate ascorbic acid-2-phosphate, the latter is hydrolyzed to form ascorbic acid (AA). AA triggers the decomposition of MnO2 nanosheets by reducing MnO2 to Mn2+, thereby weakening the enzyme mimicking activity of the MnO2 nanosheets and causing a drop in absorbance. The drop in absorbance at 652 nm is related to the ALP activity in the range from 0.05-10 m-units per mL (mU·mL-1), and the detection limit is 0.05 mU·mL-1. The method was applied to the determination of ALP in spiked calf serum samples and gave satisfactory results. Graphical abstract Schematic presentation of a facile and sensitive colorimetric method for detecting the activity of alkaline phosphatase (ALP) based on enzymatic regulation of the oxidase-mimicking activity of MnO2 nanosheets.

Feasibility of balanced steady-state free precession sequence at 1.5T for the evaluation of hepatic steatosis in obese children and adolescents.

OBJECTIVES: To determine the feasibility of balanced steady-state free precession (b-SSFP) imaging for measuring hepatic steatosis in obese children and adolescents, using proton magnetic resonance spectroscopy (1H MRS) as reference standard. METHODS: 182 obese Chinese paediatric patients underwent conventional T1-weighted dual echo MRI, 1H MRS and b-SSFP imaging for non-invasive assessment of hepatic steatosis. RESULTS: There was a strong positive correlation between liver fat fraction (FF) on T1-weighted dual echo MRI and 1H MRS-determined liver fat content (LFC) (r = 0.964, p < .001), and a strong negative correlation between the ratio of liver signal intensity (SI) to spleen SI (L/S) on b-SSFP and LFC (r = -0.896, p < .001). ROC curve analysis based on a diagnostic threshold of 1H MRS-determined LFC >50 mg/g (>5 % by wet weight) showed areas under the curves for FF and L/S at 0.989 (0.976-1.000) and 0.926 (0.888-0.964), respectively. Optimal FF and L/S cut-off values identified patients with hepatic steatosis with 97.9 % and 86.5 % sensitivity and 93.4 % and 93.4 % specificity, respectively. CONCLUSIONS: Following further validation, b-SSFP at 1.5T has potential as a feasible technique for evaluation of hepatic steatosis in obese paediatric patients with limited breath-holding capacity. KEY POINTS: • L/S on b-SSFP images closely correlated with 1 H MRS-determined LFC. • b-SSFP has high diagnostic accuracy for hepatic steatosis in obese children. • 100% of obese paediatric subjects are imaged successfully using b-SSFP sequence. • b-SSFP has potential to evaluate hepatic steatosis in children with poor breath-hold.

Regularized Instance Weighting Multiview Clustering via Late Fusion Alignment.

Multiview clustering has become a prominent research topic in data analysis, with wide-ranging applications across various fields. However, the existing late fusion multiview clustering (LFMVC) methods still exhibit some limitations, including variable importance and contributions and a heightened sensitivity to noise and outliers during the alignment process. To tackle these challenges, we propose a novel regularized instance weighting multiview clustering via late fusion alignment (R-IWLF-MVC), which considers the instance importance from various views, enabling information integration to be more effective. Specifically, we assign each sample an importance attribute to enable the learning process to focus more on the key sample nodes and avoid being influenced by noise or outliers, while laying the groundwork for the fusion of different views. In addition, we continue to employ late fusion alignment to integrate base clustering from various views and introduce a new regularization term with prior knowledge to ensure that the learning process does not deviate too much from the expected results. After that, we design a three-step alternating optimization strategy with proven convergence for the resultant problem. Our proposed approach has been extensively evaluated on multiple real-world datasets, demonstrating its superiority to state-of-the-art methods.

Improving management in gastroesophageal reflux disease through leveraging WeChat platform for mobile health care: A randomized control trial.

BACKGROUND: Gastroesophageal reflux disease (GERD) refers to a clinical condition characterized by gastric content reflux into the esophagus, causing symptoms like acid regurgitation and heartburn. While patient education is essential for GERD treatment, traditional educational models often struggle to effectively improve treatment outcomes. METHODS: Between January 2021 and April 2022, we enrolled 257 patients and assessed their GERD knowledge. The patients were randomly assigned to either the WeChat group (60 participants) for health education via WeChat platform or the control group (60 participants) for conventional education only. GERD-Q scores were collected at 1, 3, and 6 months post-intervention, with compliance and satisfaction assessed at the study's conclusion. RESULTS: The overall awareness rate of GERD among patients was approximately 22.3 %. The WeChat group showed better compliance than the control group in terms of adhering to a proper diet, taking medication on time, and engaging in moderate exercise (P < 0.05 for all). Furthermore, the WeChat group demonstrated significantly higher treatment effectiveness and satisfaction than the control group (P < 0.05 for all). CONCLUSION: Patients have a relatively low level of knowledge regarding GERD. WeChat has the potential to facilitate lifestyle changes and improve compliance, treatment effectiveness, and treatment satisfaction among patients with gastroesophageal reflux disease.

The state of biosafety across China's CDC microbiology laboratories: insights from a nationwide survey (2021-2023).

Background: The COVID-19 pandemic underscored the critical importance of biosafety in microbiology laboratories worldwide. In response, China has ramped up its efforts to enhance biosafety measures within its Centers for Disease Control and Prevention (CDC) laboratories. This study provides the first comprehensive assessment of biosafety practices across provincial, city, and county levels of CDC microbiology laboratories in China. Methods: We conducted a nationwide cross-sectional survey from 2021 to 2023, targeting staff from microbiology laboratories within CDCs at all administrative levels in China. Stratified sampling was employed to select respondents, ensuring a representative mix across different CDC hierarchies, job titles, and academic qualifications. The survey encompassed questions on biosafety training, the presence of BSL-2 and BSL-3 laboratories, adherence to general biosafety guidelines, and management practices regarding specimens, reagents, and consumables. Statistical analysis was performed to identify significant differences in biosafety practices among different CDC levels. Results: A total of 990 valid responses were received, highlighting a nearly universal presence (98.69%) of BSL-2 laboratories and a significant yet varied presence of BSL-3 laboratories across the CDC network. The survey revealed high levels of biosafety training (98.69%) and adherence to biosafety protocols. However, challenges remain in the consistent application of certain safety practices, especially at lower administrative levels. Notable differences in the management of specimens, reagents, and consumables point to areas for improvement in ensuring biosecurity. Conclusion: Our findings indicate a robust foundation of biosafety practices within CDC microbiology laboratories in China, reflecting significant advancements in the wake of the Biosecurity Law's implementation. Nevertheless, the variability in adherence to specific protocols underscores the need for ongoing training, resources allocation, and policy refinement to enhance biosafety standards uniformly across all levels. This study's insights are crucial for guiding future improvements in laboratory biosafety, not just in China but potentially in other countries enhancing their public health infrastructures.

One-pot solvothermal preparation of the porous NiS2//MoS2 composite catalyst with enhanced low-temperature hydrodesulfurization activity.

The simple preparation of mesoporous NiS2//MoS2 composite catalyst through a one-pot solvothermal method is presented. The improvement of the specific surface area (220 m2/g) and the construction of the porous structure are realized by this method in the case of no support. The organics acts as a microscopic binder contribute to uniform stacking of MoS2 with NiS2 clusters. The composite structure including NiS2 and MoS2 was obtained (proved by XRD, XPS, TEM, IR, UV-vis and RAMAN) and changed the microelectronic environment of the active metal surface (DFT calculation). The mesoporous NiS2//MoS2 catalyst (Ni1Mo1-200) showed an excellent hydrodesulfurization performance of dibenzothiophene (DBT conversion: 78 % at 260 °C) and a high ratio of direct desulfurization pathway (SDDS/HYD = 16.6) at a low reaction temperature. By combining the characterization and theoretical calculation results, the advantages of this NiS2//MoS2 composite structure in synergistic catalysis was further confirmed.

One-step photodeposition of spatially separated CuOx and MnOx dual cocatalysts on g-C3N4 for enhanced CO2 photoreduction.

The rapid recombination of photogenerated carriers of photocatalysts greatly limits their actual application in CO2 conversion into valuable chemicals. Herein, dual CuOx and MnOx cocatalysts are decorated on g-C3N4 nanosheets via a one-step photodeposition strategy. Benefiting from the repulsion between Cu2+ and Mn2+ cations, a novel g-C3N4-based heterostructure loaded with spatially separated CuOx and MnOx nanoparticle dual cocatalysts has been successfully fabricated. Cu favors the trapping of electrons, while MnOx tends to collect holes. Moreover, the Cu2O/g-C3N4 p-n heterojunction also accelerates the charge separation. As a result, the photogenerated holes and electrons flow into and out of the photocatalyst, respectively, resulting in enhanced charge separation for achieving efficient CO2 photoreduction over CuOx/g-C3N4/MnOx. Accordingly, the optimized CuOx/g-C3N4/MnOx exhibits an improved CO production rate of 5.49 µmol g-1 h-1, which is 27.5 times higher than that of bare g-C3N4.

A collagen-immobilized nanodevice for in situ ratiometric imaging of cancer biomarkers in the tumor microenvironment.

Monitoring the spatiotemporal dynamics of cancer biomarkers within the tumor microenvironment (TME) is critical to understanding their roles in tumorigenesis. Here, we reported a multifunctional fusion protein (collagen-binding domain and duck circovirus tag fused to mCherry, CBD-mCherry-DCV) capable of binding collagen with high affinity and covalently binding specific nucleic acids with exceptional efficiency. We then constructed a chimeric protein-nucleic acid nanodevice (CPNN) using CBD-mCherry-DCV and an aptamer-based sensing module to enable spatially controlled ratiometric imaging of cancer biomarkers in the TME. The collagen-anchoring module CBD-mCherry-DCV allowed specific immobilization of CPNN on 3D multicellular tumor spheroids, enabling the sensing module to achieve "off-on" fluorescence imaging of cancer biomarkers upon specific target recognition by an aptamer. Taking advantage of the constant fluorescence signal of mCherry and the activatable fluorescence response of Cy5 to specific cancer biomarkers, the detection sensitivity and reliability of CPNN were improved by self-calibrating the signal intensity. Specifically, CPNN enabled ratiometric fluorescence imaging of varying concentrations of exogenous PDGF-BB and ATP in tumor spheroids with a high signal-to-background ratio. Furthermore, it allowed the visual monitoring of endogenous PDGF-BB and ATP released from cells. Overall, this study demonstrates the potential of the nanodevice as a versatile approach for the visualization and imaging of cancer biomarkers in the TME.

RNA-sequencing-based detection of human viral pathogens in cerebrospinal fluid and serum samples from children with meningitis and encephalitis.

Encephalitis and meningitis are notable global public health concerns, especially among infants or children. Metagenomic next-generation sequencing (mNGS) has greatly advanced our understanding of the viruses responsible for these diseases. However, the detection rate of the aetiology remains low. We conducted RNA sequencing and virome analysis on cerebrospinal fluid (CSF) and serum samples commonly used in the clinical diagnosis to detect viral pathogens. In total, 226 paired CSF and serum samples from 113 children with encephalitis and meningitis were enrolled. The results showed that the diversity of viruses was higher in CSF, with a total of 12 viral taxa detected, including one case each of herpesvirus, coronavirus and enterovirus, and six cases of adenovirus related to human diseases. In contrast, the Anelloviridae was the most abundant viral family detected in serum, and only a few samples contained human viral pathogens, including one case of enterovirus and two cases of adenovirus. The detection rate for human viral pathogens increases to 10.6 %(12/113) when both types of samples are used simultaneously, compared to CSF along 7.9 % (9/113) or serum alone 2.6 % (3/113). However, we did not detect these viruses simultaneously in paired samples from the same case. These results suggest that CSF samples still have irreplaceable advantages for using mNGS to detect viruses in patients with meningitis and encephalitis, and serum can supplement to improve the detection rate of viral encephalitis and meningitis. The findings of this study could help improve the etiological diagnosis, clinical management and prognosis of patients with meningitis and encephalitis in children.

A Rapid and Sensitive Detection of HIV-1 with a One-Pot Two-Stage Reverse Transcription Recombinase Aided Real-Time PCR Assay.

Human immunodeficiency virus 1 (HIV-1) attacks the immune system, making people susceptible to various diseases, thus increasing their risk of death. Comprehensive detection of major HIV-1 strains circulating in China is vital for effective HIV-1 infection prevention and treatment. HIV-1 nucleic acid detection is considered effective for HIV-1 diagnosis since traditional immunological testing may fail to detect HIV-1 infection during the window period. This work demonstrates a one-pot two-stage amplification assay (RT-RAP), a combination of reverse transcription recombinase (RT- RAA), and quantitative real-time polymerase chain reaction (qRT-PCR). The turn-around time of the assay is only 50 min and can be performed with commonly available laboratory equipment, the qPCR devices. The RT-RAP assay could detect approximately 5 and 14 copies/reaction of HIV-1 DNA and RNA using recombinant plasmids and standard reference strains, respectively. Additionally, we found that the clinical performance of RT-RAP (detected 169 samples out of 170 specimens) was consistent with that of qRT-PCR. The sensitivity and specificity of RT-RAP were 100.00% (99/99) and 98.59% (70/71), respectively, while its positive and negative predictive values were 99.00% (99/100) and 100.00% (70/70), respectively. The total coincidence rate of the RT-RAP was 99.41% (169/170), with a kappa value of 0.988 (p < 0.05). We demonstrated that RT-RAP could rapidly detect the common HIV-1 subtypes commonly circulating in China with comparable sensitivity and specificity to qRT-PCR.

Multiplex LNA probe-based RAP assay for rapid and highly sensitive detection of rifampicin-resistant Mycobacterium tuberculosis.

Objectives: The World Health Organization (WHO) Global tuberculosis Report 2021 stated that rifampicin-resistant tuberculosis (RR-TB) remains a major public health threat. However, the in-practice diagnostic techniques for RR-TB have a variety of limitations including longer time, lack of sensitivity, and undetectable low proportion of heterogeneous drug resistance. Methods: Here we developed a multiplex LNA probe-based RAP method (MLP-RAP) for more sensitive detection of multiple point mutations of the RR-TB and its heteroresistance. A total of 126 clinical isolates and 78 sputum samples collected from the National Tuberculosis Reference Laboratory, China CDC, were tested by MLP-RAP assay. In parallel, qPCR and Sanger sequencing of nested PCR product assay were also performed for comparison. Results: The sensitivity of the MLP-RAP assay could reach 5 copies/µl using recombinant plasmids, which is 20 times more sensitive than qPCR (100 copies/µl). In addition, the detection ability of rifampicin heteroresistance was 5%. The MLP-RAP assay had low requirements (boiling method) for nucleic acid extraction and the reaction could be completed within 1 h when placed in a fluorescent qPCR instrument. The result of the clinical evaluation showed that the MLP-RAP method could cover codons 516, 526, 531, and 533 with good specificity. 41 out of 78 boiled sputum samples were detected positive by MLP-RAP assay, which was further confirmed by Sanger sequencing of nested PCR product assay, on the contrary, qPCR was able to detect 32 samples only. Compared with Sanger sequencing of nested PCR product assay, both the specificity and sensitivity of the MLP-RAP assay were 100%. Conclusion: MLP-RAP assay can detect RR-TB infection with high sensitivity and specificity, indicating that this assay has the prospect of being applied for rapid and sensitive RR-TB detection in general laboratories where fluorescent qPCR instrument is available.