Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing.

Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.

Intestinal Bacterial Translocation Contributes to Diabetic Kidney Disease.

BACKGROUND: In recent years, many studies have focused on the intestinal environment to elucidate pathogenesis of various diseases, including kidney diseases. Impairment of the intestinal barrier function, the "leaky gut," reportedly contributes to pathologic processes in some disorders. Mitochondrial antiviral signaling protein (MAVS), a component of innate immunity, maintains intestinal integrity. The effects of disrupted intestinal homeostasis associated with MAVS signaling in diabetic kidney disease remains unclear. METHODS: To evaluate the contribution of intestinal barrier impairment to kidney injury under diabetic conditions, we induced diabetic kidney disease in wild-type and MAVS knockout mice through unilateral nephrectomy and streptozotocin treatment. We then assessed effects on the kidney, intestinal injuries, and bacterial translocation. RESULTS: MAVS knockout diabetic mice showed more severe glomerular and tubular injuries compared with wild-type diabetic mice. Owing to impaired intestinal integrity, the presence of intestine-derived Klebsiella oxytoca and elevated IL-17 were detected in the circulation and kidneys of diabetic mice, especially in diabetic MAVS knockout mice. Stimulation of tubular epithelial cells with K. oxytoca activated MAVS pathways and the phosphorylation of Stat3 and ERK1/2, leading to the production of kidney injury molecule-1 (KIM-1). Nevertheless, MAVS inhibition induced inflammation in the intestinal epithelial cells and KIM-1 production in tubular epithelial cells under K. oxytoca supernatant or IL-17 stimulation. Treatment with neutralizing anti-IL-17 antibody treatment had renoprotective effects. In contrast, LPS administration accelerated kidney injury in the murine diabetic kidney disease model. CONCLUSIONS: Impaired MAVS signaling both in the kidney and intestine contributes to the disrupted homeostasis, leading to diabetic kidney disease progression. Controlling intestinal homeostasis may offer a novel therapeutic approach for this condition.

Is Social Support Associated with Colorectal Cancer Care Utilization? A Multilevel Mixed-Effects Model of a Cross-Sectional Cohort Study in Vietnam.

OBJECTIVE: To investigate the relationship between the social support (SS) and colorectal cancer (CRC) care utilization of patients in the central region of Vietnam. METHODS: This was a cross-sectional cohort study in which the cohort was defined as all residential patients diagnosed with CRC in a tertiary hospital, Hue Central Hospital (HCH), in central Vietnam from 2013 to 2019. Social support was considered the main independent variable and was evaluated using the Medical Outcomes Study Social Support Survey (MOS-SSS), a self-administered 19-item SS survey. MOS-SSS is a widely used scale for assessing social support in CRC patients because it is brief, easy to use, reliable, and valid. In this study, we considered a data framework with a multilevel structure that included the patient level and duration of diagnosis as the second level. We estimated the magnitude of SS and CRC-specific treatment modalities using multilevel mixed-effects (MM) models under a hierarchical approach. RESULTS: The findings indicated that CRC care utilization rates were 89.9%, 48.5%, and 30.6% for surgical resection, chemotherapy, and radiation therapy, respectively. The overall trend of SS decreased significantly and affected the CRC care utilization. We found a positive effects of overall SS, as well as emotional and tangible support, on the number of hospitalization admissions and chemotherapy utilization. CONCLUSION: This study suggests that the use of the MOS-SSS should be continued in the long term for CRC patients to enhance medical accessibility and care utilization.

Digital Health Literacy About COVID-19 as a Factor Mediating the Association Between the Importance of Online Information Search and Subjective Well-Being Among University Students in Vietnam.

Introduction: Digital health literacy (DHL) has recently been proposed as a means of enabling healthy decisions for protective behavior, preventive measures, and adherence with COVID-19 policies and recommendations especially in the era of the "infodemic". This study aimed to (1) identify COVID-19 related DHL and its association with online information seeking; (2) to elucidate COVID-19 related DHL as a mediator predictor between the importance of online information search and its association with subjective well-being among Vietnamese university students. Methods: A cross-sectional web-based survey was used to elicit the responses of Vietnamese students over 2 consecutive weeks (from April 25 to May 9, 2020, n = 1,003, 70.1% female students, mean age 21.4 ± 3.1). The online survey questionnaire collected data on the sociodemographic characteristics of participants, DHL about COVID-19, information seeking behavior, and subjective well-being. Mediation analysis was conducted using the importance of searching COVID-19 related information as independent variables, subjective well-being as a dependent variable, and DHL as a mediator variable. Results: Among 1,003 students, the mean (SD) of DHL related to COVID-19 was 2.87 ± 0.32. In the survey, 87.2% of the students reported sufficient well-being, while almost 13% reported low or very low well-being. The findings also indicated that search engines were the most popular platform for information seeking by Vietnamese students (95.3%) and 92.8% of participants had searched for information related to the current spread of COVID-19. Not searching for hygiene regulation as part of infection control and an average level of information satisfaction were associated with limited DHL (p < 0.05). The importance of online information searching related to COVID-19 increased the subjective well-being of students significantly and limited DHL (p < 0.05). DHL was found to mediate the relationship between the importance of online information searching and the subjective well-being of students. Conclusion: The finding provides insight into DHL about COVID-19 among university students, and their ability to find, understand, appraise, and use online health related information during lockdown throughout the first COVID-19 pandemic wave. DHL should be highlighted as a mediating factor that enhances the positive effect of the importance of information seeking on psychological well-being. However, further studies are needed to better define the mediating role of DHL across other factors.

The Production of Standardized Samples with Known Concentrations for Severe Acute Respiratory Syndrome Coronavirus 2 RT-qPCR Testing Validation for Developing Countries in the Period of the Pandemic Era.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic of pneumonia spreading around the world, leading to serious threats to public health and attracting enormous attention. There is an urgent need for sensitive diagnostic testing implementation to control and manage SARS-CoV-2 in public health laboratories. The quantitative reverse transcription PCR (RT-qPCR) assay is the gold standard method, but the sensitivity and specificity of SARS-CoV-2 testing are dependent on a number of factors. METHODS: We synthesized RNA based on the genes published to estimate the concentration of inactivated virus samples in a biosafety level 3 laboratory. The limit of detection (LOD), linearity, accuracy, and precision were evaluated according to the bioanalytical method validation guidelines. RESULTS: We found that the LOD reached around 3 copies/reaction. Furthermore, intra-assay precision, accuracy, and linearity met the accepted criterion with an RSD for copies of less than 25%, and linear regression met the accepted R 2 of 0.98. CONCLUSIONS: We suggest that synthesized RNA based on the database of the NCBI gene bank for estimating the concentration of inactivated virus samples provides a potential opportunity for reliable testing to diagnose coronavirus disease 2019 (COVID-19) as well as limit the spread of the disease. This method may be relatively quick and inexpensive, and it may be useful for developing countries during the pandemic era. In the long term, it is also applicable for evaluation, verification, validation, and external quality assessment.

Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

BACKGROUND: There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. METHODS: We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master. RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.