Evaluation of RT-LAMP Assay for Rapid Detection of SARS-CoV-2.

OBJECTIVE: To evaluate the accuracy of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in community or primary-care settings. METHOD: We systematically searched the Web of Science, Embase, PubMed, and Cochrane Library databases. We conducted quality evaluation using ReviewManager software (version 5.0). We then used MetaDisc software (version 1.4) and Stata software (version 12.0) to build forest plots, along with a Deeks funnel plot and a bivariate boxplot for analysis. RESULT: Overall, the sensitivity, specificity, and diagnostic odds ratio were 0.79, 0.97, and 328.18, respectively. The sensitivity for the subgroup with RNA extraction appeared to be higher, at 0.88 (0.86-0.90), compared to the subgroup without RNA extraction, at 0.50 (0.45-0.55), with no significant difference in specificity. CONCLUSION: RT-LAMP assay exhibited high specificity regarding current SARS-CoV-2 infection. However, its overall sensitivity was relatively moderate. Extracting RNA was found to be beneficial in improving sensitivity.

Effect of BCG Vaccination against SARS-CoV-2 Infection.

Based on previous studies, we found that Bacillus Calmette-Guérin (BCG) vaccination may play a role in preventing SARS-CoV-2 infection. Therefore, we conducted a meta-analysis to investigate this protective effect. We searched the Embase, PubMed, Web of Science, Cochrane Library, BioRxiv, and MedRxiv databases for studies that evaluated the relationship between BCG vaccination and SARS-CoV-2 infection or COVID-19 disease. The quality of all included studies was assessed using the Risk of Bias in Non-randomized Studies of Interventions and the Agency for Healthcare Research and Quality data tools. Review Manager (Version 5.3) was used to conduct all the data analyses. A total of eight studies were ultimately included in our meta-analysis. Our primary analysis found a significantly lower SARS-CoV-2 infection rate in the BCG vaccination group compared to the control group, with an odds ratio of 0.61, (95% confidence interval 0.39 to 0.95, P = 0.03; I2 = 31%, and P = 0.21, respectively). Our study indicates that BCG vaccination can protect against SARS-CoV-2 infection. However, there is insufficient evidence that BCG vaccination can reduce the severity of COVID-19.

Evaluation of CRISPR-Based Assays for Rapid Detection of SARS-CoV-2: A Systematic Review and Meta-Analysis.

PURPOSE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen of coronavirus disease 2019. Diagnostic methods based on the clustered regularly interspaced short palindromic repeats (CRISPR) have been developed to detect SARS-CoV-2 rapidly. Therefore, a systematic review and meta-analysis were performed to assess the diagnostic accuracy of CRISPR for detecting SARS-CoV-2 infection. MATERIALS AND METHODS: Studies published before August 2021 were retrieved from four databases, using the keywords "SARS-CoV-2" and "CRISPR." Data were collected from these publications, and the sensitivity, specificity, negative likelihood ratio (NLR), positive likelihood ratio (PLR), and diagnostic odds ratio (DOR) were calculated. The summary receiver operating characteristic curve was plotted for analysis with MetaDiSc 1.4. The Stata 15.0 software was used to draw Deeks' funnel plots to evaluate publication bias. RESULTS: We performed a pooled analysis of 38 independent studies shown in 30 publications. The reference standard was reverse transcription-quantitative PCR. The results indicated that the sensitivity of CRISPR-based methods for diagnosis was 0.94 (95% CI 0.93-0.95), the specificity was 0.98 (95% CI 0.97-0.99), the PLR was 34.03 (95% CI 20.81-55.66), the NLR was 0.08 (95% CI 0.06-0.10), and the DOR was 575.74 (95% CI 382.36-866.95). The area under the curve was 0.9894. CONCLUSION: Studies indicate that a diagnostic method based on CRISPR has high sensitivity and specificity. Therefore, this would be a potential diagnostic tool to improve the accuracy of SARS-CoV-2 detection.

The Diagnostic Accuracy of Xpert Xpress to SARS-CoV-2: A systematic review.

The SARS-CoV-2 infection rate, as well as mortality rate, is high. There is an urgent need for a high-throughput, accurate and reliable method of diagnosing COVID-19 pneumonia. We included references from databases, such as PubMed, Cochrane Library, Web of Science, and Embase, and extracted data. Then, MetaDisc and STATA were used to establish forest plots and funnel plots for meta-analysis. We collected 14 articles and performed a systematic review. The following results were obtained: sensitivity and specificity were 0.97 (0.96 to 0.98) and 0.97 (0.96 to 0.98) respectively; PLR and NLR were 24.51 (16.63-36.12) and 0.03 (0.01 to 0.10) respectively, DOR was 975.15 (430.11-2210.88), and AUC was 0.9926. When Xpress detects SARS-CoV-2 in different samples, the heterogeneity is small and the specificity and sensitivity are extremely high. We recommend the employment of Xpert Xpress analysis in rapid screening.

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids.

BACKGROUND: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. RESULTS: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. CONCLUSIONS: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.