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Objective. Most respiratory infections have similar symptoms, so it is clinically difficult to determine their etiology. This study aimed to show the importance of molecular diagnostics in identifying the etiological agent of respiratory infections, especially during the coronavirus disease 2019 (COVID-19) pandemic. Methods. A total of 849 samples from patients hospitalized at the University Clinical Center Kragujevac (from January 1 to August 1, 2022) were examined using automated multiplex-polymerase chain reaction (PCR) tests. The BioFire-FilmArray-Respiratory Panel 2.1 test was used for 742 nasopharyngeal swabs [identification of 19 viruses (including SARS-CoV-2) and four bacteria], while the BioFire-FilmArray-Pneumonia Panel was used [identification of 18 bacteria and nine viruses] (BioMerieux, Marcy l'Etoile, France) for 107 tracheal aspirates. The tests were performed according to the manufacturer's instructions, and the results were available within an hour. Results. In 582 (78.4%) samples, the BioFire-FilmArray-Respiratory Panel 2.1 plus test identified at least one pathogen. The rhinovirus (20.6%), SARS-CoV-2 (17.7%), influenza A (17.5%), respiratory syncytial virus (12.4%), and parainfluenza 3 (10.1%) were the most common. Other viruses were found less frequently, and Bordetella parapertussis was detected in one sample. In 85 (79.4%) samples, the BioFire-FilmArray-Pneumonia Panel test identified at least one bacterium or virus. The most prevalent bacteria were Staphylococcus aureus (42.4%), Haemophilus influenzae (41.2%), Streptococcus pneumoniae (36.5%), Moraxella catarrhalis (22.3%), and Legionella pneumophila (2.4%). Among viruses, rhinovirus (36.5%), adenovirus (23.5%), influenza A (11.8%), and the genus Coronavirus (4.7%), were detected. Conclusion. Multiplex-PCR tests improved the implementation of therapeutic and epidemiological measures, preventing the spread of the COVID-19 infection and Legionnaires' disease.Copyright © 2022, Serbian Medical Society. All rights reserved.
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Canine parvovirus (CPV), canine coronavirus (CCoV) and canine rotavirus (CRV) are the three main causative viruses of diarrhea in dogs with similar clinical symptoms;thereby it is necessary to establish a high effective molecular detection method for differentiating the above pathogens. By optimizing the primer concentration and annealing temperature, a triple PCR method was established for simultaneous detection of CPV, CCoV and CRV, and then the specificity, sensitivity and repeatability of the method were tested. The results showed that the target fragments of CPV VP2 gene (253 bp), CCoV ORF-1b gene (379 bp) and CRV VP6 gene (852 bp) could be accurately amplified by the triple PCR method with high specificity, the detection limits of CPV, CCOV and CRV were 6.44x10-1 pg/L, 8.72x10-1 pg/L and 8.35x10-1 pg/L respectively with high sensitivity, and the method had good stability. Using this triple PCR method, 135 canine diarrhea fecal samples collected in Chengdu region from 2019 to 2020 were detected, and compared with those of single PCR method. The detection rates of CPV, CCoV and CRV were 16.30%, 20.74% and 4.44%, respectively, and the total infection rate was 51.11% (65/135) with 20.00% (13/65) co-infection rate. The detection results were consistent with three single PCR methods. In conclusion, CPV/CCoV/CRV triple PCR method successfully established in this paper can be applied as an effective molecular method to detection of related pathogens and to the epidemiological investigation.
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The COVID-19 pandemic, emerging/re-emerging infections as well as other non-communicable chronic diseases, highlight the necessity of smart microfluidic point-of-care diagnostic (POC) devices and systems in developing nations as risk factors for infections, severe disease manifestations and poor clinical outcomes are highly represented in these countries. These POC devices are also becoming vital as analytical procedures executable outside of conventional laboratory settings are seen as the future of healthcare delivery. Microfluidics have grown into a revolutionary system to miniaturize chemical and biological experimentation, including disease detection and diagnosis utilizing muPads/paper-based microfluidic devices, polymer-based microfluidic devices and 3-dimensional printed microfluidic devices. Through the development of droplet digital PCR, single-cell RNA sequencing, and next-generation sequencing, microfluidics in their analogous forms have been the leading contributor to the technical advancements in medicine. Microfluidics and machine-learning-based algorithms complement each other with the possibility of scientific exploration, induced by the framework's robustness, as preliminary studies have documented significant achievements in biomedicine, such as sorting, microencapsulation, and automated detection. Despite these milestones and potential applications, the complexity of microfluidic system design, fabrication, and operation has prevented widespread adoption. As previous studies focused on microfluidic devices that can handle molecular diagnostic procedures, researchers must integrate these components with other microsystem processes like data acquisition, data processing, power supply, fluid control, and sample pretreatment to overcome the barriers to smart microfluidic commercialization.Copyright © 2023 by Begell House, Inc.
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Given the scale of the ongoing COVID-19 pandemic, the need for reliable, scalable testing, and the likelihood of reagent shortages, especially in resource-poor settings, we have developed an RTqPCR assay that relies on an alternative to conventional viral reverse transcriptases, a thermostable reverse transcriptase/DNA polymerase (RTX) (Ellefson et al., 2016). Here we show that RTX performs comparably to the other assays sanctioned by the CDC and validated in kit format. We demonstrate two modes of RTX use - (i) dye-based RT-qPCR assays that require only RTX polymerase, and (ii) TaqMan RT-qPCR assays that use a combination of RTX and Taq DNA polymerases (as the RTX exonuclease does not degrade a TaqMan probe). We also provide straightforward recipes for the purification of this alternative reagent RTX. We anticipate that in low resource or point-of-need settings researchers could obtain the available constructs and begin to develop their own assays, within whatever regulatory framework exists for them.Copyright © 2021 Bio-protocol LLC. All Rights Reserved.
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Objectives: Reverse transcription and real-time polymerase chain reaction (RT-qPCR) based on the SARS-CoV-2 viral RNA demonstration is the gold standard in diagnosis. Data files obtained from PCR devices should be analysed by a specialist physician and results should be transferred to Laboratory Information Management System (LIMS). CAtenA Smart PCR (Ventura, Ankara, Turkiye) program is a local bioinformatics software that assess PCR data files with artificial intelligence, submits to expert approval and transfers the approved results to LIMS. The aim of this study is to investigate its accuracy and matching success rate with expert analysis. Method(s): A total of 9400 RT-qPCR test results studied in Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory were compared with respect to expert evaluation and CAtenA results. Result(s): It was determined that the preliminary evaluation results of the CAtenA matched 86% of the negative and 90% of the positive results provided by expert analysis. 987 tests which CAtenA determined as inconclusive and suggested repeating PCR were found either negative or positive by expert analysis. A significant difference between positive and negative matching success rates and artificial intelligence (AI) based software overall accuracy was found and associated with the missed tests of the AI. Conclusion(s): As a result, it was suggested there is a low risk of confirming false positive results without expert analysis and test repetitions would cause losing time along with extra test costs. It was agreed that the PCR analysis used in CAtenA should be improved particularly in terms of test repetitions.Copyright © 2023 by Prusa Medical Publishing.
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Since late December 2019, coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been rapidly spread across the globe. The early, safe, sensitive, and accurate diagnosis of viral infection is required to decrease and control contagious infection and improve public health surveillance. The diagnosis generally is made by detecting SARS-CoV-2-related agents, including a range of nucleic acid detection-based, immunoassay-based, radiographic-based, and biosensor-based methods. This review presents the progress of various detection tools for diagnosing COVID-19 and addresses the advantages and restrictions of each detection method. Given that diagnosis of a contagious various like SARS-COV-2 can improve patient survival rates and break the transmission chain, there is no surprise that significant efforts should be made to reduce the limitations of tests that lead to false-negative results and to develop a substantial test for COVID-19 diagnosis.
Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2 , COVID-19 TestingABSTRACT
Purpose of Review: This review gives an overview of the diseases caused by Aspergillus, including a description of the species involved and the infected clinical systems. We provide insight into the various diagnostic methods available for diagnosing aspergillosis, particularly invasive aspergillosis (IA), including the role of radiology, bronchoscopy, culture, and non-culture-based microbiological methods. We also discuss the available diagnostic algorithms for the different disease conditions. This review also summarizes the main aspects of managing infections due to Aspergillus spp., such as antifungal resistance, choice of antifungals, therapeutic drug monitoring, and new antifungal alternatives. Recent Findings: The risk factors for this infection continue to evolve with the development of many biological agents that target the immune system and the increase of viral illnesses such as coronavirus disease. Due to the limitations of present mycological test methods, establishing a fast diagnosis is frequently difficult, and reports of developing antifungal resistance further complicate the management of aspergillosis. Many commercial assays, like AsperGenius®, MycAssay Aspergillus®, and MycoGENIE®, have the advantage of better species-level identification and concomitant resistance-associated mutations. Fosmanogepix, ibrexafungerp, rezafungin, and olorofim are newer antifungal agents in the pipeline exhibiting remarkable activity against Aspergillus spp. Summary: The fungus Aspergillus is found ubiquitously around the world and can cause various infections, from harmless saprophytic colonization to severe IA. Understanding the diagnostic criteria to be used in different patient groups and the local epidemiological data and antifungal susceptibility profile is critical for optimal patient management.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann-Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath.
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The use of a timely and appropriate antibiotic therapy, which requires early and accurate microorganisms' detection in pneumonia. Currently, the identification of microorganisms in pneumonia is limited by the low sensitivity and long response time of standard culture-based diagnostic tools. For this reason, treatment in pneumonia is empirical. An inadequate empirical treatment is related to poor outcomes in patients with pneumonia. The microbiological diagnosis is key to improve the outcomes in patient with pneumonia. Over the past years there was a significant advance in the molecular diagnosis of infectious diseases including pneumonia. Also the impact of the COVID-19 pandemic has impacted the development and application of these new molecular techniques. This review summarizes the advances in molecular diagnosis of community-acquired pneumonia.Copyright © 2022 EDIZIONI MINERVA MEDICA.
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Background: Most patients with heterozygous familial hypercholesterolemia (FH) do not achieve current LDL-C goals proposed by European guidelines with conventional lipid-lowering therapy (LLT). Chronic use of PCSK9 inhibitors (PCSK9i) have shown to reduce LDL-C levels up to 61% on top of statins. Persistence to chronic LLT is important to reduce the burden of atherosclerotic cardiovascular disease (ASCVD). Purpose(s): To analyze persistence and effectiveness of PCSK9i in clinical practice setting in FH patients from the SAFEHEART register with longterm follow-up. Method(s): SAFEHEART is an open, long-term prospective study of a cohort of subjects with molecular diagnosis of FH. Follow-up is carried out every year through a standardized phone-call to collect clinical conditions, persistence to medications, lipid profile, and cardiovascular events. This study analyses subjects >=18 years of age on stable LLT who have received PCSK9i. Result(s): 696 individuals (46% females), median age 56.4 years (IQR 49- 66) started with PCSK9i (49% alirocumab and 51% evolocumab). Out of them 38% had history of ASCVD, and 89% were on maximum LLT. Median LDL-C at the moment of starting PCSK9i was 145 mg/dL (IQR, 123- 177), representing a poor 2016 & 2019 ESC/EAS guidelines achievement (3% and 0.1% respectively). After a median follow-up of 3.7 years (IQR, 2.3-4.8), 669 patients (96%) remained on PCSK9i treatment during entire follow-up. Only 27 patients (4%) discontinued, 5 temporarily (0.7%) and 22 permanently (3.2%). Most common reasons for PCSK9i treatment interruption were medical decision (n=6), adverse event (AE) (n=5), patient decision not related with AE (n=5) and comorbidity (n=5). Median time to permanent discontinuation was 15 months (IQR, 4-33). Median LDL-C levels observed and % of LDL-C reduction obtained after 1 year of treatment and in the last follow-up visit were: 63 mg/dL (IQR, 43- 88), 61 mg/dL (IQR, 44-82), 57.6% (IQR, 39.5-69) and 58% (IQR, 44-68), respectively. 2016 ESC/EAS guidelines LDL-C goals was achieved by 70% of patients at year 1 and 77% in the last follow-up visit after the introduction of PCSK9i (p<0.001). 2019 ESC/EAS goals were achieved by 44.5% and 48% (p=0.1). Conclusion(s): Long-term persistence to PCSK9i treatment in FH patients is very high (96%) and reasons for discontinuation are diverse. This study shows that COVID-19 pandemic did not affected persistence to treatment. Effectiveness in LDL-C reduction and LDL-C goal achievement improved significantly with introduction of PCSK9i in clinical practice setting.
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SARS-CoV-2 is a highly pathogenic novel ongoing-pandemic virus. It causes COVID-19. Little is known about SARS-CoV-2 biology, countermeasure, and its origin. SARS-CoV-2 is characterized by high infectiousness and sever pathogenesis. COVID-19 crosses the bounders of all continents in a high spreading manner. Here, several aspects regarding the origin and the molecular structure of this novel virus as well as the production of effective vaccines have been addressed. This article illustrated that SARS-CoV-2 was not being recombined inside laboratory and it has a complicated genome that led to sophisticated pathogenesis. Additionally, an important structural protein known as spike S was demonstrated by researchers as an important protein used by the virus for host cell entry as well as for vaccine development. However, the efforts for viral diagnosis and genomic demonstration as well as vaccine production are promising to tackle COVID-19. These perspectives will help in COVID-19 control. However, further investigations are urgently needed to figure out which controlling tactic is more efficient not only in the case of SARS-CoV-2 but also for future pandemics.Copyright © Mohammed Hamzah Abdulkadhim Al-Saadi and Wisam Hindawi Hoidy.
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Asymptomatic subjects account for 25 to 45% of SARS-CoV-2 infections, and in particular, subjects on mild immunosuppressive therapy may have symptoms masked and could spread virus for an extended period of time. To determine the cumulative incidence of symptomatic and asymptomatic SARS-CoV-2 infections and associated risk factors, we conducted a prospective clinical and serological survey in a cohort of 278 liver transplant recipients (LTRs) from Central Italy. Three different serology tests were performed every 4 months in 259 LTRs between April 2020 and April 2021: one based on raw extract of whole SARS-CoV-2 virus and two on specific viral antigens (nucleoprotein and receptor binding domain) to detect specific IgG, IgM and IgA. Hundred fifteen LTRs who reported symptoms or close contact with a SARS-CoV-2-positive subject, or had a positive serological result underwent molecular testing by standard screening procedures (RT-PCR on naso-pharyngeal swab). Thirty-one past or active SARS-CoV-2 infections were identified: 14 had positive molecular test (64% symptomatic), and 17 had positive serology only (18% symptomatic). SARS-CoV-2 infection was not statistically related to gender, age, obesity, diabetes, renal impairment, type of anti-rejection therapy or time from transplant. Asymptomatic SARS-CoV-2 cases (61.3%) were more frequent in males and in those with glomerular filtrate rate >50 ml/min. Overall, the addition of repeated serology to standard diagnostic molecular protocols increased detection of SARS-CoV-2 infection from 5.1% to 10.9%. Anti-SARS-CoV-2 seroprevalence among our LTRs (11.2%) is comparable to the general population of Central Italy, considered a medium-impact area. Only one asymptomatic subject (6%) was found to carry SARS-CoV-2 in respiratory tract at the time of serological diagnosis.Copyright © 2021 The Authors
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The pandemic outbreak of COVID-19 has posed a threat to public health globally, and rapid and accurate identification of the viruses is crucial for controlling COVID-19. In recent years, nanomaterial-based electrochemical sensing techniques hold immense potential for molecular diagnosis with high sensitivity and specificity. In this review, we briefly introduced the structural characteristics and routine detection methods of SARS-CoV-2, then summarized the associated properties and mechanisms of the electrochemical biosensing methods. On the above basis, the research progress of electrochemical biosensors based on gold nanomaterials, oxide nanomaterials, carbon-based nanomaterials and other nanomaterials for rapid and accurate detection of virus were reviewed. Finally, the future applications of nanomaterial-based biosensors for biomolecular diagnostics were pointed out. © 2023 Science Press. All rights reserved.
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Polydimethylsiloxane (PDMS) has been widely used to make lab-on-a-chip devices, such as reactors and sensors, for biological research. Real-time nucleic acid testing is one of the main applications of PDMS microfluidic chips due to their high biocompatibility and transparency. However, the inherent hydrophobicity and excessive gas permeability of PDMS hinder its applications in many fields. This study developed a silicon-based polydimethylsiloxane-polyethylene-glycol (PDMS-PEG) copolymer microfluidic chip, the PDMS-PEG copolymer silicon chip (PPc-Si chip), for biomolecular diagnosis. By adjusting the modifier formula for PDMS, the hydrophilic switch occurred within 15 s after contact with water, resulting in only a 0.8% reduction in transmittance after modification. In addition, we evaluated the transmittance at a wide range of wavelengths from 200 nm to 1000 nm to provide a reference for its optical property study and application in optical-related devices. The improved hydrophilicity was achieved by introducing a large number of hydroxyl groups, which also resulted in excellent bonding strength of PPc-Si chips. The bonding condition was easy to achieve and time-saving. Real-time PCR tests were successfully conducted with higher efficiency and lower non-specific absorption. This chip has a high potential for a wide range of applications in point-of-care tests (POCT) and rapid disease diagnosis.
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Introduction: The ongoing 2019 coronavirus disease pandemic (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, is a global public health threat. Early diagnosis and identification of SARS-CoV-2 and its variants plays a critical role in COVID-19 prevention and control. Currently, the most widely used technique to detect SARS-CoV-2 is quantitative reverse transcription real-time quantitative PCR (RT-qPCR), which takes nearly 1 hour and should be performed by experienced personnel to ensure the accuracy of results. Therefore, the development of a nucleic acid detection kit with higher sensitivity, faster detection and greater accuracy is important. Methods: Here, we optimized the system components and reaction conditions of our previous detection approach by using RT-RAA and Cas12b. Results: We developed a Cas12b-assisted one-pot detection platform (CDetection.v2) that allows rapid detection of SARS-CoV-2 in 30 minutes. This platform was able to detect up to 5,000 copies/ml of SARS-CoV-2 without cross-reactivity with other viruses. Moreover, the sensitivity of this CRISPR system was comparable to that of RT-qPCR when tested on 120 clinical samples. Discussion: The CDetection.v2 provides a novel one-pot detection approach based on the integration of RT-RAA and CRISPR/Cas12b for detecting SARS-CoV-2 and screening of large-scale clinical samples, offering a more efficient strategy for detecting various types of viruses.
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The pandemic outbreak of COVID-19 has posed a threat to public health globally, and rapid and accurate identification of the viruses is crucial for controlling COVID-19. In recent years, nanomaterial-based electrochemical sensing techniques hold immense potential for molecular diagnosis with high sensitivity and specificity. In this review, we briefly introduced the structural characteristics and routine detection methods of SARS-CoV-2, then summarized the associated properties and mechanisms of the electrochemical biosensing methods. On the above basis, the research progress of electrochemical biosensors based on gold nanomaterials, oxide nanomaterials, carbon-based nanomaterials and other nanomaterials for rapid and accurate detection of virus were reviewed. Finally, the future applications of nanomaterial-based biosensors for biomolecular diagnostics were pointed out. © 2023 Science Press. All rights reserved.
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Horses may act as incidental host and experience silent infection following spillover from humans with COVID-19. SARS-CoV-2-infected humans should avoid close contact with equids during the time of their illness.