scholarly journals LabDisk with complete reagent prestorage for sample-to-answer nucleic acid based detection of respiratory pathogens verified with influenza A H3N2 virus

Lab on a Chip ◽  
2016 ◽  
Vol 16 (1) ◽  
pp. 199-207 ◽  
Author(s):  
F. Stumpf ◽  
F. Schwemmer ◽  
T. Hutzenlaub ◽  
D. Baumann ◽  
O. Strohmeier ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Influenza A ◽  
Pathogen Detection ◽  
Point Of Care ◽  
H3n2 Virus ◽  
Respiratory Pathogens ◽  
Manual Handling

Sample supply remains the only manual handling step for pathogen detection at the point-of-care.

scholarly journals Multiplex Tests for Respiratory Tract Infections: The Direct Utility of the FilmArray Respiratory Panel in Emergency Department

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Siyuan Yang ◽  
Hui Li ◽  
Yunxia Tang ◽  
Fengting Yu ◽  
Chengjie Ma ◽  
...  
Keyword(s):  
Emergency Department ◽  
Respiratory Tract ◽  
Influenza A ◽  
Respiratory Tract Infections ◽  
Pathogen Detection ◽  
Point Of Care ◽  
Respiratory Pathogens ◽  
Point Of Care Testing ◽  
Tract Infections ◽  
First Time

Background. The FilmArray Respiratory Panel with multiplex targets for respiratory pathogens has been widely used and verified in clinical trials in special test settings. However, it is necessary to evaluate the panel’s performance at the point of care directly, in nonspecific test settings. Methods. Patients with respiratory tract infections were enrolled from among emergency department visitors, and all steps, including the collection of specimens and testing, were performed by our clinicians. Results. Among 270 patients, 196 (72.6%) patients were found to have one or more pathogens. For signal pathogen detection, influenza A virus had the highest rate of detection; 45 (16.7%) of the patients had two or more respiratory pathogens codetected, and most of the multiplex pathogens were rhinovirus/enterovirus codetected with Bordetella pertussis (17.8%). The information provided by the FilmArray had an impact on the prescription of antimicrobials, and there were differences in the rates of antibiotic prescriptions and anti-influenza prescriptions among patients. Conclusions. Use of the FilmArray by clinical staff was successfully implemented in the emergency department for the first time in China. The FilmArray has the potential for point-of-care testing in nonspecific settings.

scholarly journals Based on Transcriptome Sequencing: Clinicians Need to Pay Attention to Fever Caused by Common Respiratory Pathogens During the Global Outbreak of COVID-19

2021 ◽  
Author(s):  
Sheng Yin ◽  
Zeyou Wang ◽  
Min Wang ◽  
Wenlong Wang
Keyword(s):  
Public Health ◽  
Nucleic Acid ◽  
Influenza A ◽  
De Novo ◽  
Respiratory Pathogens ◽  
Public Health Decision ◽  
Significant Difference ◽  
B Virus ◽  
Health Decision ◽  
Observational Cohort

Abstract Objectives:During the COVID-19 pandemic, clinicians and public health decision-makers especially focus on fever patients. Other common pathogens that may cause fever are easily overlooked. We aimed to describe the pathogen infection and epidemic trend of non-SARS-CoV-2 occurring in hospitalized patients.Methods:An observational cohort study of 733 consecutive patients admitted to Hospital Clinic of the Second Xiangya Hospital for COVID-19. All samples of a pharyngeal swab from patients with fever have been tested for nucleic acid and immune antigens of SARS-CoV-2 and Influenza A/B virus. 649 fever patients have been tested for nucleic acid in ten respiratory pathogens. Macrotranscriptome sequencing was performed on 26 samples.Results:Of a total of 733 patients with fever, 2.05% patients had confirmed SARS-CoV-2 infections. Fever patients with common respiratory pathogens in fever patients was 8.78%. There is no integration phenomenon between SARS-Cov-2 and the human genome. SARS-CoV-2 positive samples will also be infected with other viruses, especially adenovirus. Macrotranscript analysis showed that there was no significant difference in the species and genus levels of pathogens between Covid-19 patients and other fever patients. The main pathways that affect human metabolism after SARS-Cov-2 infection are the Calvin-Benson-Bassham cycle, pyrimidine deoxyribonucleotides de novo biosynthesis I and D-galactose degradation V.Conclusions:Most patients have a fever caused by common respiratory pathogens. Clinicians still need to pay more attention to infections of common respiratory pathogens in addition to SARS-CoV-2. China's public health measures to stop the spread of the epidemic have proven effective.

scholarly journals A robust, hand-powered, instrument-free sample preparation system for point-of-care pathogen detection

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fei Zhao ◽  
Eun Yeong Lee ◽  
Geun Su Noh ◽  
Jaehyup Shin ◽  
Huifang Liu ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Pathogen Detection ◽  
Point Of Care ◽  
Low Cost ◽  
Sample Pretreatment ◽  
Sample Volume ◽  
Nucleic Acid Isolation ◽  
Point Of Care Diagnostics ◽  
Reaction Matrix

Abstract Here, we describe a simple, universal protocol for use in nucleic acid testing-based pathogen diagnostics, which requires only hand-powered sample preparation, including the processes of pathogen enrichment and nucleic acid isolation. The protocol uses low-cost amine-functionalized diatomaceous earth with a 1-μm Teflon filter as a reaction matrix in both stages of the process, using homobifunctional imidoesters. Using a simple syringe as a pump, the capture efficiency for a large sample volume (<50 mL) was enhanced by up to 98.3%, and the detection limit was 1 CFU/mL, 100-fold better than that of common commercial nucleic acid isolation kit. This protocol can also be combined with commercialized 96-well filter plates for robust sample preparation. Our proposed system is robust, simple, low-cost, universal, and rapid (taking <20 min), and it works regardless of the ambient environment and sample pretreatment, requiring no electricity or instruments. Its benefits include the simplicity of producing its components and its ease of operation, and it can be readily integrated with other assays for point-of-care diagnostics.

scholarly journals Comparison of the ID Now Influenza A & B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in Children

2020 ◽  
Vol 58 (3) ◽  
Author(s):  
Neena Kanwar ◽  
Jeffrey Michael ◽  
Kathryn Doran ◽  
Emily Montgomery ◽  
Rangaraj Selvarangan
Keyword(s):  
Nucleic Acid ◽  
Influenza A ◽  
Point Of Care ◽  
Virus Detection ◽  
Reference Method ◽  
Nucleic Acid Amplification ◽  
Molecular Assays ◽  
B Virus ◽  
Flu Virus ◽  
Xpert Assay

ABSTRACT Early diagnosis of influenza (Flu) is critical for patient management and infection control. The ID Now influenza A & B 2 (ID Now) assay (Abbott Laboratories), Cobas influenza A/B nucleic acid test (LIAT; Roche Molecular Systems, Inc.), and Xpert Xpress Flu (Xpert; Cepheid) are rapid, point-of-care molecular assays for Flu virus detection. The study aim was to compare the performances of these three commercially available Clinical Laboratory Improvement Amendments (CLIA)-waived Flu virus assays. We prospectively enrolled 201 children <18 years old from January to April 2018 and collected nasopharyngeal swab specimens in viral medium. Aliquots were frozen for testing on different diagnostic platforms, as per the manufacturers’ instructions. CDC Flu A/B PCR was used as a reference method to evaluate the performances of these three platforms. Among the 201 specimens tested, the CDC Flu A/B PCR assay detected Flu A/B virus in 107 samples (Flu A virus, 73 samples; Flu B virus, 36 samples; dual Flu A/B virus positive, 2 samples), while the ID Now virus detected 102 samples (Flu A virus, 69 samples; Flu B virus, 37 samples; dual Flu A/B virus positive, 4 samples; invalid rate, 1/201 [0.5%]), the LIAT detected 112 samples (Flu A virus, 74 samples; Flu B virus, 38 samples; invalid rate, 11/201 [5.5%]), and the Xpert assay detected 112 samples (Flu A virus, 76 samples; Flu B virus, 36 samples; invalid rate, 6/201 [3.0%]). The overall sensitivities for the ID Now assay, LIAT, and Xpert assay for Flu A virus detection (93.2%, 100%, and 100%, respectively) and Flu B virus detection (97.2%, 94.4%, and 91.7%, respectively) were comparable. The specificity for Flu A and B virus detection by all methods was >97%. These molecular assays had higher sensitivity than did a historical standard-of-care test from the BD Veritor antigen test (Flu A virus, 79.5%; Flu B virus, 66.7%).

scholarly journals Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza

Biosensors ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 47 ◽  
Author(s):  
Samantha J. Courtney ◽  
Zachary R. Stromberg ◽  
Jessica Z. Kubicek-Sutherland
Keyword(s):  
Influenza Virus ◽  
Nucleic Acid ◽  
Diagnostic Test ◽  
Influenza A ◽  
Direct Detection ◽  
Point Of Care ◽  
Influenza Viruses ◽  
Nucleic Acid Amplification ◽  
High Genetic Diversity ◽  
Mild Disease

Influenza virus poses a threat to global health by causing seasonal outbreaks as well as three pandemics in the 20th century. In humans, disease is primarily caused by influenza A and B viruses, while influenza C virus causes mild disease mostly in children. Influenza D is an emerging virus found in cattle and pigs. To mitigate the morbidity and mortality associated with influenza, rapid and accurate diagnostic tests need to be deployed. However, the high genetic diversity displayed by influenza viruses presents a challenge to the development of a robust diagnostic test. Nucleic acid-based tests are more accurate than rapid antigen tests for influenza and are therefore better candidates to be used in both diagnostic and surveillance applications. Here, we review various nucleic acid-based techniques that have been applied towards the detection of influenza viruses in order to evaluate their utility as both diagnostic and surveillance tools. We discuss both traditional as well as novel methods to detect influenza viruses by covering techniques that require nucleic acid amplification or direct detection of viral RNA as well as comparing advantages and limitations for each method. There has been substantial progress in the development of nucleic acid-based sensing techniques for the detection of influenza virus. However, there is still an urgent need for a rapid and reliable influenza diagnostic test that can be used at point-of-care in order to enhance responsiveness to both seasonal and pandemic influenza outbreaks.

scholarly journals Cleavable hairpin beacon-enhanced fluorescence detection of nucleic acid isothermal amplification and smartphone-based readout

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiong Ding ◽  
Kun Yin ◽  
Ziyue Li ◽  
Vikram Pandian ◽  
Joan A. Smyth ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Fluorescence Detection ◽  
Pathogen Detection ◽  
Point Of Care ◽  
Lamp Assay ◽  
Dna Amplification ◽  
Isothermal Amplification ◽  
Specific Method ◽  
Enhanced Fluorescence ◽  
Resource Limited

Abstract Fluorescence detection of nucleic acid isothermal amplification utilizing energy-transfer-tagged oligonucleotide probes provides a highly sensitive and specific method for pathogen detection. However, currently available probes suffer from relatively weak fluorescence signals and are not suitable for simple, affordable smartphone-based detection at the point of care. Here, we present a cleavable hairpin beacon (CHB)-enhanced fluorescence detection for isothermal amplification assay. The CHB probe is a single fluorophore-tagged hairpin oligonucleotide with five continuous ribonucleotides which can be cleaved by the ribonuclease to specifically initiate DNA amplification and generate strong fluorescence signals. By coupling with loop-mediated isothermal amplification (LAMP), the CHB probe could detect Borrelia burgdorferi (B. burgdorferi) recA gene with a sensitivity of 100 copies within 25 min and generated stronger specific fluorescence signals which were easily read and analysed by our programmed smartphone. Also, this CHB-enhanced LAMP (CHB-LAMP) assay was successfully demonstrated to detect B. burgdorferi DNA extracted from tick species, showing comparable results to real-time PCR assay. In addition, our CHB probe was compatible with other isothermal amplifications, such as isothermal multiple-self-matching-initiated amplification (IMSA). Therefore, CHB-enhanced fluorescence detection is anticipated to facilitate the development of simple, sensitive smartphone-based point-of-care pathogen diagnostics in resource-limited settings.

scholarly journals Detection of Coronaviruses Using RNA Toehold Switch Sensors

2021 ◽  
Vol 22 (4) ◽  
pp. 1772
Author(s):  
Soan Park ◽  
Jeong Wook Lee
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Test ◽  
Pathogen Detection ◽  
Point Of Care ◽  
Colorimetric Detection ◽  
Cross Reactivity ◽  
Amplification Method ◽  
Reactivity Test ◽  
Target Rna ◽  
Microbiome Profiling

A rapid, sensitive and simple point-of-care (POC) nucleic acid diagnostic test is needed to prevent spread of infectious diseases. Paper-based toehold reaction, a recently emerged colorimetric POC nucleic acid diagnostic test, has been widely used for pathogen detection and microbiome profiling. Here, we introduce an amplification method called reverse transcription loop-mediated amplification (RT-LAMP) prior to the toehold reaction and modify it to enable more sensitive and faster colorimetric detection of RNA viruses. We show that incorporating the modified RT-LAMP to the toehold reaction detects as few as 120 copies of coronavirus RNA in 70 min. Cross-reactivity test against other coronaviruses indicates this toehold reaction with the modified RT-LAMP is highly specific to the target RNA. Overall, the paper-based toehold switch sensors with the modified RT-LAMP allow fast, sensitive, specific and colorimetric coronavirus detection.

scholarly journals Coinfections with Respiratory Pathogens among COVID-19 Patients in Korea

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Kyoung Ho Roh ◽  
Yu Kyung Kim ◽  
Shin-Woo Kim ◽  
Eun-Rim Kang ◽  
Yong-Jin Yang ◽  
...  
Keyword(s):  
Influenza A ◽  
Pathogen Detection ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Diagnostic Value ◽  
Respiratory Pathogen ◽  
Nasopharyngeal Swab ◽  
Respiratory Pathogens ◽  
Oropharyngeal Swab ◽  
Syncytial Virus

The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) was investigated. Study subjects (N = 342) were retrospectively enrolled after being confirmed as SARS-CoV-2 positive, and their nasopharyngeal swab (NPS), oropharyngeal swab (OPS), and sputum specimens were restored for SARS-CoV-2 retesting and respiratory pathogen detection. The majority of the subjects (96.5%, N = 330) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens. Among the COVID-19 patients (N = 342), 7.9% (N = 27) and 0.9% (N = 3) were coinfected with respiratory viruses and Mycoplasma pneumoniae, respectively, yielding an 8.8% (N = 30) overall respiratory pathogen coinfection rate. Of the respiratory virus coinfection cases (N = 27), 92.6% (N = 25) were coinfected with a single respiratory virus and 7.4% (N = 2) with two viruses (metapneumovirus/adenovirus and rhinovirus/bocavirus). No triple coinfections of other respiratory viruses or bacteria with SARS-CoV-2 were detected. Respiratory viruses coinfected in the patients with COVID-19 were as follows: rhinovirus (N = 7, 2.1%), respiratory syncytial virus A and B (N = 6, 1.8%), non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.5%), metapneumovirus (N = 4, 1.2%), influenza A (N = 3, 0.9%), adenovirus (N = 3, 0.9%), and bocavirus (N = 1, 0.3%). In conclusion, the diagnostic value of utilizing NPS/OPS specimens is excellent, and, as the first report in Korea, coinfection with respiratory pathogens was detected at a rate of 8.8% in patients with COVID-19.

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