scholarly journals The performance of RT-PCR compared with a rapid serological assay for acute dengue fever in a diagnostic laboratory

2006 ◽  
Vol 100 (2) ◽  
pp. 142-148 ◽  
Author(s):  
Timothy M. Barkham ◽  
Youne Kow Chung ◽  
Kin Fai Tang ◽  
Eng Eong Ooi
Keyword(s):  
Dengue Fever ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
Serological Assay

scholarly journals Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency

2021 ◽  
Vol 11 ◽  
Author(s):  
Linda Mueller ◽  
Valentin Scherz ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Turnaround Time ◽  
Quality Monitoring ◽  
Rt Pcr ◽  
Monitoring Tool ◽  
Diagnostic Laboratory ◽  
Important Health ◽  
Polymerase Chain ◽  
Automated Processes ◽  
Regulatory Decisions ◽  
Case Validation

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

scholarly journals APPLICATION OF ELISA-IGM (MAC-ELISA) FOR DETERMINING ETIOLOGICAL LINK VIRUS TYPES IN CONCRET CASES OF THE DISEASE

2017 ◽  
Vol 22 (3) ◽  
pp. 116-121
Author(s):  
Yuliya A. Akinshina ◽  
V. F Larichev ◽  
M. A Sayfullin ◽  
S. G Mardanly ◽  
A. M Butenko
Keyword(s):  
Dengue Fever ◽  
Rt Pcr ◽  
Serum Samples ◽  
Dengue Viruses ◽  
Etiological Role ◽  
Igm Elisa ◽  
Pcr Method

105 sera from 101 patients with a confirmed diagnosis of dengue fever (LD) were examined using monospecific ELISA-IgM test. Monospecific results were observed in 39 samples (37.1%). 27 sample of them were taken during the first 7 days of the disease. In those systems were examined 23 serum samples of 23 patients, in which etiological role of one of the four dengue viruses was been established by the RT-PCR method. In this case, the coincidence-IgM ELISA results and the RT-PCR took place in 14 sera (60.9%).

scholarly journals Development of a Mobile Laboratory for Sudden Onset Disasters

2019 ◽  
Vol 34 (s1) ◽  
pp. s24-s24
Author(s):  
Ian Marr ◽  
Dianne Stephens ◽  
Rob Baird ◽  
Josh Francis ◽  
David Read ◽  
...  
Keyword(s):  
Sudden Onset ◽  
Clinical Diagnostics ◽  
Cold Chain ◽  
Major Advance ◽  
Mobile Laboratory ◽  
Rt Pcr ◽  
Field Hospital ◽  
Diagnostic Laboratory ◽  
Pcr Multiplex ◽  
Timor Leste

Introduction:Clinical diagnostics in sudden-onset disasters (SOD) has historically been limited. With poor supply routes, lack of a cold chain, and challenging environmental conditions, many diagnostic platforms are unsuitable.Aim:We set out to design, implement, and evaluate a mobile diagnostic laboratory accompanying a type II emergency medical team (EMT) field hospital.Methods:Available diagnostic platforms were reviewed and selected against infield need. Platforms included HemoCue301/WBC DIFF, i-STAT, BioFire multiplex RT-PCR, Olympus BX53 microscopy, ABO/Rh Grouping, and specific rapid diagnostic tests (RDT). This equipment was trialed in Katherine, Australia and Dili, Timor-Leste.Results:During the initial deployment, validation of FilmArray rt-PCR multiplex tests was successful on blood culture, gastrointestinal, and respiratory panels. HemoCue301 (n = 20) haemoglobin values were compared on Sysmex XN 550 (r = 0.94). Analysis of HemoCue WBC DIFF samples had some variation when compared to Sysmex XN 550, (neutrophils r = 0.88, lymphocytes r = 0.49, monocytes r = 0.16, eosinophils r = 0.70, basophils r = 0.16). i-STAT showed non-significant differences for CHEM4 (n=10), CG8 (n = 10), and TnI (n = 5) against Vitros 250. A further trial of BioFire rt-PCR testing in Dili, Timor-Leste diagnosed 117 causative pathogens on 168 FilmArray test cartridges.Discussion:This mobile laboratory represents a major advance in SOD. Setup of the service was quick (<24hr) and transport to site rapidly. Training was simple and performance consistent. Future deployment in fragmented health systems after sudden onset disasters with EMT2 will now allow broader diagnostics.

scholarly journals Computer-aided medical microbiology monitoring tool: a strategy to adapt to the SARS-CoV-2 epidemic and that highlights RT-PCR consistency

2020 ◽  
Author(s):  
Linda Mueller ◽  
Valentin Scherz ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Turnaround Time ◽  
Quality Monitoring ◽  
Rt Pcr ◽  
Monitoring Tool ◽  
Diagnostic Laboratory ◽  
Health Authorities ◽  
Important Health ◽  
Public Health Authorities ◽  
Automated Processes ◽  
Case Validation

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR, with up to 1,007 tests per day. To maintain a rapid turnaround time to support patient management and public health authorities' decisions, we moved from a case-by-case validation of RT-PCR to an automated validation and immediate transmission of the results to clinicians. To maintain high quality and to track possible aberrant results, we developed a quality-monitoring tool based on a homemade algorithm coded in R. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results corresponding to 30,198 patients. Patients tested several times led to 4,939 pairwise comparisons; 88% concordant and 12% discrepant. Among the 573 discrepancies, 428 were automatically solved by the algorithm. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to "Clinical evolution", 27.9% to "Preanalytical" problems, and 25.3% to "Stochastic". Finally, 11 discrepant results could not be explained, including 8 received from external partners for which clinical data were not available. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable TAT. This work highlighted the high RT-PCR consistency for the detection of SARS-CoV-2 and the importance of automated processes to handle a huge number of samples while preserving quality.

scholarly journals Typing of Dengue Viruses in Clinical Specimens and Mosquitoes by Single-Tube Multiplex Reverse Transcriptase PCR

1998 ◽  
Vol 36 (9) ◽  
pp. 2634-2639 ◽  
Author(s):  
Eva Harris ◽  
T. Guy Roberts ◽  
Leila Smith ◽  
John Selle ◽  
Laura D. Kramer ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Dengue Fever ◽  
Internal Control ◽  
Extraction Procedure ◽  
Rna Degradation ◽  
Viral Rna ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Single Tube ◽  
Dengue Viruses

In recent years, dengue viruses (serotypes 1 to 4) have spread throughout tropical regions worldwide. In many places, multiple dengue virus serotypes are circulating concurrently, which may increase the risk for the more severe form of the disease, dengue hemorrhagic fever. For the control and prevention of dengue fever, it is important to rapidly detect and type the virus in clinical samples and mosquitoes. Assays based on reverse transcriptase (RT) PCR (RT-PCR) amplification of dengue viral RNA can offer a rapid, sensitive, and specific approach to the typing of dengue viruses. We have reduced a two-step nested RT-PCR protocol to a single-tube reaction with sensitivity equivalent to that of the two-step protocol (1 to 50 PFU) in order to maximize simplicity and minimize the risk of sample cross-contamination. This assay was also optimized for use with a thermostable RT-polymerase. We designed a plasmid-based internal control that produces a uniquely sized product and can be used to control for both reverse transcription or amplification steps without the risk of generating false-positive results. This single-tube RT-PCR procedure was used to type dengue viruses during the 1995 and 1997-1998 outbreaks in Nicaragua. In addition, an extraction procedure that permits the sensitive detection of viral RNA in pools of up to 50 mosquitoes without PCR inhibition or RNA degradation was developed. This assay should serve as a practical tool for use in countries where dengue fever is endemic, in conjunction with classical methods for surveillance and epidemiology of dengue viruses.

scholarly journals An automated Dashboard to improve laboratory COVID-19 diagnostics management

2021 ◽  
Author(s):  
Emma Maury ◽  
Marc-Olivier Boldi ◽  
Gilbert Greub ◽  
Valerie Chavez ◽  
Katia Jaton ◽  
...  
Keyword(s):  
Influenza A ◽  
Data Extraction ◽  
Resource Planning ◽  
Added Value ◽  
University Hospital ◽  
Molecular Diagnostic ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
R Shiny ◽  
And Gender

Background: In response to the CoVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. Thanks to our automated molecular diagnostic platform, more than 140 000 SARS-CoV-2 RT-PCR tests were achieved over 12 months, with peaks higher than 1 500 daily tests. A dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses - SARS-CoV-2, influenza A and B and RSV - from our laboratory information system (LIS), was automated. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Information is updated every 4 hours. Results: The dashboard is organized into three main parts. The Filter page presents all the KPIs, divided into five sections: i) general and gender-related indicators, ii) number of tests and positivity rate, iii) cycle threshold and viral load, iv) test durations, and v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, or a requester for instance. The Comparison page allows a custom charting of all the available variables, which represents more than 182 combinations. The Data page gives the user access to the raw data in table format, with the possibility of filtering, allowing for a deeper analysis and data download in Excel format. Conclusions: The dashboard, that gives a rapid access to a huge number of up-to-date information, represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management. The dashboard represent an added value for diagnosric laboratories during a pandemic, where rapid and efficient adaptation is mandatory.

scholarly journals An Automated Dashboard to Improve Laboratory COVID-19 Diagnostics Management

2021 ◽  
Vol 3 ◽  
Author(s):  
Emma Maury ◽  
Marc-Olivier Boldi ◽  
Gilbert Greub ◽  
Valérie Chavez ◽  
Katia Jaton ◽  
...  
Keyword(s):  
Influenza A ◽  
Data Extraction ◽  
Resource Planning ◽  
Test Reliability ◽  
University Hospital ◽  
Sample Type ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
And Gender ◽  
User Friendly

Background: In response to the COVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. More than 148,000 tests have been performed over 12 months, which represents about 405 tests per day, with peaks to more than 1,500 tests per days during the second wave. This was only possible thanks to automation and digitalization, to allow high throughput, acceptable time to results and to maintain test reliability. An automated dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management.Methods: RT-PCR data extraction of four respiratory viruses—SARS-CoV-2, influenza A and B and RSV—from our laboratory information system (LIS), was automated. This included age, gender, test result, RT-PCR instrument, sample type, reception time, requester, and hospitalization status etc. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny).Results: The dashboard is organized into three main parts. The “Filter” page presents all the KPIs, divided into five sections: (i) general and gender-related indicators, (ii) number of tests and positivity rate, (iii) cycle threshold and viral load, (iv) test durations, and (v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, an age range or a requester. The “Comparison” page allows a custom charting of all the available variables, which represents more than 182 combination. The “Data” page, gives the user an access to the raw data in tables format, with possibility of filtering, allowing for a deeper analysis and data download. Informations are updated every 4 h.Conclusions: By giving a rapid access to a huge number of up-to-date information, represented using the most relevant visualization types, without the burden of timely data extraction and analysis, the dashboard represents a reliable and user-friendly tool for operational laboratory management. The dashboard represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management.

scholarly journals COVID-19 and Dengue infection in Bangladesh: a case of coinfection where hemoptysis as first presentation

2021 ◽  
Author(s):  
Mohammad Ashraful Amin ◽  
Md. Taufiqul Islam ◽  
Ishtiakul Islam Khan ◽  
Zahid Hasan Khan ◽  
Firdausi Qadri ◽  
...  
Keyword(s):  
Dengue Fever ◽  
Sore Throat ◽  
Dengue Infection ◽  
High Grade ◽  
Rt Pcr ◽  
High Grade Fever

Bangladesh recently faced large outbreaks of both COVID-19 and Dengue fever. A 28-year-old woman suffered from symptoms including hemoptysis as first presentation followed by high-grade fever, sore throat, and fatigue. SARS-CoV-2 was confirmed by RT-PCR and also diagnosed dengue later on.COVID-19 and dengue fever could be a harmful combination.

scholarly journals Improved performance of saliva for the detection of the B.1.351 variant in South Africa

2021 ◽  
Author(s):  
Chun Yat Chu ◽  
Gert Marais ◽  
Christoffel Opperman ◽  
Deelan Doolabh ◽  
Arash Iranzadeh ◽  
...  
Keyword(s):  
South Africa ◽  
Marked Improvement ◽  
Molecular Detection ◽  
Cape Town ◽  
The Novel ◽  
Wild Type ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
Percent Agreement ◽  
Improved Performance

Assessment of the unknown performance of saliva for the detection of the novel SARS-CoV-2 variant of concern (VOC) B.1.351 (501Y.V2) lineage is essential as saliva has been shown to be an equivalent, less invasive and a less costly alternative to nasopharyngeal swabs for the molecular detection of SARS-CoV-2 infection in pre-variant studies. Between 1st August 2020 and 16th January 2021, we enrolled 410 eligible ambulatory participants who presented to Groote Schuur Hospital (GSH) in Cape Town, South Africa for SARS-CoV-2 testing. Of these, 300 were enrolled prior to, and 110 after, the initial detection and replacement of wild-type by the B.1.351 variant. All participants provided a supervised self-collected mid-turbinate (MT) and saliva (SA) swab, in addition to the standard HCW collected NP swab which were all tested by RT-PCR in an accredited diagnostic laboratory. Positive percent agreement to NP swab for SA swabs pre- and post-variant were 51.5% and 72.5% respectively while these values for MT swabs were 75.8% and 77.5%. The negative percent agreement for all swab types during all periods was >98%. The basis for this marked improvement of SA swabs as a diagnostic sample for B.1.351 virus is still being investigated.

scholarly journals Detection of Bovine Torovirus and other Enteric Pathogens in Feces from Diarrhea Cases in Cattle

2003 ◽  
Vol 15 (3) ◽  
pp. 205-212 ◽  
Author(s):  
Armando E. Hoet ◽  
Paul R. Nielsen ◽  
Mustafa Hasoksuz ◽  
Christopher Thomas ◽  
Thomas E. Wittum ◽  
...  
Keyword(s):  
Etiologic Agent ◽  
Enteric Pathogens ◽  
Clinical Samples ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Salmonella Spp ◽  
Diagnostic Laboratory ◽  
Fecal Samples ◽  
Polymerase Chain

The objectives of this study were to determine the prevalence of bovine torovirus (BoTV) in bovine fecal samples from diarrhea cases submitted to the Ohio Animal Disease Diagnostic Laboratory (ADDL) and to assess if a relationship exists between BoTV and the other enteric pathogens detected. From November 1999 to May 2001, 259 specimens from 53 calves (≤6 months old), 27 young adults (≤2 years), 125 adults (≥2 years), and 54 animals of unknown age were examined by an antigen-capture enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) assay developed to detect BoTV Testing for other enteric pathogens was performed by ADDL, and the results were analyzed with the BoTV data. The BoTV was detected using ELISA or RT-PCR in 9.7% (25/259) of the clinical samples, 56% (14/25) of which were from calves ( P < 0.001) representing 26.4% (14/53) of the calves tested. Of the BoTV-positive calves, 71% (10/14) were less than 3 weeks of age. In 11/25 positive specimens, BoTV was the only pathogen detected among those examined. Other enteric organisms detected alone or in combination with BoTV in calf samples were rotavirus, coronavirus, Salmonella spp., Cryptosporidium spp., and Giardia spp.; but no consistent association between BoTV and these organisms was observed. In summary, BoTV was detected in fecal samples from cattle with diarrhea, principally in young calves less than 3 weeks of age. Future studies of infectious diarrhea in cattle should also include assays for this etiologic agent.

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