scholarly journals Inclusion of cycle threshold (CT) values when reporting SARS-CoV-2 RT-PCR results improves clinical Interpretation in suspected and confirmed COVID-19

2021 ◽  
Author(s):  
Peter V. Coyle ◽  
Naema Hassan Al Molawi ◽  
Mohamed Ali Ben Hadj Kacem ◽  
Reham Awni El Kahlout ◽  
Einas Al Kuwari ◽  
...  
Keyword(s):  
Patient Management ◽  
Respiratory Infections ◽  
Routine Practice ◽  
Rt Pcr ◽  
Kappa Score ◽  
Clinical Interpretation ◽  
Cycle Threshold ◽  
Clearance Kinetics ◽  
Accepted Practice ◽  
Management Staff

IntroductionThe Cycle Threshold (CT) value in Real-time Polymerase Chain Reaction (RT-PCR) is where a target specific amplification signal becomes detectable and can infer viral load, risk of transmission and recovery in SARS-CoV-2 infections. Adoption into routine practice is however uncommon.Gap StatementThe lack of inclusion of CT values when reporting SARS-CoV-2 RT-PCR results in routine practice.AimTo use CT values when reporting SARS-CoV-2 RT-PCR results in Qatar to aid clinical interpretation and patient management.MethodologyRoutine CT values across 3 different RT-PCR platforms were reviewed for concordance at presentation and clearance in patients with COVID-19. An Indicative Threshold of CT 30 based on viral clearance kinetics categorized low and high CT values.ResultsThere was very high Correlation and Kappa Score agreement between the different gene targets in each platform (p<0.001). Using the Indicative Threshold it was possible to autoverify and add average CT values and append Interpretive Comments to all RT-PCR reports. The new reporting algorithm impacted immediately and safely on: physician interpretation of SARS-CoV-2 results; patient management; staff surveillance protocols; length of stay in quarantine; a redefinition of patient recovery.ConclusionIncorporation of CT values into routine practice is possible across different RT-PCR platforms and adds useful information for patient management. The use of an Indicative Threshold and interpretive comments improves clinical interpretation of the result and could be a model for reporting other respiratory infections. The current accepted practice of withholding CT values should be reviewed by the profession, accreditation bodies and regulators.

scholarly journals Preanalytical Issues and Cycle Threshold Values in SARS-CoV-2 Real-Time RT-PCR Testing: Should Test Results Include These?

ACS Omega ◽  
2021 ◽  
Author(s):  
Ilka Engelmann ◽  
Enagnon Kazali Alidjinou ◽  
Judith Ogiez ◽  
Quentin Pagneux ◽  
Sana Miloudi ◽  
...  
Keyword(s):  
Real Time ◽  
Test Results ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold

scholarly journals Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ramesh Yelagandula ◽  
◽  
Aleksandr Bykov ◽  
Alexander Vogt ◽  
Robert Heinen ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Infections ◽  
High Sensitivity ◽  
Cost Effective ◽  
Massively Parallel ◽  
Rt Pcr ◽  
Viral Spread ◽  
Saliva Analysis ◽  
Double Blinded ◽  
Generation Sequencing

AbstractThe COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing, a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic.

Đánh giá nồng độ lactate và procalcitonin ở bệnh nhân Covid-19

2022 ◽  
Author(s):  
Thanh Xuan Nguyen
Keyword(s):  
Serum Level ◽  
Respiratory Infections ◽  
Severe Pneumonia ◽  
Cross Sectional Study ◽  
Multiple Organ ◽  
High Rate ◽  
Rt Pcr ◽  
Wuhan City ◽  
Cross Sectional ◽  
The Relationship

TÓM TẮT Đặt vấn đề: Bệnh COVID-19 đa dạng từ không có triệu chứng đến có các triệu chứng nhẹ cho đến viêm phổi nặng, hội chứng suy hô hấp cấp tiến triển (ARDS), nhiễm khuẩn huyết suy đa tạng và tử vong. Người cao tuổi, người có bệnh mạn tính sẽ có nguy cơ diễn biến nặng nhiều hơn. Nghiên cứu này nhằm xác định nồng độ lactate và PCT ở những bệnh nhân Covid-19 và xét mối liên quan giữa lactate và PCT trên bệnh nhân Covid-19. Đối tượng và phương pháp: Nghiên cứu mô tả cắt ngang trên 126 bệnh nhân được chẩn đoán nhiễm Sars-Cov-2 bằng xét nghiệm RT PCR. Kết quả: Tuổi trung bình 55,98 ± 17,1 tuổi (4 - 98 tuổi). Bệnh nhân > 60 tuổi chiếm tỉ lệ cao nhất (42,8%). Trung vị PCT: 3,6 (95%CI:3,21 - 3,75) ng/ml; trung vị lactate 1,5 (95%CI:1,21 - 1,91) mmol/L; lactate có tương quan thuận và yếu với procalcitonin với r = 0,241; p < 0,001. Nồng độ procalcitonin > 0,1 ng/ml; lactate > 2 mmol/l ở bệnh nhân Covid-19 chiếm tỷ lệ cao với 89,7% và 39,7%. Kết luận: Chỉ điểm procalcitonin, lactate tăng cao ở bệnh nhân Covid-19. ABSTRACT ASSESSMENT OF SERUM LEVEL OF LACTATE AND PROCALCITONIN IN COVID-19 PATIENTS Background: Sars-CoV-2 has been identified as the cause of acute respiratory infections in Wuhan city, Hubei province, China, and has since spread worldwide. Sars-CoV-2 is capable of aerosol transmission in enclosed, crowded, and poorly ventilated spaces. COVID-19 illness ranges from asymptomatic to mild symptoms to severe pneumonia, acute respiratory distress syndrome (ARDS), sepsis, multiple organ failure, and death. This study aims to determine lactate and PCT levels in Covid-19 patients and examine the relationship between lactate and PCT in Covid-19 patients. Methods: A cross-sectional study was performed on 126 patients diagnosed with Sars-Cov-2 infection by RT-PCR. Results: Mean age was 55.98 ± 17.1 years (range: 4-98 years). Patients more than 60 years old were accounted for the highest rate (42.8%). Median PCT: 3.6 (95%CI:3.21 - 3.75) ng/ml; median lactate 1.5 (95%CI:1.21 - 1,91) mmol/L; lactate has a positive and weak correlation with procalcitonin with r = 0.241; p < 0.001. Procalcitonin concentration > 0.1 ng/ml; lactate > 2 mmol/l in patients with Covid-19 accounted for a high rate with 89.7% and 39.7%. Conclusion: Serum level of procalcitonin and lactate raise highly in Covid-19 patients. Keywords: Covid-19, procalcitonin, lactate.

scholarly journals Cycle Threshold Values in the Context of Multiple RT-PCR Testing for SARS-CoV-2

2021 ◽  
Vol Volume 14 ◽  
pp. 1311-1317
Author(s):  
Daniel Romero-Alvarez ◽  
Daniel Garzon-Chavez ◽  
Franklin Espinosa ◽  
Edison Ligña ◽  
Enrique Teran ◽  
...  
Keyword(s):  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold

scholarly journals Duration of viral detection in throat and rectum of a patient with COVID-19

2020 ◽  
Author(s):  
Le Van Tan ◽  
Nghiem My Ngoc ◽  
Bui Thi Ton That ◽  
Le Thi Tam Uyen ◽  
Nguyen Thi Thu Hong ◽  
...  
Keyword(s):  
Infection Control ◽  
Patient Management ◽  
Ho Chi Minh City ◽  
Rt Pcr ◽  
Viral Detection ◽  
Oral Transmission ◽  
Viral Shedding ◽  
Clinical Recovery ◽  
Global Pandemic ◽  
Rapid Spread

AbstractThe rapid spread of coronavirus disease 2019 (COVID-19) raises concern about a global pandemic. Knowledge about the duration of viral shedding remains important for patient management and infection control. We report the duration of viral detection in throat and rectum of a COVID-19 patient treated at the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam. Despite clinical recovery, SARS-CoV-2 RNA remained detectable by real time RT-PCR in throat and rectal swabs until day 11 and 18 of hospitalization, respectively. Because live SARS-CoV-2 has been successfully isolated from a stool sample from a COVID-19 patient in China, the results demonstrate that COVID-19 patients may remain infectious for long periods, and fecal-oral transmission may be possible. Therefore, our finding has important implications for infection control.

scholarly journals Human Rhinovirus Molecular Epidemiology and Genotyping in Iranian Military Trainees with Acute Respiratory Symptoms

2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Fahimeh Safarnezhad Tameshkel ◽  
Ali Salimi Jeda ◽  
Ahmad Tavakoli ◽  
Mohammad Hadi Karbalaie Niya ◽  
Morteza Izadi ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Clinical Symptoms ◽  
Respiratory Infections ◽  
Direct Sequencing ◽  
Human Rhinovirus ◽  
P Value ◽  
Rt Pcr ◽  
Respiratory Problems ◽  
Pcr Products ◽  
Tract Infections

Background: Human rhinovirus (HRV) is still the most prevalent viral infection in humans and a significant cause of acute respiratory tract infections (ARTIs) in many communities, including military personnel undergoing basic training. Objectives: In this research, we assessed the molecular epidemiology, genotyping, and phylogenetic classification of HRVs in Iranian military trainees with respiratory infections (RI). Methods: For HRV identification and genotyping, respiratory specimens were obtained, and RT-PCR was conducted for genotyping and phylogenetic analysis of HRV utilizing primers for the 5-UTR region. Results: Among 400 Iranian military trainees (average age of 21 ± 4 years, the range of 18 - 57 years) with respiratory infections, HRV was detected in 29 patients (7%) using RT-PCR. The direct sequencing of PCR products from 10 specimens showed that the incidence of type A (n = 5, 50%) was higher than that of type B (n = 4, 40%) and type C (n = 1, 10%). There were no significant associations between HRV and respiratory and clinical symptoms, blood group, and indoor or outdoor conditions (P-value > 0.05). Conclusions: This research was the first to record HRV as a significant cause of respiratory problems among military trainees in Iran, with a frequency of 7%. The most prevalent genotype was HRV-A, which may be applicable in epidemiological and clinical studies, as well as vaccination plans.

scholarly journals Distribution of SARS-CoV-2 PCR Cycle Threshold Values Provide Practical Insight Into Overall and Target-Specific Sensitivity Among Symptomatic Patients

2020 ◽  
Vol 154 (4) ◽  
pp. 479-485 ◽  
Author(s):  
Blake W Buchan ◽  
Jessica S Hoff ◽  
Cameron G Gmehlin ◽  
Adriana Perez ◽  
Matthew L Faron ◽  
...  
Keyword(s):  
Viral Load ◽  
Limit Of Detection ◽  
False Negative ◽  
Age Group ◽  
Rt Pcr ◽  
Patient Age ◽  
Cycle Threshold ◽  
Negative Results ◽  
Patient Âgé ◽  
False Negative Results

Abstract Objectives We examined the distribution of reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values obtained from symptomatic patients being evaluated for coronavirus disease 2019 (COVID-19) to determine the proportion of specimens containing a viral load near the assay limit of detection (LoD) to gain practical insight to the risk of false-negative results. We also examined the relationship between CT value and patient age to determine any age-dependent difference in viral load or test sensitivity. Methods We collected CT values obtained from the cobas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay corresponding to 1,213 combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals that were reported as positive or presumptive positive for SARS-CoV-2. CT values were stratified by SARS-CoV target and patient age group. Results In total, 93.3% to 98.4% of specimens demonstrated CT values greater than 3× the assay LoD, at which point false-negative results would not be expected. The mean of CT values between age groups was statistically equivalent with the exception of patients in age group 80 to 89 years, which demonstrated slightly lower CTs. Conclusions Based on the distribution of observed CT values, including the small proportion of specimens with values near the assay LoD, there is a low risk of false-negative RT-PCR results in combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals.

scholarly journals SARS-CoV-2 y RT-PCR en pacientes asintomáticos: resultados de una cohorte de trabajadores del Aeropuerto Internacional El Dorado de Bogotá, 2020

Biomédica ◽  
2020 ◽  
Vol 40 (Supl. 2) ◽  
pp. 166-172 ◽  
Author(s):  
Jeadran Malagón-Rojas ◽  
Claudia Gómez-Rendón ◽  
Eliana L. Parra ◽  
Julia Almentero ◽  
Ruth Palma ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Cycle Threshold ◽  
El Dorado

Introducción. La pandemia de COVID-19 ha ocasionado cerca de 25 millones de casos en el mundo. Se ha descrito que los pacientes asintomáticos pueden ser fuentes de transmisión. Sin embargo, es difícil detectarlos y no es claro su papel en la dinámica de transmisión del virus, lo que obstaculiza la implementación de estrategias para la prevención.Objetivo. Describir el comportamiento de la infección asintomática por SARS-CoV-2 en una cohorte de trabajadores del Aeropuerto Internacional El Dorado “Luis Carlos Galán Sarmiento” de Bogotá, Colombia.Materiales y métodos. Se diseñó una cohorte prospectiva de trabajadores del Aeropuerto El Dorado. El seguimiento se inició en junio de 2020 con una encuesta a cada trabajador para caracterizar sus condiciones de salud y trabajo. Cada 21 días se tomó una muestra de hisopado nasofaríngeo para detectar la presencia del SARS-CoV-2 mediante reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR). Se analizó el comportamiento del umbral del ciclo (cycle threshold) de los genes ORF1ab y N según el día de seguimiento. Resultados. En los primeros tres seguimientos de la cohorte se encontró una incidencia de la infección por SARS-CoV-2 del 16,51 %. La proporción de contactos positivos fue del 14,08 %. La mediana del umbral del ciclo fue de 33,53.Conclusión. Se determinaron las características de la infección asintomática por el SARSCoV-2 en una cohorte de trabajadores. La detección de infectados asintomáticos sigue siendo un reto para los sistemas de vigilancia epidemiológica.

scholarly journals Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources

2020 ◽  
Vol 153 (6) ◽  
pp. 715-718 ◽  
Author(s):  
Baha Abdalhamid ◽  
Christopher R Bilder ◽  
Emily L McCutchen ◽  
Steven H Hinrichs ◽  
Scott A Koepsell ◽  
...  
Keyword(s):  
Incidence Rate ◽  
Group Testing ◽  
Viral Rna ◽  
Optimal Parameters ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Web Based ◽  
Negative Patient ◽  
Cycle Threshold ◽  
Unselected Group

Abstract Objectives To establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2. Methods The most efficient pool size was determined to be five specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 µL from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 µL each) for a total volume of 250 µL. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12 pools. Results All 25 pools were positive with cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that 2 pools were positive followed by identification of 2 individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions. Conclusions When the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.

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