Detection of SARS-CoV-2 RNA in Upper Respiratory Swap Samples by Pooling Method

Tok, Yeşim Tuyji; Kuşkucu, Mert Ahmet; Sarıbal, Devrim; Yilmaz, Seda; Nohut, Okan Kadir; Balkan, İ̇lker İnanç; Aygün, Gökhan; Midilli, Kenan

doi:10.5152/balkanmedj.2021.21135

Cited by 4 publications

(4 citation statements)

References 15 publications

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“…The pooling of specimens for testing has been shown to be an effective approach to expand detection capacity, reduce per specimen costs, and shorten turnaround time (TAT). However, false-negative results are more likely due to specimen dilution after pooling [ 24 , 25 ]. Watkins et al suggested that the pooling ratio can be evaluated using the community positivity rate.…”

Section: Discussionmentioning

confidence: 99%

Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making

Yang

Hsu

Chan

et al. 2023

Life

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This study aimed to compare the SARS-CoV-2 nucleic acid detection results of the BD MAX™ System and other platforms to formulate an optimized laboratory verification process. The re-examination of 400 samples determined as positive by BD MAX™ indicated that the inconsistency rate between BD MAX™ and the other platforms was 65.8%; the inconsistency rate of single-gene-positive results was as high as 99.2%. A receiver operating characteristic curve was drawn for the relative light unit (RLU) values of samples positive for a single gene, and RLU 800 was used as the cutoff. After setting the retest standard as single-gene positive and RLU ≥ 800, the number of the 260 BD MAX™ single-gene positives that needed to be confirmed again was 36 (13.8%) and the number that could be directly reported as negative was 224 (86.2%). This verification process can shorten the reporting period and speed up the epidemic adjustment time and turnover rate of special wards, thereby improving SARS-CoV-2 detection efficiency and clinical decision-making.

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Section: Discussionmentioning

confidence: 99%

Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making

Yang

Hsu

Chan

et al. 2023

Life

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“…The study included all children who required HFNC upon admission or during follow-up. Patients were split into two groups: Group 1 included the patients who tested positive for SARS-CoV-2, group 2 included the patients who tested and found negative for SARS-CoV-2 COVID-19 infection was diagnosed using quantitative real-time reverse transcriptase-PCR positivity with detection of double targets, N-gene and ORF ab1 region at cycling threshold value under 35 cycles [SARS-CoV-2 (2019-nCoV) qPCR Detection Kit, Bio-Speedy, Turkey] [11]. The respiratory viruses were detected using a multiplex real-time PCR test (Bosphore Respiratory Pathogens Panel Kit V4,Anato lia Geneworks, Turkey) that is capable of identifying viral pathogens including in uenza viruses (in uenza A, pandemic H1N1 in uenza A, seasonal H1N1 in uenza A, and in uenza B), parain uenza viruses (PIVs; PIV-1, PIV-2, PIV-3, and PIV-4), human coronaviruses (CoV OC43, CoV NL63, CoV HKU1, and CoV 229E), RSV A/B, rhinovirus, hMPV, enterovirus, bocavirus, adenovirus, and parechovirus.…”

Section: Material-methodsmentioning

confidence: 99%

A comparison of the characteristics and outcomes of children with COVID-19 infections and children with other respiratory tract viral infections requiring high-flow nasal cannula

Besin,

Böncüoğlu,

Kıymet

et al. 2023

Preprint

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Background The aim of this single-center retrospective cohort study was to compare the clinical and laboratory differences, response, and outome of the patients requiring HFNC between two distinct groups, children with SARS-CoV-2 infection and children infected with other types of respiratory tract viruses during the COVID-19 pandemic. Methods This single-center cross-sectional study was conducted in the Pediatric Infectious Disease Ward and COVID-19 pademic wardç Data of the patients was collected from medical records including information on demographic characteristics (age, gender, and medical history); underlying diseases or co-morbidities, indications for HFNC and physical examination findings. If present laboratory examinations taken from the submissions were recorded. The indication and duration of HFNC, the length of hospital stay, admission or transfer to the PICU each patient’s stay in the hospital and if present the mortality rates by group were recorded.. Results During the study period a total of 171 patients were followed-up under HFNC. Among them, 8 patients were excluded from the study due to absence of arterial blood gas results before HFNC and 6 patients were excluded due to absence of PCR testing for COVID-19. At the final analysis, 157 patients under HFNC treatment were included including 22 COVID-19 PCR positive (group I ) and 135 COVID-19 PCR negative patients(Group II). Conclusions This study, patients with COVID-19 infections had longer durations of HFNC and hospital stay, in addition to high rate of transmission to PICU, suggesting a worser clinical outcome compared to infections with other viruses.

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“…The rate of invalid samples/total samples by RT-qPCR in the routine of our lab is 1.3%, and considering that ddPCR is more resistant to inhibitors, this percentage may be even lower. Nevertheless, this problem arises in every pool testing diagnostic strategy and recommendations are to pay special attention to adequate sample collection so that pre-analytical processes do not lead to major signal losses [36,44]. Then, if we take into consideration that pooling by ddPCR is thought for screening, this has an even less negative connotation.…”

Section: Plos Onementioning

confidence: 99%

Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR

et al. 2022

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Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.

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Detection of SARS-CoV-2 RNA in Upper Respiratory Swap Samples by Pooling Method

Cited by 4 publications

References 15 publications

Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making

Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making

A comparison of the characteristics and outcomes of children with COVID-19 infections and children with other respiratory tract viral infections requiring high-flow nasal cannula

Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR

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