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Article ; Online: Pooling of nasopharyngeal swab specimens for SARS-CoV-2 detection by RT-PCR.

Torres, Ignacio / Albert, Eliseo / Navarro, David

2020 Volume 92, Issue 11, Page(s) 2306–2307

MeSH term(s)	COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing/methods ; Humans ; Nasopharynx/virology ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Specimen Handling/methods
Keywords	covid19
Language	English
Publishing date	2020-06-02
Publishing country	United States
Document type	Letter
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25971
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Article ; Online: Pooling of nasopharyngeal swab specimens for SARS‐CoV‐2 detection by RT‐PCR

Torres, Ignacio / Albert, Eliseo / Navarro, David

Journal of Medical Virology

2020 Volume 92, Issue 11, Page(s) 2306–2307

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25971
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR

Torres, Ignacio / Albert, Eliseo / Navarro, David

Abstract: ... for RT-PCR has been effectively used to detect community transmission of SARS CoV-2 ... of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E ... Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy ...

Abstract	Systematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.04.22.20075598
Database	COVID19

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Article ; Online: Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR

Torres, Ignacio / Albert, Eliseo / Navarro, David

medRxiv

Abstract	Systematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding C<sub>T</sub> <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying C<sub>Ts</sub> > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.
Keywords	covid19
Language	English
Publishing date	2020-04-25
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.04.22.20075598
Database	COVID19

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Article: Pooling Strategy for Detection of SARS-CoV-2 RNA by Real-Time RT-PCR: Comparison of Pooling 5 and 10 Samples.

Alacam, Sema / Bakir, Ayfer

Clinical laboratory

2023 Volume 69, Issue 8

Abstract: ... groups according to their Ct values as high, medium, and low viral load. SARS-CoV-2 RNA in nasopharyngeal ... strategies that allow mass screening of SARS-CoV-2 can contribute to early detection of patients at high risk ... Background: We evaluated whether it was appropriate to screen SARS-CoV-2 in sample pools of 5 and ...

Abstract	Background: We evaluated whether it was appropriate to screen SARS-CoV-2 in sample pools of 5 and 10. This study was aimed to evaluate whether the pooling strategy would be an appropriate strategy for SARS-CoV-2 screening. Methods: In the study, 5 and 10 sample pools were formed using 720 nasopharyngeal swab samples, of which 72 were positive, and 648 were negative. The samples were analyzed in three groups according to their Ct values as high, medium, and low viral load. SARS-CoV-2 RNA in nasopharyngeal swab samples was detected by the real-time PCR method on the Bio-Rad platform. Results: The sensitivity of 5-sample pooling was 77.8%, and the sensitivity of 10-sample pooling was 75%. The false-negative rate was 22.2% in 5 sample poolings and 25% in 10 sample poolings. Out of the samples with medium and high viral loads, none of the positive samples were lost in either pool. In pools containing both 5 samples and 10 samples, the individual mean Ct values of the samples detected as false-negative were significantly higher (low viral load) than those of the other samples (p < 0.001). Conclusions: In this study, 5 and 10 pooling seems useful in detecting patients with medium and high viral loads. Pooling strategies that allow mass screening of SARS-CoV-2 can contribute to early detection of patients at high risk of SARS-CoV-2 transmission in low prevalence areas, as well as timely public health interventions.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; COVID-19 Testing ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction ; Specimen Handling/methods ; Sensitivity and Specificity
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-08-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1307629-2
ISSN	1433-6510 ; 0941-2131
ISSN	1433-6510 ; 0941-2131
DOI	10.7754/Clin.Lab.2023.220830
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Article ; Online: Pooling Nasopharyngeal Swab Specimens to Increase Testing Capacity for SARS-CoV-2.

Anderson, Cole / Castillo, Fritz / Koenig, Michael / Managbanag, Jim-Ray

Medical journal (Fort Sam Houston, Tex.)

2021 , Issue PB 8-21-01/02/03, Page(s) 8–11

Abstract: ... Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by reverse transcription ... polymerase chain reaction (RT-PCR) in upper and lower respiratory specimens. While sensitive and specific ... The recent emergence of SARS-CoV-2 has led to a global pandemic of unprecedented proportions ...

Abstract	The recent emergence of SARS-CoV-2 has led to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR) in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing ; Humans ; Nasopharynx/virology ; RNA, Viral/isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity ; Specimen Handling
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-03-05
Document type	Journal Article
ISSN	2694-3611
ISSN (online)	2694-3611
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR.

Handous, Imene / Hannachi, Naila / Marzouk, Manel / Hazgui, Olfa / Bouafif Ep Ben Alaya, Nissaf / Boukadida, Jalel

Biological procedures online

2021 Volume 23, Issue 1, Page(s) 19

Abstract: Background: The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce ... 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 ... nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and ...

Abstract	Background: The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. Results: In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean C Conclusions: In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered.
Language	English
Publishing date	2021-09-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2027823-8
ISSN	1480-9222
ISSN	1480-9222
DOI	10.1186/s12575-021-00156-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test.

Sun, Qing / Li, Jonathan / Ren, Hui / Pastor, Larry / Loginova, Yulia / Madej, Roberta / Taylor, Kristopher / Wong, Joseph K / Zhang, Zhao / Zhang, Aiguo / Lu, Chuanyi M / Sha, Michael Y

PloS one

2021 Volume 16, Issue 2, Page(s) e0243183

Abstract: ... SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) or ... to that of NPS-based testing. Pooling of saliva specimens for SARS-CoV-2 detection is feasible. Saliva based and ... of QuantiVirus™ SARS-CoV-2 test using saliva as the testing specimens with or without pooling.: Methods ...

Abstract	Background: Sensitive and high throughput molecular detection assays are essential during the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) or oropharyngeal swab (OPS) specimens collected from suspected individuals. However, using NPS or OPS as specimens has apparent drawbacks, e.g. the collection procedures for NPS or OPS specimens can be uncomfortable to some people and may cause sneezing and coughing which in turn generate droplets and/or aerosol particles that are of risk to healthcare workers, requiring heavy use of personal protective equipment. There have been recent studies indicating that self-collected saliva specimens can be used for molecular detection of SARS-CoV-2 and provides more comfort and ease of use for the patients. Here we report the performance of QuantiVirus™ SARS-CoV-2 test using saliva as the testing specimens with or without pooling. Methods: Development and validation studies were conducted following FDA-EUA and molecular assay validation guidelines. Using SeraCare Accuplex SARS-CoV-2 reference panel, the limit of detection (LOD) and clinical performance studies were performed with the QuantiVirus™ SARS-CoV-2 test. For clinical evaluation, 85 known positive and 90 known negative clinical NPS samples were tested. Additionally, twenty paired NPS and saliva samples collected from recovering COVID-19 patients were tested and the results were further compared to that of the Abbott m2000 SARS-CoV-2 PCR assay. Results of community collected 389 saliva samples for COVID-19 screening by QuantiVirus™ SARS-CoV-2 test were also obtained and analyzed. Additionally, testing of pooled saliva samples was evaluated. Results: The LOD for the QuantiVirus™ SARS-CoV-2 test was confirmed to be 100-200 copies/mL. The clinical performance studies using contrived saliva samples indicated that the positive percentage agreement (PPA) of the QuantiVirus™ SARS-CoV-2 test is 100% at 1xLOD, 1.5xLOD and 2.5xLOD. No cross-reactivity was observed for the QuantiVirus™ SARS-CoV-2 test with common respiratory pathogens. Testing of clinical samples showed a positive percentage agreement (PPA) of 100% (95% CI: 94.6% to 100%) and a negative percentage agreement (NPA) of 98.9% (95% CI: 93.1% to 99.9%). QuantiVirus™ SARS CoV-2 test had 80% concordance rate and no significant difference (p = 0.13) between paired saliva and NPS specimens by Wilcoxon matched pairs signed rank test. Positive test rate was 1.79% for 389 saliva specimens collected from local communities for COVID-19 screening. Preliminary data showed that saliva sample pooling up to 6 samples (1:6 pooling) for SARS-CoV-2 detection is feasible (sensitivity 94.8% and specificity 100%). Conclusion: The studies demonstrated that the QuantiVirus™ SARS-CoV-2 test has a LOD of 200 copies/mL in contrived saliva samples. The clinical performance of saliva-based testing is comparable to that of NPS-based testing. Pooling of saliva specimens for SARS-CoV-2 detection is feasible. Saliva based and high-throughput QuantiVirus™ SARS-CoV-2 test offers a highly desirable testing platform during the ongoing COVID-19 pandemic.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Multiplex Polymerase Chain Reaction/methods ; Pandemics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2/pathogenicity ; Saliva/virology ; Specimen Handling/methods ; Young Adult
Language	English
Publishing date	2021-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0243183
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2

Anderson, Cole / Castillo, Fritz / Koenig, Michael / Managbanag, Jim

bioRxiv

Abstract: ... Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower ... respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and ... The recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions ...

Abstract	The recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.22.110932
Database	COVID19

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Article ; Online: Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR

Imene Handous / Naila Hannachi / Manel Marzouk / Olfa Hazgui / Nissaf Bouafif Ep Ben Alaya / Jalel Boukadida

Biological Procedures Online, Vol 23, Iss 1, Pp 1-

2021 Volume 6

Abstract: Abstract Background The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples ... coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 ... nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and ...

Abstract	Abstract Background The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. Results In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean Ct values obtained with the 5-sample pooled testing exceeded individual sample testing by 1.85 ± 1.09 cycles, while Ct values obtained with the 10-sample pooling exceeded individual sample testing by 3.4 ± 1.65 cycles. Conclusions In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered.
Keywords	SARS-CoV-2 ; COVID-19 ; RT-qPCR ; Pooling ; Nasopharyngeal ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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