Pooling of SARS-CoV-2 samples to increase molecular testing throughput

Perchetti, Garrett A.; Sullivan, KaWing; Pepper, Greg; Huang, Meei‐Li; Breit, Nathan; Mathias, Patrick C.; Jerome, Keith R.; Greninger, Alexander L.

doi:10.1016/j.jcv.2020.104570

Cited by 54 publications

(58 citation statements)

References 18 publications

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“…Lohse et al, (13) could be consistently identified when the N-gene Ct value of the Individual sample making up the pool was <35 for pools of 5 and <31 for pools of 10. These results are consistent with those of another study (17) and suggest that smaller pool sizes will help in improving sensitivity of detection.…”

Section: Discussionsupporting

confidence: 91%

“…Several pooling strategies and PCR protocols have been studied for COVID-19 diagnosis (13,14,17,18). In most studies, samples were pooled before RNA extraction, however, pooling of extracted RNA has also been reported for COVID-19 testing (15,33).…”

Section: Discussionmentioning

confidence: 99%

“…in herds/flocks of animals (7-10). A similar concept of pooling has been recognized for COVID-19 diagnosis by different groups (11)(12)(13)(14)(15)(16)(17)(18) for successful screening of samples with variable detection sensitivity.…”

Section: Introductionmentioning

confidence: 90%

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Pooling of Nasopharyngeal Swab Samples To Overcome a Global Shortage of Real-Time Reverse Transcription-PCR COVID-19 Test Kits

Narayanan

Patil

et al. 2021

J Clin Microbiol

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The global outbreak and rapid spread of SARS-CoV-2 created an urgent need for large scale testing of populations. There is a demand for high throughput testing protocols that can be used for efficient and rapid testing of clinical specimens. We evaluated a pooled-PCR protocol for testing nasopharyngeal swabs using known positive/negative and untested clinical samples that were assigned to pools of 5 or 10. Six-hundred and thirty (630) samples were used in this study. Individual positive samples with Ct values as high as 33 could be consistently detected when pooled with 4 negative samples (pool of 5) and individual positive samples with Ct values up to 31 could be consistently detected when pooled with 9 negative samples (pool of 10). Pooling of up to 5 samples can be employed in laboratories for the diagnosis of COVID-19 for efficient utilization of resources, rapid screening of a greater number of people, and faster reporting of test results.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

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Pooling of Nasopharyngeal Swab Samples To Overcome a Global Shortage of Real-Time Reverse Transcription-PCR COVID-19 Test Kits

Narayanan

Patil

et al. 2021

J Clin Microbiol

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“…Pool testing has gained importance to fight the COVID-19 pandemic, as challenges involving cost and logistics are at the core of shared struggles to promote large-scale screenings worldwide 10 . Traditional pooling methods proposed 9-15 rely on the combination of multiple individual samples prior to RNA extraction or RT-qPCR, leading to a dilution factor directly related to the number of samples in the pool 9,[11][12][13][14][15] . This dilution effect has been of major concern over the diagnostic performance of pool testing procedures 26 .…”

Section: Discussionmentioning

confidence: 99%

Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2

Christoff¹,

Cruz²,

Sereia³

et al. 2020

Preprint

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Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Here, we describe a pooling procedure in which nasopharyngeal swabs are pooled together at the time of sample collection (swab pooling), decreasing laboratory manipulation and minimizing dilution of the viral RNA present in the samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96.9% to 100%) and a specificity of 99.8% (Cr.I. 99.4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0.1 Cq (Cr.I. -0.98 to 1.17) to 2.09 Cq (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1.26%). This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Finally, these data demonstrate that swab pooling can significantly minimize sample dilution and sensitivity issues commonly seen in its traditional counterpart. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.

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“…The detection of the positive samples with low viral load was not feasible by pooling. On the other hand, all the samples which individually determined as negative, were also negative when tested in pools ( Perchetti et al, 2020b ).…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%