Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR
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...
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doaj-172386f8fb51468e8fa95a7d75d5084e2021-10-03T11:06:46ZengBMCBiological Procedures Online1480-92222021-09-012311610.1186/s12575-021-00156-6Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCRImene Handous0Naila Hannachi1Manel Marzouk2Olfa Hazgui3Nissaf Bouafif Ep Ben Alaya4Jalel Boukadida5Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de SousseLaboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de SousseLaboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de SousseLaboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de SousseMinistère de la Santé, Observatoire national des maladies nouvelles et émergentesLaboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de SousseAbstract 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.https://doi.org/10.1186/s12575-021-00156-6SARS-CoV-2COVID-19RT-qPCRPoolingNasopharyngeal |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Imene Handous Naila Hannachi Manel Marzouk Olfa Hazgui Nissaf Bouafif Ep Ben Alaya Jalel Boukadida |
spellingShingle |
Imene Handous Naila Hannachi Manel Marzouk Olfa Hazgui Nissaf Bouafif Ep Ben Alaya Jalel Boukadida Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR Biological Procedures Online SARS-CoV-2 COVID-19 RT-qPCR Pooling Nasopharyngeal |
author_facet |
Imene Handous Naila Hannachi Manel Marzouk Olfa Hazgui Nissaf Bouafif Ep Ben Alaya Jalel Boukadida |
author_sort |
Imene Handous |
title |
Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR |
title_short |
Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR |
title_full |
Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR |
title_fullStr |
Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR |
title_full_unstemmed |
Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR |
title_sort |
pooling nasopharyngeal swab specimens to improve testing capacity for sars-cov-2 by real-time rt-pcr |
publisher |
BMC |
series |
Biological Procedures Online |
issn |
1480-9222 |
publishDate |
2021-09-01 |
description |
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. |
topic |
SARS-CoV-2 COVID-19 RT-qPCR Pooling Nasopharyngeal |
url |
https://doi.org/10.1186/s12575-021-00156-6 |
work_keys_str_mv |
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