Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling

Objectives: Limited testing capacity has characterized the ongoing coronavirus disease 2019 (COVID-19) pandemic in Spain, hampering timely control of outbreaks and opportunities to reduce the escalation of community transmission. This study investigated the potential to use sample pooling, followed by onestep retrotranscription and real-time quantitative reverse transcription polymerase chain reaction (RTqPCR) to increase testing capacity for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: Various pool sizes (five, 10 and 15 samples) were evaluated prior to RNA extraction followed by standard RT-qPCR for the diagnosis of COVID-19. The pool size achieving reproducible results with individual sample testing was subsequently used to assess nasopharyngeal samples in a tertiary hospital in August 2020. Results: A pool size of five samples had higher sensitivity compared with pool sizes of 10 and 15 samples, showing a mean cycle threshold (Ct) shift of 3.5 [standard deviation (SD) 2.2] between the pooled test and positive samples in the pool. Next, a pool size of five was used to test a total of 895 pools (4475 prospective samples) using two different RT-qPCR kits. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct shift [2.2 (SD 2.4)] between the pool and individual samples. This strategy enables detection of individual positive samples in positive pools with Ct of 16.7-39.4. Conclusions: Grouping samples into pools of five for RT-qPCR resulted in an increase in SARS-CoV-2 testing capacity with minimal loss of sensitivity compared with testing each sample individually. (c) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-ncnd/4.0/).

Automated summary

This study aimed to increase testing capacity for COVID-19 in Spain through sample pooling and found that a pool size of five samples had higher sensitivity compared to larger pool sizes. Utilizing sample pooling strategy with a pool size of five allowed for efficient detection of individual positive samples in positive pools with minimal loss of sensitivity.