Evaluation of pooling strategy of SARS-CoV-2 RT-PCR in limited resources setting in Egypt at low prevalence

Abstract

Sample pooling testing for SARS-COV-2 can be an effective tool in COVID-19 screening when resources are limited, yet it is important to assess the performance before implementation as pooling has its limitations. Our objective was to assess the efficacy of pooling samples for coronavirus 2019 (COVID-19) compared to an individual analysis by using commercial platforms for nucleic acid testing. A total of 2200 nasopharyngeal swabs for SARS-COV-2 were tested individually and in pools of 4, 8, and 10. The cycle threshold (Ct) values of the positive pooled samples were compared to their corresponding individual positive samples. In pool size 10 samples, an estimated increase of 3-Ct was obtained, which led to false negative results in low viral load positive samples. Pooling SARS COV-2 samples is an effective strategy of screening to increase laboratories' capacity and reduce costs without affecting diagnostic performance. A pool size of 8 is recommended.

Keywords: COVID-19; Limited resources; RT-PCR; SARS-COV-2; Sample pooling; Screening.

Fig. 1

Scatter plots showing cycle threshold (Ct) values and Ct shifts detected by rRT-PCR in four sample pools, composed of three negative and one positive sample, with respect to the individual positive samples for the ORF1ab gene

Fig. 2

Scatter plots showing cycle threshold (Ct) values and Ct shifts detected by rRT-PCR in eight sample pools, composed of seven negative and one positive sample, with respect to the individual positive samples for the ORF1ab gene

Fig. 3

Ct value shift due to sample pooling. Scatter plots showing cycle threshold (Ct) values and Ct shifts detected by rRT-PCR in ten sample pools, composed of nine negative and one positive sample, with respect to the individual positive samples for the ORF1ab gene