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Performance Evaluation of Nasopharyngeal Swab Pooling to Improve SARS-CoV-2 Testing Capacity via Closed Real-Time
Betselot Ayano1,2, Solomon Gebre-Selassie2, Habtamu Biazin Kebede2
1Referral and Reference Laboratories Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
Background:
The consistency of GeneXpert and Cobas RT-PCR assays for detecting SARS-CoV-2 in pooled versus individual samples remains uncertain. Sample pooling combines multiple patient samples into a single test reaction to increase efficiency. Only one study in Ethiopia has evaluated pooling performance for SARS-CoV-2 detection, but it failed to directly compare these two widely used diagnostic tests.
Purpose:
This study evaluated the performance of the Cepheid Xpert® Xpress (Xpert) and Roche Cobas® (Cobas) SARS-CoV-2 assays for SARS-CoV-2 detection in pooled nasopharyngeal swab samples.
Patients And Methods:
The study used a cross-sectional study design on 50 confirmed SARS-CoV-2-positive samples grouped by their Cycle Threshold (CT) values. These samples were pooled with SARS-CoV-2-negative samples and tested using both assays. A total of 200 pooled samples were tested.
Results:
Of the 200 poled samples tested, 91.0% and 81.0% tested positive with Xpert and Cobas, respectively, with an overall agreement of 89% (κ=0.552). Strong correlation was observed between the CT values of the initial individual samples and the pooled samples for both assays. In pool-4 and pool-6, the Xpert assay detected 94.0% of positives, while Cobas assay detected 82.0%. Overall, 80.5% of pooled samples were positive and 8.5% were negative with both assays (overall concordance of 89.0%), Percent Positive Agreement of 93.6%, and Negative Agreement of 60.7%.
Conclusion:
Overall, these findings suggest that implementing sample pooling can be particularly beneficial in low-resource settings where testing resources are limited, enabling an increase in overall testing capacity. Xpert assay performed effectively for pooling up to six samples, whereas the Cobas assay showed reduced sensitivity, especially with low viral loads. This implies that pooling of nasopharyngeal samples from asymptomatic individuals may be missed by the Cobas assay, underscoring the importance of considering pool size, viral load and assay choices when implementing pooled SARS-CoV-2 testing.
