key: cord-1055645-jc2a5vkz
authors: McMillen, Tracy; Jani, Krupa; Babady, N. Esther
title: Evaluation of Sample Pooling for SARS-CoV-2 RNA Detection in Nasopharyngeal Swabs and Salivas on the Roche Cobas 6800
date: 2021-03-10
journal: J Clin Virol
DOI: 10.1016/j.jcv.2021.104790
sha: fb3b7ad41489ef38025e5a53453ffaa5fd2f3de0
doc_id: 1055645
cord_uid: jc2a5vkz

The Roche Cobas SARS-CoV-2 test recently received an Emergency Use Authorization from the U.S. Food and Drug Administration UA for pooling of up to six nasopharyngeal swab samples (NPS). We evaluated the 6-pool approach on both NPS and saliva samples using 564 samples (20 positive NPS and saliva samples each and 262 negative NPS and saliva samples each). The sensitivity of the Roche SARS-CoV-2 RNA test for pooled NPS samples was 100% (95%CI: 83.2-100%) and the sensitivity for pooled saliva samples was 90% (95% CI: 68.3-98.8%). Given the high throughput of the Roche Cobas 6800, pooling of 6 samples has the potential to significantly increase testing capacity without significant loss in sensitivity.

samples (20 positive NPS and saliva samples each and 262 negative NPS and saliva samples each). The sensitivity of the Roche SARS-CoV-2 RNA test for pooled NPS samples was 100% (95%CI: 83.2-100%) and the sensitivity for pooled saliva samples was 90% (95% CI: 68.3-98.8%). Given the high throughput of the Roche Cobas 6800, pooling of 6 samples has the potential to significantly increase testing capacity without significant loss in sensitivity.

Keywords: Sample pooling, SARS-CoV-2, RT-PCR EUA, Saliva

The first reported case of the Coronavirus 2019 disease in the United States was diagnosed in January (1) . Since then, the number of cases in the United States has surpassed 15,000, 000 in less than 12 months (2) . Testing for SARS-CoV-2 infection continues to face several challenges due in part this rapid increase in cases but also to continued supply chain issues from collection devices to testing reagents. In order to increase testing throughput, pooling of multiple samples has been proposed as a strategy. As pooling may result in loss of sensitivity, the approach that minimizes the loss in sensitivity while increasing throughput needs to be validated and optimized prior to implementation.

We have previously validated the use of saliva collected in sterile tubes for the detection of SARS-CoV-2 using a modified CDC SARS-CoV-2 RT-PCR, the Cepheid Xpert SARS-CoV-2 and the Roche Cobas SARS-CoV-2 EUA assays and showed a sensitivity of greater than 90% when compared to either throat swabs or nasopharyngeal swabs (NPS) (3) . Recently, the Roche Cobas SARS-CoV-2 received an EUA for pooling of up to six NPS.

The goal of this study was to evaluate the impact of pooling on both NPS and saliva samples on the Roche Cobas 6800.

We evaluated the 6-pool approach on both NPS and saliva samples. 

Results are summarized in Table 1 

In this study, the sensitivity of the Roche SARS-CoV-2 RNA EUA test for NPS samples, False-negative results were primarily due to samples with Ct values >34, again, similar to data presented in this study (7) .

We additionally evaluated pooling on saliva samples. We and others have previously shown that saliva was an acceptable sample for SARS-CoV-2 nucleic acid detection with the added advantage of allowing for self-collection and circumventing the need for swabs and viral transport media (3, 8) . Combining pooling with saliva collection could further expand the availability of testing and while published studies are scarce, the approach has been used for wide surveillance testing at colleges and universities. We have previously shown that there were no differences in performance between symptomatic and asymptomatic patients and high viral loads could be detected in saliva of asymptomatic or pre-symptomatic patients, further supporting the potential use of saliva pool testing (3) . In their study, Barat Further studies with greater sample set will help clarify impact of pooling on saliva viral loads.

In conclusion, we report a sensitivity of greater than 90% for SARS-CoV-2 nucleic detection using the Roche Cobas SARS-CoV-2 assay and pooling protocol of 6 samples for both NPS and saliva samples. Laboratory considering testing and pooling saliva samples would need to perform in-house validation. Given the high throughput of the Roche Cobas 6800, pooling of 6 samples without significant loss of sensitivity would result in a significant increase in testing capacity.

The authors report no conflict of interest. 

Washington State -nCo VCIT. 2020. First Case of 2019 Novel Coronavirus in the United States

Anonymous. 2020. CDC COVID Data Tracker

Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Real-Time RT-PCR Tests on Oral Rinses and Saliva Samples

Pooled Saliva Specimens for SARS-CoV-2 Testing

Pooling Upper Respiratory Specimens for Rapid Mass Screening of COVID-19 by Real-Time RT-PCR

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

Performance of Nucleic Acid Amplification Tests for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Prospectively Pooled Specimens

Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2