Implementation of a Sample Pooling Strategy for the Direct Detection of SARS-CoV-2 by Real-Time Polymerase Chain Reaction During the COVID-19 Pandemic

Abstract

Objectives: To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3-month period in the fall of 2020.

Methods: The widespread testing implemented in the United States for detecting SARS-CoV-2 infection in response to the coronavirus disease 2019 pandemic has led to a significant shortage of testing supplies and therefore has become a major impediment to the public health response. To date, several institutions have implemented sample pooling, but publications documenting these experiences are sparse. Nasal and nasopharyngeal samples collected from low-positivity (<5%) areas were tested in pools of five on the Roche cobas 6800 analyzer system. Routine SARS-CoV-2 RT-PCR turnaround times between sample collection to result reporting were monitored and compared before and after sample pooling implementation.

Results: A total of 4,131 sample pools were tested over a 3-month period (during which 39,770 RT-PCR results were reported from the Roche system), allowing our laboratory to save 13,824 tests, equivalent to a conservation rate of 35%. A 48-hour or less turnaround time was generally maintained throughout the pooling period.

Conclusions: Sample pooling offers a viable means to mitigate shortfalls of PCR testing supplies in the ongoing pandemic without significantly compromising overall turnaround times.

Keywords: COVID-19; PCR; Pooled testing; Pooling; RT-PCR; SARS-CoV-2; Test reagents.

Figure 1

Sample pooling workflow at University of Chicago Medical Center for coronavirus disease 2019 testing on the Roche cobas 6800 analyzer system. Pooled testing was conducted on samples derived from sites with overall positivity rates of less than 5%. Positive pools necessitated repeat testing of the individual specimens making up the pool, and those results were automatically reported, whereas manual reporting of individual results was required for negative pools.

Figure 2

Mockup of rack organization for sample pooling. Empty rows were used to help organize and prevent mixing of sample tubes from separate pools. N and NP represent nasal and nasopharyngeal swab tubes, respectively. The sample pools consisted of either N or NP tubes but not a mix of both specimen types.

Figure 3

Cumulative coronavirus disease 2019 tests reported, used, and saved before and after sample pooling implementation. The cumulative number of tests reported, used, and saved (as a result of pooling) is shown in green, blue, and orange, respectively.

Figure 4

Seven-day results, case positivity, and pooled tests of coronavirus disease 2019 (COVID-19) before and after implementation of sample pooling on the Roche cobas 6800 platform. The gray and blue lines represent the 7-day number of COVID-19 results reported before and after pooling, respectively, whereas the green line shows the 7-day number of COVID-19 tests used after pooling. Of note, the number of tests used and results reported were equivalent before pooling. The orange line represents the 7-day number of COVID-19–positive results, while the red line shows the 7-day COVID-19 positivity rate (or percent positive).