Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Abstract

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

Keywords: COVID-19; Kenya; Kilifi; Pooled testing; SARS-CoV-2.

Figure 1.. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) laboratory testing in Kenya between 21 ^th March and 15 ^th July 2020.

Panel A, the bars show reported daily nationwide tests. Panel B, bars show the daily tests undertaken at the KEMRI-Kilifi laboratory and when major protocol changes were implemented. In both panels the secondary y-axis shows the daily proportion of tests positive indicated by the dashed line.

Figure 2.. A schema of how the pooled testing strategy works.

The example illustrates that if an infection is occurring at about 5.6% (i.e. 1/18) then by the pooled testing, a total of 9 tests can identify the infected individual. In Kenya, the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity rate is ~5.0% thus pooled testing can conserve 50% of testing kits.

Figure 3.. Summary results from the analysis of the 1500 samples analyzed at KEMRI-Kilifi using the pooled testing strategy.

Panel A, shows the number of positives from the created pools. Panel B, comparison of Ct values from pooled tests versus individual sample tests.