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.

Analysis of SARS-CoV-2 RT-PCR Testing and Pooling Strategies for Screening of Asymptomatic Individuals - The Philippine Children's Medical Center Experience

“…Moreover, pooled samples with multiple positive individuals had an average decrease of Ct-value by 1.59 in comparison to pooled samples with single positive individual. 17 A pooled study involving hospitalized patients that have low risk for SARS-CoV-2 was done using Xpert Xpress SARS-CoV-2 test which involved 530 samples pooled in groups of 3. This resulted in 4 positive pools and a total of 179 pooled samples with a positivity rate of 0.8%.…”

Pooled Testing Strategies for SARS-CoV-2 diagnosis: A comprehensive review

“…Owing to the non-invasive nature of sample collection, the feasibility of utilising pooled saliva has also been tested and found that detection is possible without much compromise in sensitivity( Barat et al, 2020 ; Fogarty et al, 2020 ; Pasomsub et al, 2020 ). Studies have reported improved test turn- around time and conservation of laboratory resources while adapting pooled testing( Abdalhamid et al, 2020a ; Agoti et al, 2020 ). The diagnostic accuracy while adapting pooled testing is found to be highly efficient in most of the studies ( Fig.4 ).…”

Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study

“…This study analyzed SARS-CoV-2 positive NP/OP swab samples that were collected by the MoH County Department of Health RRTs, across all the six counties of Coastal Kenya. SARS-CoV-2 positive diagnosis was made at the KWTRP in Kilifi County (Agoti et al, 2021). The RRTs delivered the NP/OP swabs to KWTRP laboratories within 48 hours of collection in cool boxes with ice packs.…”

“…This work was supported by the National Institute for Health Research (NIHR) (project references 17/63/82 (PI Prof. James Nokes) and 16/136/33 (PI Prof. Mark Wooolhouse) using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office and Wellcome Trust (grant# 220985). The views expressed in this publication are those of the author (s) and not necessarily those of NIHR, the Supplementary Material for Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study Agoti et al, 2021 Corresponding author: Dr Charles N. Agoti Email : cnyaigoti@kemri-wellcome.org…”