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

Agoti, Charles N.; Mutunga, Martin; Lambisia, Arnold W.; Kimani, Domtila; Cheruiyot, Robinson; Kiyuka, Patience; Lewa, Clement; Gicheru, Elijah; Tendwa, Metrine; Said Mohammed, Khadija; Osoti, Victor; Makale, Johnstone; Tawa, Brian; Odundo, Calleb; Cheruiyot, Wesley; Nyamu, Wilfred; Gumbi, Wilson; Mwacharo, Jedidah; Nyamako, Lydia; Otieno, Edward; Amadi, David; Thoya, Janet; Karani, Angela; Mugo, Daisy; Musyoki, Jennifer; Gumba, Horace; Mwarumba, Salim; M. Gichuki, Bonface; Njuguna, Susan; Riako, Debra; Mutua, Shadrack; Gitonga, John N.; Sein, Yiakon; Bartilol, Brian; Mwangi, Shaban J.; O. Omuoyo, Donwilliams; M. Morobe, John; de Laurent, Zaydah R.; Bejon, Philip; Ochola-Oyier, Lynette Isabella; Tsofa, Benjamin; Agoti, Charles N; Lambisia, Arnold W; M Gichuki, Bonface; Gitonga, John N; Mwangi, Shaban J; O Omuoyo, Donwilliams; M Morobe, John; de Laurent, Zaydah R

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.