An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams

Mohammed KS, de Laurent ZR, Omuoyo DO, Lewa C, Gicheru E, Cheruiyot R, Bartilol B, Mutua S, Musyoki J, Gumba H, Mwacharo J, Riako D, Mwangi SJ, Gichuki BM, Nyamako L, Karani A, Karanja H, Mugo D, Gitonga JN, Njuguna S, Gumbi W, Tawa B, Tendwa M, Cheruiyot W, Sein Y, Nyambu JK, Patta SO, Thani TS, Maitha EK, Kitole B, Mwakinangu MS, Muslih BS, Otieno JO, Nyiro JU, Kiyuka P, Ndwiga L, Wamae K, Kimani D, Makale J, Morobe JM, Osoti V, Lambisia AW, Odundo C, Mwarumba S, Mutunga M, Bejon P, Tsofa B, Agoti CN, Ochola-Oyier LI
Wellcome Open Res. 2020;5

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Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers' recommendations to sustain the testing capability in a resource-limited setting. Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charite Berlin primer-probe set, ii) European Virus Archive - GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values. Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components. Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit's performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results.