TY - JOUR
AU - Said Mohammed, Khadija
AU - de Laurent, Zaydah R.
AU - Omuoyo, Donwilliams O.
AU - Lewa, Clement
AU - Gicheru, Elijah
AU - Cheruiyot, Robinson
AU - Bartilol, Brian
AU - Mutua, Shadrack
AU - Musyoki, Jennifer
AU - Gumba, Horace
AU - Mwacharo, Jedidah
AU - Riako, Debra
AU - Mwangi, Shaban J.
AU - Gichuki, Bonface M.
AU - Nyamako, Lydia
AU - Karani, Angela
AU - Karanja, Henry
AU - Mugo, Daisy
AU - Gitonga, John N.
AU - Njuguna, Susan
AU - Gumbi, Wilson
AU - Tawa, Brian
AU - Tendwa, Metrine
AU - Cheruiyot, Wesley
AU - Sein, Yiakon
AU - Nyambu, John K.
AU - Patta, Shem O.
AU - Thani Suleiman, Thani
AU - Maitha, Eric K.
AU - Kitole, Benson
AU - Mwakinangu, Mohamed S.
AU - Muslih, Barke S.
AU - Otieno, John
AU - Nyiro, Joyce U.
AU - Kiyuka, Patience K.
AU - Ndwiga, Leonard
AU - Wamae, Kevin
AU - Kimani, Domtila
AU - Makale, Johnstone
AU - Morobe, John Mwita
AU - Osoti, Victor
AU - Lambisia, Arnold W.
AU - Odundo, Calleb
AU - Mwarumba, Salim
AU - Mutunga, Martin
AU - Bejon, Philip
AU - Tsofa, Benjamin
AU - Agoti, Charles N.
AU - Ochola-Oyier, Lynette Isabella
PY - 2022
DA - March
TI - An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams
JO - Wellcome Open Research
VL - 5
DO - https://doi.org/10.12688/wellcomeopenres.16063.2
AB - 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) Charité 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.
PB - F1000 Research
UR - https://eprints.gla.ac.uk/325340/
KW - Coronavirus (COVID-19)
ER