Lessons from the Field

COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya

John N. Waitumbi, Esther Omuseni, Josphat Nyataya, Clement Masakhwe, Faith Sigei, Allan Lemtudo, George Awinda, Eric Muthanje, Brian Andika, Rachel Githii, Rehema Liyai, Gathii Kimita, Beth Mutai
African Journal of Laboratory Medicine | Vol 11, No 1 | a1737 | DOI: https://doi.org/10.4102/ajlm.v11i1.1737 | © 2022 John N. Waitumbi, Esther Omuseni, Josphat Nyataya, Clement Masakhwe, Faith Sigei, Allan Lemtudo, George Awinda, Eric Muthanje, Brian Andika, Rachel Githii, Rehema Liyai, Gathii Kimita, Beth Mutai | This work is licensed under CC Attribution 4.0
Submitted: 21 September 2021 | Published: 22 July 2022

About the author(s)

John N. Waitumbi, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Esther Omuseni, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Josphat Nyataya, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Clement Masakhwe, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Faith Sigei, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Allan Lemtudo, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
George Awinda, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Eric Muthanje, Department of Biological Sciences, University of Embu, Embu, Kenya
Brian Andika, Department of Molecular Biology and Bioinformatics, Jomo Kenyatta, University of Agriculture and Technology, Juja, Kenya
Rachel Githii, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Rehema Liyai, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Gathii Kimita, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya
Beth Mutai, Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, Kisumu, Kenya


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Abstract

Background: The Basic Science Laboratory (BSL) of the Kenya Medical Research Institute/Walter Reed Project in Kisumu, Kenya addressed mass testing challenges posed by the emergent coronavirus disease 2019 (COVID-19) in an environment of global supply shortages. Before COVID-19, the BSL had adequate resources for disease surveillance and was therefore designated as one of the testing centres for COVID-19.

Intervention: By April 2020, the BSL had developed stringent safety procedures for receiving and mass testing potentially infectious nasal specimens. To accommodate increased demand, BSL personnel worked in units: nucleic acid extraction, polymerase chain reaction, and data and quality assurance checks. The BSL adopted procedures for tracking sample integrity and minimising cross-contamination.

Lessons learnt: Between May 2020 and January 2022, the BSL tested 63 542 samples, of which 5375 (8.59%) were positive for COVID-19; 1034 genomes were generated by whole genome sequencing and deposited in the Global Initiative on Sharing All Influenza Data database to aid global tracking of viral lineages. At the height of the pandemic (August and November 2020, April and August 2021 and January 2022), the BSL was testing more than 500 samples daily, compared to 150 per month prior to COVID-19. An important lesson from the COVID-19 pandemic was the discovery of untapped resilience within BSL personnel that allowed adaptability when the situation demanded. Strict safety procedures and quality management that are often difficult to maintain became routine.

Recommendations: A fundamental lesson to embrace is that there is no ‘one-size-fits-all’ approach and adaptability is the key to success.


Keywords

COVID-19; coronavirus; SARS-CoV-2; nasal swab; nasopharyngeal swabs; mass testing; genome sequencing

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