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

African Journal of Laboratory Medicine

 
 
Field Value
 
Title COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya
 
Creator Waitumbi, John N. Omuseni, Esther Nyataya, Josphat Masakhwe, Clement Sigei, Faith Lemtudo, Allan Awinda, George Muthanje, Eric Andika, Brian Githii, Rachel Liyai, Rehema Kimita, Gathii Mutai, Beth
 
Subject Biological Sciences; Microbiology; Virology COVID-19; coronavirus; SARS-CoV-2; nasal swab; nasopharyngeal swabs; mass testing; genome sequencing
Description 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.
 
Publisher AOSIS
 
Contributor Kenya Ministry of Health Armed Forces Health Surveillance Division (AFHSD) and its Global Emerging Infections Surveillance and Research Branch
Date 2022-07-22
 
Type info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion — Laboratory Analysis
Format text/html application/epub+zip text/xml application/pdf
Identifier 10.4102/ajlm.v11i1.1737
 
Source African Journal of Laboratory Medicine; Vol 11, No 1 (2022); 6 pages 2225-2010 2225-2002
 
Language eng
 
Relation
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https://ajlmonline.org/index.php/ajlm/article/view/1737/2325 https://ajlmonline.org/index.php/ajlm/article/view/1737/2326 https://ajlmonline.org/index.php/ajlm/article/view/1737/2327 https://ajlmonline.org/index.php/ajlm/article/view/1737/2328
 
Coverage Kenya COVID-19 Epidemic —
Rights Copyright (c) 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 https://creativecommons.org/licenses/by/4.0
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