COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya
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...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
AOSIS
2022-07-01
|
| Series: | African Journal of Laboratory Medicine |
| Subjects: | |
| Online Access: | https://ajlmonline.org/index.php/ajlm/article/view/1737 |
| _version_ | 1811315891756859392 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | John N. Waitumbi |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-13T11:39:37Z |
| format | Article |
| id | doaj.art-4a1d3659d5b144ec9c1c687320442b3b |
| institution | Directory Open Access Journal |
| issn | 2225-2002 2225-2010 |
| language | English |
| last_indexed | 2024-04-13T11:39:37Z |
| publishDate | 2022-07-01 |
| publisher | AOSIS |
| record_format | Article |
| series | African Journal of Laboratory Medicine |
| spelling | doaj.art-4a1d3659d5b144ec9c1c687320442b3b2022-12-22T02:48:21ZengAOSISAfrican Journal of Laboratory Medicine2225-20022225-20102022-07-01111e1e610.4102/ajlm.v11i1.1737385COVID-19 mass testing and sequencing: Experiences from a laboratory in Western KenyaJohn N. Waitumbi0Esther Omuseni1Josphat Nyataya2Clement Masakhwe3Faith Sigei4Allan Lemtudo5George Awinda6Eric Muthanje7Brian Andika8Rachel Githii9Rehema Liyai10Gathii Kimita11Beth Mutai12Kenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuDepartment of Biological Sciences, University of Embu, EmbuDepartment of Molecular Biology and Bioinformatics, Jomo Kenyatta, University of Agriculture and Technology, JujaKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuKenya Medical Research Institute (KEMRI)/United States Army Medical Research Directorate-Africa, Basic Science Laboratory, Kisumu Field Station, KisumuBackground: 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.https://ajlmonline.org/index.php/ajlm/article/view/1737covid-19coronavirussars-cov-2nasal swabnasopharyngeal swabsmass testinggenome sequencing |
| spellingShingle | 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 COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya African Journal of Laboratory Medicine covid-19 coronavirus sars-cov-2 nasal swab nasopharyngeal swabs mass testing genome sequencing |
| title | COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya |
| title_full | COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya |
| title_fullStr | COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya |
| title_full_unstemmed | COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya |
| title_short | COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya |
| title_sort | covid 19 mass testing and sequencing experiences from a laboratory in western kenya |
| topic | covid-19 coronavirus sars-cov-2 nasal swab nasopharyngeal swabs mass testing genome sequencing |
| url | https://ajlmonline.org/index.php/ajlm/article/view/1737 |
| work_keys_str_mv | AT johnnwaitumbi covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT estheromuseni covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT josphatnyataya covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT clementmasakhwe covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT faithsigei covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT allanlemtudo covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT georgeawinda covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT ericmuthanje covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT brianandika covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT rachelgithii covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT rehemaliyai covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT gathiikimita covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya AT bethmutai covid19masstestingandsequencingexperiencesfromalaboratoryinwesternkenya |