Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic
Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities....
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/119719 |
| _version_ | 1855528585957212160 |
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| author | Nasimiyu, C. Matoke-Muhia, D. Rono, Gilbert K. Osoro, E. Ouso, Daniel O. Mwangi, J.M. Mwikwabe, N. Thiong’o, K. Dawa, J. Ngere, I. Gachohi, J. Kariuki, S. Amukoye, E. Mureithi, M. Ngere, P. Amoth, P. Were, I. Makayotto, L. Nene, Vishvanath M. Okoth, Edward A. Njenga, M.K. Seifert, S.N. Oyola, Samuel O. |
| author_browse | Amoth, P. Amukoye, E. Dawa, J. Gachohi, J. Kariuki, S. Makayotto, L. Matoke-Muhia, D. Mureithi, M. Mwangi, J.M. Mwikwabe, N. Nasimiyu, C. Nene, Vishvanath M. Ngere, I. Ngere, P. Njenga, M.K. Okoth, Edward A. Osoro, E. Ouso, Daniel O. Oyola, Samuel O. Rono, Gilbert K. Seifert, S.N. Thiong’o, K. Were, I. |
| author_facet | Nasimiyu, C. Matoke-Muhia, D. Rono, Gilbert K. Osoro, E. Ouso, Daniel O. Mwangi, J.M. Mwikwabe, N. Thiong’o, K. Dawa, J. Ngere, I. Gachohi, J. Kariuki, S. Amukoye, E. Mureithi, M. Ngere, P. Amoth, P. Were, I. Makayotto, L. Nene, Vishvanath M. Okoth, Edward A. Njenga, M.K. Seifert, S.N. Oyola, Samuel O. |
| author_sort | Nasimiyu, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Over the pandemic duration (March 2020–January 2022), Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. In conclusion, the emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country. |
| format | Journal Article |
| id | CGSpace119719 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1197192025-12-08T10:29:22Z Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic Nasimiyu, C. Matoke-Muhia, D. Rono, Gilbert K. Osoro, E. Ouso, Daniel O. Mwangi, J.M. Mwikwabe, N. Thiong’o, K. Dawa, J. Ngere, I. Gachohi, J. Kariuki, S. Amukoye, E. Mureithi, M. Ngere, P. Amoth, P. Were, I. Makayotto, L. Nene, Vishvanath M. Okoth, Edward A. Njenga, M.K. Seifert, S.N. Oyola, Samuel O. severe acute respiratory syndrome coronavirus 2 covid-19 health Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Over the pandemic duration (March 2020–January 2022), Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. In conclusion, the emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country. 2022-05-05 2022-06-01T06:35:53Z 2022-06-01T06:35:53Z Journal Article https://hdl.handle.net/10568/119719 en Open Access MDPI Nasimiyu, C., Matoke-Muhia, D., Rono, G.K., Osoro, E., Ouso, D.O., Mwangi, J.M., Mwikwabe, N., Thiong’o, K., Dawa, J., Ngere, I., Gachohi, J., Kariuki, S., Amukoye, E., Mureithi, M., Ngere, P., Amoth, P., Were, I., Makayotto, L., Nene, V., Abworo, E.O., Njenga, M.K., Seifert, S.N. and Oyola, S.O. 2022. Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic. COVID 2(5): 586–598. |
| spellingShingle | severe acute respiratory syndrome coronavirus 2 covid-19 health Nasimiyu, C. Matoke-Muhia, D. Rono, Gilbert K. Osoro, E. Ouso, Daniel O. Mwangi, J.M. Mwikwabe, N. Thiong’o, K. Dawa, J. Ngere, I. Gachohi, J. Kariuki, S. Amukoye, E. Mureithi, M. Ngere, P. Amoth, P. Were, I. Makayotto, L. Nene, Vishvanath M. Okoth, Edward A. Njenga, M.K. Seifert, S.N. Oyola, Samuel O. Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title | Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title_full | Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title_fullStr | Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title_full_unstemmed | Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title_short | Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic |
| title_sort | imported sars cov 2 variants of concern drove spread of infections across kenya during the second year of the pandemic |
| topic | severe acute respiratory syndrome coronavirus 2 covid-19 health |
| url | https://hdl.handle.net/10568/119719 |
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