Nasimiyu Carolyne, Matoke-Muhia Damaris, Rono Gilbert K, Osoro Eric, Obado Daniel O, Mwangi J Milkah, Mwikwabe Nicholas, Thiong'o Kelvin, Dawa Jeanette, Ngere Isaac, Gachohi John, Kariuki Samuel, Amukoye Evans, Mureithi Marianne, Ngere Philip, Amoth Patrick, Were Ian, Makayotto Lyndah, Nene Vishvanath, Abworo Edward O, Njenga M Kariuki, Seifert Stephanie N, Oyola Samuel O
Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya.
Paul G. Allen School for Global Health, Washington State University, Pullman, USA.
medRxiv. 2022 Feb 28:2022.02.28.22271467. doi: 10.1101/2022.02.28.22271467.
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 (74.9% genomes), (98.7%), and (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country.
The emergence of , , and variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.
我们运用经典流行病学和基因组流行病学方法，对肯尼亚长达23个月的新冠疫情进行追踪，以确定严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变异株对疫情发展的影响。
SARS-CoV-2监测和检测数据来自肯尼亚卫生部，数据每日从306家医疗机构收集。与新冠病毒病相关的死亡数据也从这些医疗机构和社区获取。对1241份样本进行了SARS-CoV-2全基因组测序。
在疫情期间（2020年3月至2022年1月），肯尼亚经历了五波疫情，发病率为每10万人65.4至137.6例，每波疫情期间的病死率平均为3.5%，比全国新冠病毒病相关病死率平均水平高出两倍。在全球关注变异株（VoC）出现之前发生的前两波疫情发病率较低（每10万人65.4例和118.2例）。第二年出现的第三、第四和第五波疫情分别由多种VoC毒株的多次传入主导，其中 （占基因组的74.9%）、 （98.7%）和 （87.8%）。在此阶段，政府实施的限制措施未能缓解疫情发展，导致全国发病率上升。
、 和 变异株的出现是一个转折点，导致该国SARS-CoV-2感染广泛传播且感染率更高。
