{"doi":"10.1101/2022.02.28.22271467","title":"Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic","abstract":"ABSTRACT Background 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. Methods 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. Results 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. Conclusions 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.","journal":"medRxiv","year":2022,"id":296848,"datarank":0.42498200160843247,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.0,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.821,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":897122,"name":"Damaris Matoke-Muhia","orcid":"0000-0001-7737-8069","position":1,"is_corresponding":false},{"id":897123,"name":"Gilbert Kibet","orcid":"0000-0001-8043-5423","position":2,"is_corresponding":false},{"id":751916,"name":"Eric Osoro","orcid":"0000-0001-5133-4279","position":3,"is_corresponding":false},{"id":984869,"name":"Daniel O. Obado","orcid":null,"position":4,"is_corresponding":false},{"id":897804,"name":"Jackline Milkah Mwangi","orcid":null,"position":5,"is_corresponding":false},{"id":897805,"name":"Nicholas Mwikwabe","orcid":null,"position":6,"is_corresponding":false},{"id":897806,"name":"Kelvin Thiong’o","orcid":null,"position":7,"is_corresponding":false},{"id":653370,"name":"Jeanette Dawa","orcid":"0000-0001-9405-148X","position":8,"is_corresponding":false},{"id":653369,"name":"Isaac Ngere","orcid":"0000-0002-6688-3390","position":9,"is_corresponding":false},{"id":653377,"name":"John Gachohi","orcid":"0000-0001-9854-7490","position":10,"is_corresponding":false},{"id":345187,"name":"Samuel Kariuki","orcid":"0000-0003-3209-9503","position":11,"is_corresponding":false},{"id":897125,"name":"Evans Amukoye","orcid":"0000-0003-0683-0585","position":12,"is_corresponding":false},{"id":750777,"name":"Marianne Mureithi","orcid":"0000-0001-9119-3167","position":13,"is_corresponding":false},{"id":897126,"name":"Philip Ngere","orcid":"0009-0004-6164-7972","position":14,"is_corresponding":false},{"id":653373,"name":"Patrick Amoth","orcid":"0000-0001-8049-0879","position":15,"is_corresponding":false},{"id":897807,"name":"Ian Were","orcid":null,"position":16,"is_corresponding":false},{"id":654335,"name":"Lyndah Makayotto","orcid":null,"position":17,"is_corresponding":false},{"id":393240,"name":"Vishvanath Nene","orcid":"0000-0001-7066-4169","position":18,"is_corresponding":false},{"id":897808,"name":"Edward Okoth Abworo","orcid":null,"position":19,"is_corresponding":false},{"id":653379,"name":"M. Kariuki Njenga","orcid":"0000-0002-7629-7002","position":20,"is_corresponding":false},{"id":225424,"name":"Stephanie N. Seifert","orcid":"0000-0002-4397-6156","position":21,"is_corresponding":false},{"id":897127,"name":"Samuel O. 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