A genomics dissection of Kenya’s COVID-19 waves: temporal lineage replacements and dominance of imported variants of concern

Abstract Kenya’s COVID-19 epidemic was slow to peak. It was seeded early in March 2020, and did not peak until late-July 2020 (wave 1), mid-November 2020 (wave 2) and late-March 2021 (wave 3). Here we present SARS-CoV-2 lineages associated with the three COVID-19 waves through analysis of 483 genomes, which included 167 Alpha (B.1.1.7), 57 Delta (B.1.617.2) and 12 Beta (B.1.351) variants of concerns (VOC) that dominated the third wave. In total, 35 lineages were identified. The early European lineages B.1 and B.1.1 were the first to be seeded in Kenya. The B.1 lineage continued to expand and remained the most dominant lineage accounting for 55.8% and 56.3% in waves 1 and 2 respectively. The alpha (B.1.1.7), delta (B.1.167.2) and beta (B.1.351) VOCs dominated in wave 3 at 59.0%, 20.1% and 4.2% respectively. Eventually, the delta variant took over at the tail end of wave 3 and at the time of going to press, it had become the major lineage in the whole country. Phylogenetic analysis suggested multiple introductions of variants from outside Kenya especially during the first and third wave. Phylogeny also highlighted local lineage diversification as local transmission events supervened. The data highlights the importance of genome surveillance in determining circulating variants to aid in public health interventions.

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Plague and trade in Lagos, 1924–1931

International Journal of Maritime History ◽

10.1177/0843871418765723 ◽

2018 ◽

Vol 30 (2) ◽

pp. 287-301 ◽

Cited By ~ 1

Author(s):

Olukayode A. Faleye

Keyword(s):

Public Health ◽

Economic Policy ◽

Medical Records ◽

Historical Analysis ◽

Public Health Intervention ◽

Health Interventions ◽

Historical Study ◽

Maritime Trade ◽

Public Health Interventions ◽

The Third

The literature on the Third Plague Pandemic in West Africa focuses on urbanisation and disease processes in colonial Senegal, Ghana, and Nigeria. Consequently, there is a dearth of historical study of the relational complexities between public health interventions and maritime trade during the outbreak in the region. It is with this in mind that this article examines the historical effects of plague control on internal commerce and international maritime trade in Lagos from 1924 to 1931. The study is based on the historical analysis of colonial administrative, sanitary and medical records as well as newspaper reports. It concludes that the nature of colonial public health intervention was determined by economic policy preferences that impacted distinctively on internal commerce and international maritime trade in Lagos.

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Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

Nature Communications ◽

10.1038/s41467-021-22366-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Manon Ragonnet-Cronin ◽

Olivia Boyd ◽

Lily Geidelberg ◽

David Jorgensen ◽

Fabricia F. Nascimento ◽

...

Keyword(s):

Public Health ◽

Phylogenetic Analysis ◽

Genetic Evidence ◽

Health Interventions ◽

Morbidity And Mortality ◽

Whole Genome ◽

Public Health Interventions ◽

Epidemic Size ◽

Travel Restrictions ◽

Pharmaceutical Interventions

AbstractUnprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.

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The impact of public health interventions on the future prevalence of ESBL-producing Klebsiella pneumoniae: a population based mathematical modelling study

10.1101/19012765 ◽

2019 ◽

Author(s):

Luisa Salazar-Vizcaya ◽

Andrew Atkinson ◽

Andreas Kronenberg ◽

Catherine Plüss-Suard ◽

Roger Kouyos ◽

...

Keyword(s):

Public Health ◽

Transmission Rate ◽

Health Interventions ◽

Resistant Bacteria ◽

Antimicrobial Consumption ◽

Public Health Interventions ◽

The Future ◽

Non Local ◽

The Impact ◽

Local Transmission

AbstractBackgroundExtended-spectrum betalactamase (ESBL-) producing K. pneumoniae is one of the most common causes of infections with antimicrobial resistant bacteria worldwide. The spread of colonization of humans with this pathogen is on the rise. The future prevalence of colonization with ESBL-producing K. pneumoniae, and the potential of public health interventions to lower it, remain uncertain.MethodsBased on detailed data on antimicrobial consumption and susceptibility systematically recorded for over 13 years in a Swiss region, we developed a mathematical model to i) reconstruct the observed course of colonization with ESBL-producing K. pneumoniae; and ii) to assess the potential impact of public health interventions on future trends in colonization.ResultsSimulated prevalence of colonization with ESBL-producing K. pneumoniae stabilized in the near future when rates of antimicrobial consumption and in-hospital transmission remained stable in the main analyses (simulated prevalence in 2025 was 5.3% (5.0%-9.1%) in hospitals and 2.7% (2.1%-4.6%) in the community versus 5.6% (5.1%-9.5%) and 2.8% (2.2%-5.0%) in 2019). The largest changes in future prevalence were observed in simulations that assumed changes in overall antimicrobial consumption. When overall antimicrobial consumption was set to decrease by 50%, prevalence in 2025 declined by 89% in hospitals and by 84% in the community. A 50% decline in transmission rate within hospitals led to a reduction in prevalence of 43% in hospitals and of 13% in the community by 2025. Prevalence changed much less (≤9%) across scenarios with reduced carbapenem consumption. Assuming higher rates for the contribution from external sources of colonization, led to decreasing estimations of future prevalence in hospitals. While high uncertainty remains on the magnitude of these contribution, the best model fit suggested that as much as 46% (95% CI: 12%-96 %) of observed colonizations could be attributable to sources other than human-to-human transmission within the geographical setting (i.e., non-local transmission).ConclusionsThis study suggests that overall antimicrobial consumption will be, by far, the most powerful driver of future prevalence and that a large fraction of colonizations could be attributed to non-local transmission.

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Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread

10.1101/2021.01.04.20232520 ◽

2021 ◽

Author(s):

Tapfumanei Mashe ◽

Faustinos Tatenda Takawira ◽

Leonardo de Oliveira Martins ◽

Muchaneta Gudza-Mugabe ◽

Joconiah Chirenda ◽

...

Keyword(s):

Public Health ◽

Demographic Data ◽

The United States ◽

International Travel ◽

Health Interventions ◽

Whole Genome Sequence ◽

Public Health Interventions ◽

Regional Migration ◽

First Case ◽

Local Transmission

AbstractZimbabwe reported its first case of SARS-Cov-2 infection in March 2020, and case numbers increased to more than 8,099 to 16th October 2020. An understanding of the SARS-Cov-2 outbreak in Zimbabwe will assist in the implementation of effective public health interventions to control transmission. Nasopharyngeal samples from 92,299 suspected and confirmed COVID-19 cases reported in Zimbabwe between 20 March and 16 October 2020 were obtained. Available demographic data associated with those cases identified as positive (8,099) were analysed to describe the national breakdown of positive cases over time in more detail (geographical location, sex, age and travel history). The whole genome sequence (WGS) of one hundred SARS-CoV-2-positive samples from the first 120 days of the epidemic in Zimbabwe was determined to identify their relationship to one another and WGS from global samples. Overall, a greater proportion of infections were in males (55.5%) than females (44.85%), although in older age groups more females were affected than males. Most COVID-19 cases (57 %) were in the 20-40 age group. Eight lineages, from at least 25 separate introductions into the region were found using comparative genomics. Of these, 95% had the D614G mutation on the spike protein which was associated with higher transmissibility than the ancestral strain. Early introductions and spread of SARS-CoV-2 were predominantly associated with genomes common in Europe and the United States of America (USA), and few common in Asia at this time. As the pandemic evolved, travel-associated cases from South Africa and other neighbouring countries were also recorded. Transmission within quarantine centres occurred when travelling nationals returning to Zimbabwe. International and regional migration followed by local transmission were identified as accounting for the development of the SARS-CoV-2 epidemic in Zimbabwe. Based on this, rapid implementation of public health interventions are critical to reduce local transmission of SARS-CoV-2. Impact of the predominant G614 strain on severity of symptoms in COVID-19 cases needs further investigation.

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