The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya

The emergence and establishment of SARS-CoV-2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS-CoV-2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wild-type virus. We estimate that more than 1000 SARS-CoV-2 introductions occurred in the two-year epidemic period (March 2020 - September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy.

Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves

BackgroundThe transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. MethodsWe undertook phylogenetic analysis of 747 SARS-CoV-2 positive samples collected across six counties in coastal Kenya during the first two waves (March 2020 - February 2021). Viral imports and exports from the region were inferred using ancestral state reconstruction (ASR) approach. ResultsThe genomes were classified into 35 Pango lineages, six of which accounted for 79% of the sequenced infections: B.1 (49%), B.1.535 (11%), B.1.530 (6%), B.1.549 (4%), B.1.333 (4%) and B.1.1 (4%). Four identified lineages were Kenya specific. In a contemporaneous global subsample, 990 lineages were documented, 261 for Africa and 97 for Eastern Africa. ASR analysis identified >300 virus location transition events during the period, these comprising: 69 viral imports into Coastal Kenya; 93 viral exports from coastal Kenya; and 191 inter-county import/export events. Most international viral imports (58%) and exports (92%) occurred through Mombasa City, a key touristic and commercial Coastal Kenya center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local virus transmission dominated, and distinct local phylogenies were seen. ConclusionsOur analysis supports moving control strategies from a focus on international travel to local transmission. FundingThis work was funded by Wellcome (grant#: 220985) and the National Institute for Health Research (NIHR), project references: 17/63/and 16/136/33 using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office.

Policy and research frame of the coronavirus disease 2019 (COVID-19) pandemic: reflections on urban informality.

How has the informality of urban slums exposed a gap in policy formulation and research questions in the wake of the coronavirus disease 2019 (COVID-19) pandemic? This paper seeks to identify the appropriate questions and policy frame that would assist future researchers and policymakers on the subject of pandemics in densely populated urban settlements. The authors argue that the nexus between asking the appropriate questions and developing appropriate policy response measures during a pandemic can significantly impact the outcome of the response. The paper examines how the government of Kenya's response to the COVID-19 pandemic reveals a deep-rooted socio-economic and cultural inequality when "blanket" policies are adopted without taking into consideration the unique dynamics characterizing the society. The findings show that the effectiveness of implementing COVID-19 containment policies such as lockdowns, the cession of movement, working from home, distance learning, and social distancing are affected by other factors such as the nature of jobs, one's income levels, where someone lives, cultural beliefs, access to water, sanitation, internet, and medical facilities. This means that a significant number of people within the society experience a double tragedy from the pandemic and impact of government response measures. Yet most of the existing literature has focused on the causes, spread, and impact of the pandemic on health institutions, economies, and public health with little emphasis on the impact on policy measures especially on the vulnerable segments of the society. This paper, therefore, looks at the question of how the various public health intervention strategies disrupt or construct the livelihood of the already complex informal settlement. It provides policymakers and researchers with a number of questions that can frame policy and research during a pandemic with important consideration to urban informality.

How urban 'informality' can inform response to COVID-19: a research agenda for the future.

In the era of increasingly defined ontological insecurity and uncertainty driven by the ravages of COVID-19, urban informal settlement has emerged as a source of resilience. Indeed, the effects of a pandemic transcends its epidemiological characteristics to political economy and societal resilience. If resilience is the capacity of a system to adapt successfully to significant challenges that threaten the function or development of the human society, then ontological insecurity is about the lack of such capacity. Drawing on Keith Hartian's understanding of 'informality' of spaces, this policy brief attempts to identify and frame a research agenda for the future. The agenda would assist future researchers and policymakers provide responses that appropriately recognize groups and actors that define the urban informal space.

Modeling a Pandemic (COVID-19) Management Strategy for Urban Slums Using Social Geometry Framework.

The purpose of this paper is to utilize social geometry framework to model a pandemic (COVID-19) management strategy in densely populated informal settlements in Kenya. Our central claim is that the containment strategy that was instituted to control spread of COVID-19 failed to recognize the socio-cultural and livelihood complexities of the urban slum residents. This unmitigated strategy predisposed the residents to risks of heightened transmission of the pandemic. Drawing on social geometry approach in the analysis of human relations, we reveal some insights offered by our experiences in theorizing about public health intervention (PHI) and in doing so develop an alternative analytical framework ('social pendulum') to support the development of a PHI strategy that is compatible with the swing-like lifestyle of residents in the informal settlements. Our conclusion revisits the reliability and validity criteria for the new framework and offers some direction for further research.

Cet article a pour but d'utiliser un cadre de géométrie sociale pour modéliser une stratégie de gestion de la pandémie (COVID-19) dans les zones d'habitation informelles et densément peuplées au Kenya. Nous partons du principe que la stratégie d'endiguement qui a été mise en place pour contrôler la propagation de la COVID-19 n'a pas réussi à prendre la mesure de la complexité socioculturelle, ni celle des moyens de subsistance, des habitants des bidonvilles urbains. Cette stratégie indiscriminée a exposé les habitants à des risques accrus de transmission de la pandémie. Le modèle de géométrie sociale, au contraire, a la possibilité d'influencer la refonte d'une stratégie alternative d'intervention de santé publique qui serait compatible avec la configuration unique des moyens de subsistance dans les zones d'habitation informelles, configuration qui adopte des mouvements de pendule. Nous élaborons un cadre analytique (du «pendule social¼) en nous basant sur ce mode de vie, pour appuyer le développement d'une stratégie alternative d'intervention de santé publique. Dans notre conclusion, nous revisitons les critères de fiabilité et de validité du nouveau cadre et offrons une orientation pour les études à venir.