Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Githinji, George; Laurent, Zaydah R. de; Mohammed, Khadija Said; Omuoyo, Donwilliams O.; Macharia, Peter M.; Morobe, John M.; Otieno, Edward; Kinyanjui, Samson; Agweyu, Ambrose; Maitha, Eric; Kitole, Ben; Suleiman, Thani; Mwakinangu, Mohamed; Nyambu, John; Otieno, John; Salim, Barke; Kasera, Kadondi; Kiiru, John; Aman, Rashid; Barasa, Edwine; Warimwe, George M.; Bejon, Philip; Tsofa, Benjamin; Ochola‐Oyier, Lynette Isabella; Nokes, D. James; Agoti, Charles N.

doi:10.1038/s41467-021-25137-x

Cited by 39 publications

(41 citation statements)

References 25 publications

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Section: Discussionmentioning

confidence: 62%

“…Of the >2,800 SARS-CoV-2 genomes reported from Kenya in the current and other recent studies [37,38], there has been no VoC emerging from the country, with only B.1.525 ( Eta ) that was detected in February 2021 in the Nairobi classified as variant of interest. Studies point at increased transmissibility and capacity to evade the immune response as the key factors associated with dominance of the VoCs [39,40].…”

Section: Discussionmentioning

confidence: 73%

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Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Nasimiyu

Matoke-Muhia

Rono

et al. 2022

Preprint

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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.

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Section: Discussionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 73%

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Nasimiyu

Matoke-Muhia

Rono

et al. 2022

Preprint

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“…The Alpha, Beta and Delta variants of SARS-CoV-2 have circulated in Kenya,[47] displaying a pattern of sequential dominance. From December 2020, Alpha and Beta variants increased in frequency ([48] Fig. S2), with a complex spatial pattern of relative frequency of Alpha vs Beta within Kenya.…”

Section: Supplementary Informationmentioning

confidence: 99%

“…S2), with a complex spatial pattern of relative frequency of Alpha vs Beta within Kenya. [48] Then, from May 2021, the frequency of Delta variant increased very rapidly to complete domination across Kenya (Fig. S2).…”

Section: Supplementary Informationmentioning

confidence: 99%

Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya

Orangi

Ojal

Brand

et al. 2022

Preprint

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BackgroundFew studies have assessed the benefits of COVID-19 vaccines in settings where most of the population had been exposed to SARS-CoV-2 infection.MethodsWe conducted a cost-effectiveness analysis of COVID-19 vaccine in Kenya from a societal perspective over a 1.5-year time frame. An age-structured transmission model assumed at least 80% of the population to have prior natural immunity when an immune escape variant was introduced. We examine the effect of slow (18 months) or rapid (6 months) vaccine roll-out with vaccine coverage of 30%, 50% or 70% of the adult (> 18 years) population prioritizing roll-out in over 50-year olds (80% uptake in all scenarios). Cost data were obtained from primary analyses. We assumed vaccine procurement at $7 per dose and vaccine delivery costs of $3.90-$6.11 per dose. The cost-effectiveness threshold was USD 919.FindingsSlow roll-out at 30% coverage largely targets over 50-year-olds and resulted in 54% fewer deaths (8,132(7,914 to 8,373)) than no vaccination and was cost-saving (ICER=US$-1,343 (-1,345 to - 1,341) per DALY averted). Increasing coverage to 50% and 70%, further reduced deaths by 12% (810 (757 to 872) and 5% (282 (251 to 317) but was not cost-effective, using Kenya’s cost-effectiveness threshold ($ 919.11). Rapid roll-out with 30% coverage averted 63% more deaths and was more cost-saving (ICER=$-1,607 (-1,609 to -1,604) per DALY averted) compared to slow roll-out at the same coverage level, but 50% and 70% coverage scenarios were not cost-effective.InterpretationWith prior exposure partially protecting much of the Kenyan population, vaccination of young adults may no longer be cost-effective.KEY QUESTIONSWhat is already known?The COVID-19 pandemic has led to a substantial number of cases and deaths in low-and middle-income countries.COVID-19 vaccines are considered the main strategy of curtailing the pandemic. However, many African nations are still at the early phase of vaccination.Evidence on the cost-effectiveness of COVID-19 vaccines are useful in estimating value for money and illustrate opportunity costs. However, there is a need to balance these economic outcomes against the potential impact of vaccination.What are the new findings?In Kenya, a targeted vaccination strategy that prioritizes those of an older age and is deployed at a rapid rollout speed achieves greater marginal health impacts and is better value for money.Given the existing high-level population protection to COVID-19 due to prior exposure, vaccination of younger adults is less cost-effective in Kenya.What do the new findings imply?Rapid deployment of vaccines during a pandemic averts more cases, hospitalisations, and deaths and is more cost-effective.Against a context of constrained fiscal space for health, it is likely more prudent for Kenya to target those at severe risk of disease and possibly other vulnerable populations rather than to the whole population.

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“…Tracking the spread and evolution of the SARS-CoV-2 virus at global, national, and regional scales has been aided by the analysis of genomic sequence and epidemiological data (1)(2)(3)(4)(5)(6)(7). SARS-CoV-2 genomics contextual data, also known as genomic sequence "metadata", includes laboratory (e.g.…”

Section: Introductionmentioning

confidence: 99%

The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information

Gill¹,

Griffiths²,

Dooley³

et al. 2022

Preprint

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Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations, as well as research. In order to make use of pathogen genomics data, it must be interpreted using contextual data (metadata). Contextual data includes sample metadata, laboratory methods, patient demographics, clinical outcomes, and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration, and its use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating, and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool’s web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission.In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

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Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Cited by 39 publications

References 25 publications

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya

The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information

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