Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kenya
- University of Leuven, Belgium
- Ministry of Health, Kenya
- Uganda Virus Research Institute, Uganda
Abstract
Background: Detailed understanding on SARS-CoV-2 regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.
Methods: Here, we analysed 1,139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction and virus dispersal between counties were estimated using discrete phylogeographic analysis.
Results: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; nine of which occurred in both waves, and four seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1 and N.8). Most of the sequenced infections belonged to lineage B.1 (n=723, 63%) which predominated in both Wave 1 (73%, followed by lineages N.8 (6%) and B.1.1 (6%)) and Wave 2 (56%, followed by lineages B.1.549 (21%) and B.1.530 (5%). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many COVID-19 government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.
Conclusions: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.
Funding: This work was funded by The Wellcome (grant numbers; 220985, 203077/Z/16/Z, and 222574/Z/21/Z) 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.
Data availability
1) Sequence data have been deposited in GISAID database under accession numbers provided in Supplement File 22) Source Data files have been provided for Figures 1-2 and 4-10.3) Source Code associated with the figures has been uploaded (Source Code File 1) and also been made available through Harvard Dataverse
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Replication Data for: Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two wavesHarvard Dataverse, V3, UNF:6:RL6Vg7q0JyS7YoCkjhHe1A== [fileUNF].
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Genomic epidemiology of SARS-CoV-2 in coastal Kenya (March - July 2020)Github; sars-cov-2-early-phase-manuscript.
Article and author information
Author details
Donwilliams O Omuoyo
Funding
National Institute for Health Research (17/63/82)
- D James Nokes
National Institute for Health Research (16/136/33)
- Charles N Agoti
- Samson Kinyanjui
- George Warimwe
- D James Nokes
- George Githinji
Wellcome Trust (220985)
- D James Nokes
- George Githinji
Wellcome Trust (203077/Z/16/Z)
- Edwine Barasa
- Benjamin Tsofa
- Philip Bejon
Wellcome Trust (220977/Z/20/Z)
- My Phan
- Matthew Cotten
Medical Research Council (NC_PC_19060)
- My Phan
- Matthew Cotten
H2020 European Research Council (n{degree sign}874850)
- Simon Dellicour
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Mary Kate Grabowski, Johns Hopkins University, United States
Ethics
Human subjects: Samples analysed here were collected under the Ministry of Health protocols as part of the national COVID-19 public health response. The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU) at Kenya Medical Research Institute (KEMRI), Nairobi, Kenya (SERU protocol #4035). Individual patient consent was not required by the committee for the use of these samples for studies of genomic epidemiology to inform public health response.
Version history
- Received: June 27, 2021
- Preprint posted: July 7, 2021 (view preprint)
- Accepted: June 10, 2022
- Accepted Manuscript published: June 14, 2022 (version 1)
- Version of Record published: July 14, 2022 (version 2)
Copyright
© 2022, Agoti et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study
eLife 11:e71703.
https://doi.org/10.7554/eLife.71703
Further reading
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- Epidemiology and Global Health
Paxlovid, a SARS-CoV-2 antiviral, not only prevents severe illness but also curtails viral shedding, lowering transmission risks from treated patients. By fitting a mathematical model of within-host Omicron viral dynamics to electronic health records data from 208 hospitalized patients in Hong Kong, we estimate that Paxlovid can inhibit over 90% of viral replication. However, its effectiveness critically depends on the timing of treatment. If treatment is initiated three days after symptoms first appear, we estimate a 17% chance of a post-treatment viral rebound and a 12% (95% CI: 0%-16%) reduction in overall infectiousness for non-rebound cases. Earlier treatment significantly elevates the risk of rebound without further reducing infectiousness, whereas starting beyond five days reduces its efficacy in curbing peak viral shedding. Among the 104 patients who received Paxlovid, 62% began treatment within an optimal three-to-five-day day window after symptoms appeared. Our findings indicate that broader global access to Paxlovid, coupled with appropriately timed treatment, can mitigate the severity and transmission of SARS-Cov-2.
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- Epidemiology and Global Health
Background:
Circulating omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) have been associated with various chronic diseases and mortality, but results are conflicting. Few studies examined the role of omega-6/omega-3 ratio in mortality.
Methods:
We investigated plasma omega-3 and omega-6 PUFAs and their ratio in relation to all-cause and cause-specific mortality in a large prospective cohort, the UK Biobank. Of 85,425 participants who had complete information on circulating PUFAs, 6461 died during follow-up, including 2794 from cancer and 1668 from cardiovascular disease (CVD). Associations were estimated by multivariable Cox proportional hazards regression with adjustment for relevant risk factors.
Results:
Risk for all three mortality outcomes increased as the ratio of omega-6/omega-3 PUFAs increased (all Ptrend <0.05). Comparing the highest to the lowest quintiles, individuals had 26% (95% CI, 15–38%) higher total mortality, 14% (95% CI, 0–31%) higher cancer mortality, and 31% (95% CI, 10–55%) higher CVD mortality. Moreover, omega-3 and omega-6 PUFAs in plasma were all inversely associated with all-cause, cancer, and CVD mortality, with omega-3 showing stronger effects.
Conclusions:
Using a population-based cohort in UK Biobank, our study revealed a strong association between the ratio of circulating omega-6/omega-3 PUFAs and the risk of all-cause, cancer, and CVD mortality.
Funding:
Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institute of Health under the award number R35GM143060 (KY). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
