Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

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.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

“…However, we may not have enough resolution in the geospatial data to know whether and to what extent they were truly cocirculating throughout these countries or whether there were regional outbreaks of Alpha and Beta within these countries. In Kenya, for example, Beta was detected more frequently in coastal regions and Alpha more frequently inland ( 26 , 44 ). By contrast, the Delta and Omicron variants sequentially dominated most infections on the entire continent shortly after their emergence (Fig.…”

“…Scaling up sequencing in Africa has provided a wealth of information on how the pandemic unfolded on the continent. The epidemic has largely been spatially heterogeneous across Africa, but most countries have experienced multiple waves of infection (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29), with substantial local and regional diversity in the first wave and to a lesser extent in the second wave, followed by successive sweeps of the continent with Delta and Omicron (Fig. 1A).…”

Temporal distribution and clinical characteristics of the Alpha, Delta and Omicron SARS-CoV-2 variants of concern in Laikipia, Kenya: institutional and community-based genomic surveillance

“…Viral ribonucleic acids (RNA) were extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Manchester, UK). SARS-CoV-2 was detected using the Da An Gene Co. detection kit (DaANGene, Guangdong, China) targeting the N and ORF1ab as previously described 3 .…”

“…Import/export analysis Mugration analysis was as previously described 3 using Kenyan sequences from other regions as background data. Briefly, Viral Import and export events were counted between Laikipia and the rest of the regions in Kenya.…”

“…In Kenya, the first positive SARS-CoV-2 case was confirmed on 12 th March 2020. During the first two waves of infection, the dominant lineages were mainly B.1 and B.1.1 3 . However, in early 2021 the VOCs replaced the ancestral strain lineages to drive the three subsequent major waves of infection, observed between March and December 2021 4,5 .…”