Materials and Correspondence
Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, George Githinji ([email protected])
This study did not generate new unique reagents, but raw data and code generated as part of this research can be found in the Supplemental files as well as on public resources as specified in the Data and Code Availability section below.
Data and Code Availability
- SARS-CoV-2 sequence data used in this analysis are publicly available from GSAID
- Source code that was used in the analysis of this work is available from GitHub ( https://github.com/george-githinji/SARS-CoV-2_KE) and data used to create the figures can also be found in the supplemental files.
Experimental model and Subject details
The samples were collected under the Kenya Ministry of Health (MoH) protocols as part of the national response to the COVID-19 pandemic. The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU) that sits at the Kenya Medical Research Institute (KEMRI) headquarters in Nairobi (SERU # 4035).
The authors would like to thank members of the county rapid response teams who collected nasal and oral swabs, and all the frontline workers at the health and testing facilities. Special thanks to the COVID-19 testing team at KWTRP who conducted the laboratory PCR assays. We are grateful to those who have shared genome sequence data on GISAID (https://www.gisaid.org/). We thank the ARTIC Network (https://artic.network/) for providing us with primers and technical input and teams from the Oxford Nanopore Technology for the technical and material support. We would also like to acknowledge Prof La Scola Bernard for providing us with a heat-inactivated SARS-CoV-2 positive control that were used to validate our sequencing assays.
This work was supported by the National Institute for Health Research (NIHR) (project references 17/63/82 and 16/136/33 using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office and Wellcome Trust (grant# 102975; 220985)
G.G. is funded and supported by NIHR funded GeMVi and TIBA projects (Grant number 17/63/82 and 16/136/33). C.A. is funded by the Initiative to Develop African Research Leaders (IDeAL) through the DELTAS Africa Initiative [DEL-15-003]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)’s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa’s Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust [107769/Z/10/Z] and the UK government. The views expressed in this publication are those of the authors and not necessarily those of AAS, NEPAD Agency, Wellcome Trust NIHR or the Department of Health and Social Care or the UK government.
This was submitted for publication with permission from Director of KEMRI.
G.G., D.J.N., C.A., I.O., G.W., S.M.K, A.A., P.B. Conceptualised and designed the study
G.G., S.K.M., Z.R.L., D.O.O., J.M.M. performed sequencing and provided laboratory support
C.A., G.G., D.J.N. Provided phylogenetic analysis
B.T., I.O., A.A., E.B., C.A., K.K., R.A., J.K., E.M., B.K., T.S., M.M., J.N., J.O., B.S., provided administration and support for sample collection
E.O., G.G., C.A., S.K.M., provided data curation and analysis
G.G., C.A., D.J.N., G.W., I.O., B.T., P.B., wrote the original manuscript draft
All contributors wrote, reviewed and edited the final manuscript
Declaration of Interests
D.J.N. is a member of the National COVID-19 Modelling Technical Committee, for the Ministry of Health, Government of Kenya. K.K., R.A., J.K. are from the Ministry of Health, Government of Kenya. E.M., B.K., T.S., M.M., J.N., J.O., B.S. are from the respective county departments of health. All other authors declare no competing interests.