SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern

The emergence of the SARS-CoV-2 Delta variant of concern (lineage B.1.617.2) in late 2020 resulted in a new wave of infections in many countries across the world, where it often became the dominant lineage in a relatively short amount of time. We here report on a novel genomic surveillance effort in Rwanda in the time period from June to September 2021, leading to 201 SARS-CoV-2 genomes being generated, the majority of which were identified as the Delta variant of concern. We show that in Rwanda, the Delta variant almost completely replaced the previously dominant A.23.1 and B.1.351 (Beta) lineages in a matter of weeks, and led to a tripling of the total number of COVID-19 infections and COVID-19-related fatalities over the course of only three months. We estimate that Delta in Rwanda had an average growth rate advantage of 0.034 (95% CI 0.025-0.045) per day over A.23.1, and of 0.022 (95% CI 0.012-0.032) over B.1.351. Phylogenetic analysis reveals the presence of at least seven local Delta transmission clusters, with two of these clusters occurring close to the border with the Democratic Republic of the Congo, and another cluster close to the border with Tanzania. A smaller Delta cluster of infections also appeared close to the border with Uganda, illustrating the importance of monitoring cross-border traffic to limit the spread between Rwanda and its neighboring countries. We discuss our findings against a background of increased vaccination efforts in Rwanda, and also discuss a number of breakthrough infections identified during our study. Concluding, our study has added an important collection of data to the available genomes for the Eastern Africa region, with the number of Delta infections close to the border with neighboring countries highlighting the need to further strengthen genomic surveillance in the region to obtain a better understanding of the impact of border crossings on lowering the epidemic curve in Rwanda. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement We would like to acknowledge the work of Christian Happi, Enatha Mukantwari, Idowu Olawoye, Paul Oluniyi, Umuringa Jeanne D arc, Esperance Umumararungu, Arlene Uwituze and Onikepe Folarin. This research was supported by the Academie de Recherche et Enseignement Superieur (ARES) and from the Government of Rwanda through RBC/National Reference Laboratory in collaboration with the Belgian Development Agency (ENABEL) for additional genomic sequencing at GIGA Research Institute-Liege/Belgium. The views expressed in this publication are those of the authors and not necessarily those of the NIHR, the National Institute of Health Research, the Department of Health and Social Care or the Rwandan Government. SLH acknowledges support from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, G0D5117N). NB, SD and GB acknowledge support from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G098321N). SD also acknowledges support from the Fonds National de la Recherche Scientifique (F.R.S.-FNRS, Bel-gium; grant number F.4515.22) and from the European Union Horizon 2020 project MOOD (grant agreement number 874850). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/M010996/1]. A.OT is supported by the Wellcome Trust Hosts, Pathogens & Global Health Programme [grant number: grant.203783/Z/16/Z] and Fast Grants [award number: 2236]. GB acknowledges support from the Internal Funds KU Leuven (Grant No. C14/18/094) and the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, G0E1420N). Computational resources have been provided by the Consortium des Equipements de Calcul Intensif (CECI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under Grant number 2.5020.11 and by the Walloon Region. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Rwanda National Ethics Committee (FWA Assurance No. 00001973 IRB 00001497 of IORG0001100/15April2020). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors