ABSTRACT
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.
Subject(s)
Hepatitis D , Breakthrough Pain , COVID-19ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 19 (COVID-19), is a single-stranded positive-sense ribonucleic acid (RNA) virus that typically undergoes one to two single nucleotide mutations per month. COVID-19 continues to spread globally, with case fatality and test positivity rates often linked to locally circulating strains of SARS-CoV-2. Furthermore, mutations in this virus, in particular those occurring in the spike protein (involved in the virus binding to the host epithelial cells) have potential implications in current vaccination efforts. In Rwanda, more than twenty thousand cases have been confirmed as of March 14th 2021, with a case fatality rate of 1.4% and test positivity rate of 2.3% while the recovery rate is at 91.9%. Rwanda started its genomic surveillance efforts, taking advantage of pre-existing research projects and partnerships, to ensure early detection of SARS-CoV-2 variants and to potentially contain the spread of variants of concern (VOC). As a result of this initiative, we here present 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in the country from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the newly emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the VOCs, B.1.1.7 and B.1.351, among incoming travelers tested at Kigali International Airport. We also discuss the potential impact of COVID-19 control measures established in the country to control the spread of the virus. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations during the time frame of interest. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences are currently available or that no longer report positive cases. Our results point to the importance of systematically screening all incoming travelers, regardless of the origin of their travels as well as regional considerations for durable response to COVID-19.