SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern
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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.
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SciScore for 10.1101/2022.05.31.22275802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We used the resulting alignment to estimate an unrooted maximum-likelihood phylogeny using IQ-TREE v2.1.2 under a general time-reversible model with empirical base frequencies and assuming among-site rate heterogeneity by means of a discretized gamma distribution with four rate categories (GTR+F+G4). IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing …SciScore for 10.1101/2022.05.31.22275802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We used the resulting alignment to estimate an unrooted maximum-likelihood phylogeny using IQ-TREE v2.1.2 under a general time-reversible model with empirical base frequencies and assuming among-site rate heterogeneity by means of a discretized gamma distribution with four rate categories (GTR+F+G4). IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, we do acknowledge a limitation in our study in the form of suboptimal sampling in the North-East of Rwanda, which is mostly covered by the Akagera National Park and where the border to Uganda had been closed from February 2019 to January 2022. We can compare our own results to those of a recent study in Benin which focused on the emergence of the Delta lineage (Yadouleton et al., 2022). In Benin, Delta first appeared around May and became dominant by June 2021, similarly to what was observed in Rwanda and in some other neighbouring African countries (see Figure 6). Shortly after Delta became dominant (in August and September 2021), a spike in cases was observed, which is again similar to what was observed in our own study. A large COVID-19 wave around this time period was also observed in Malawi, Zambia, Kenya and Uganda. While Benin is far removed geographically from Rwanda, we also observe notable similarities when comparing the Rwandan lineage replacement patterns with those of Uganda, Rwanda’s neighboring country to the north. A recent Ugandan study using 266 naso-oropharyngeal samples collected during June-December 2021 shows the same pattern of replacement of A.23.1 by Delta, starting March 2021 and peaking in June 2021 (Bbosa et al., 2022). This similarity in patterns is not surprising as this was previously observed with A.23.1, when it became the dominant lineage in both countries by the end of 2020 (Figure 5, (Bugembe et al., 2021). Moreover, our previous s...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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