Publication online - Rapid replacement of the SARS-CoV-2 Beta variant by the Delta variant in South Africa - ceri.africa/publication/?t… 
The Delta variant was imported to South Africa primarily from India, spread rapidly in all provinces, and became dominant within 3 months of introduction. Associated with a resurgence in community transmission and a 3rd wave which was associated with a high number of deaths
We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant.
As the second wave decreased, Beta disappears (in green) and as Delta increased prevalence (in red) the third wave starts in South Africa. We also mapped a new lineage, the C.1.2 (yellow) in time and space in South Africa.
These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat.
Phylogenetic reconstruction of the Delta variant with 5602 SARS-CoV-2 Delta sequences from South Africa. We identifying a very large monophyletic cluster and inference of viral introduction events Spatiotemporal reconstruction of the spread of Delta in South Africa.
These findings provide more support that, at this stage in the pandemic, the inherent increased transmissibility of the Delta variant compared to ancestral strains and other VOCs (like Beta), gives it a transmission fitness advantage.
Although genomic surveillance in Africa remains heterogeneous there is good evidence that Delta has also rapidly replaced Beta in many other African countries - see our dashboard in Africa - genomics.africa/sars-cov-2-das… from previous paper (Wilkinson et al Science 2021).
In conclusion, the Delta variant rapidly replaced the Beta variant in South Africa and fueled a 3rd wave which was associated with a high number of deaths. This again highlights the importance of strengthening genomic surveillance to support the ongoing pandemic response.
To this end, we recently reported the emergence
and functional characterization one such lineage (C.1.2) and we are monitoring this closely to assess how
it competes with the dominant Delta.
and functional characterization one such lineage (C.1.2) and we are monitoring this closely to assess how
it competes with the dominant Delta.
The continued evolution of SARS-CoV-2 is a reminder of
the ongoing public health threat and highlights the importance of addressing vaccine inequity and
accelerating vaccine delivery in all parts of the world.
the ongoing public health threat and highlights the importance of addressing vaccine inequity and
accelerating vaccine delivery in all parts of the world.
So many people to thank! @houzhou @rjlessells @EduanWilkinson @Mittenavoig and all of the supporting funders @AfricaCDC @RockefellerFdn @RickABright @NICD @DrPatSoonShiong @MRCza @dsigovza @illumina @NIH
As we release this paper, we launch the Centre for Epidemic Response and Innovation (CERI) @StellenboschUni @UKZN @DrPatSoonShiong @RockefellerFdn and bringing the largest @illumina @fdesouza sequencers so Africa can lead in genomics surveillance - ceri.africa
Manuscript submitted for per review and deposited in medRxiv - until come online, we are making open access in the CERI website - ceri.org.za/publication/?t…
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