The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The Kaapvaal Craton, South Africa: no evidence for a supercontinental affinity prior to 2.0 Ga?

We briefly examine the possible antiquity of the supercontinental cycle while noting the likely unreliability of palaeomagnetic data >ca.1.8 Ga, assuming a gradual change from a magmatically dominated Hadean Earth to a plate tectonically dominated Neoarchaean system. A brief review of one of Earth’s oldest cratons, Kaapvaal, where accent is placed on the lithostratigraphic and geodynamic-chronological history of its cover rocks from ca. 3.1 to 2.05 Ga, forms the factual basis for this article. The ca. 3.1–2.8 Ga Witwatersrand–Pongola (Supergroups) complex retroarc flexural foreland basin developed while growth and stabilization of the craton were still underway. Accretion of relatively small composite granite-gneiss-greenstone terranes (island arc complexes) from both north and west does not support the formation of a Neoarchaean supercontinent, but may well have been related to a mantle plume which enhanced primary gold sources in the accreted terranes and possibly controlled the timing and rate of craton growth through plate convergent processes. Subsequent deformation of the Witwatersrand Basin fill with concomitant loss of ≤1.5 km of stratigraphy must have been due to far-field tectonic effects, but no known mobile belt or even greenstone belts can be related to this contractional event. At ca. 2714–2709 Ma, a large mantle plume impinged beneath the thinned crust underlying theWitwatersrand Basin forming thick, locally komatiitic flood basalts at the base of the Ventersdorp Supergroup, with subsequent thermal doming leading to graben basins within which medial bimodal volcanics and immature sediments accumulated. Finally (possibly at ca. 2.66–2.68 Ga), thermal subsidence enabled the deposition of uppermost Ventersdorp sheet-like lavas and sediments, with minor komatiites still present. Ongoing plume-related influences are thus inferred, and an analogous cause is ascribed to a ca. 2.66–2.68 Ga dike swarm to the north of the Ventersdorp, where associated rifting allowed formation of discrete ‘protobasinal’ depositories of the Transvaal (ca. 2.6–2.05 Ga Supergroup, preserved in three basins). Thin fluvial sheet sandstones (Black Reef Formation, undated) above these lowermost rift fills show an association with localized compressive deformation along the palaeo-Rand anticline, north of Johannesburg, but again with no evidence of any major terrane amalgamations with the Kaapvaal. From ca. 2642 to 2432 Ma, the craton was drowned with a long-lived epeiric marine carbonate-banded iron formation platform covering much of it and preserved in all three Transvaal Basins (TB). During this general period, at ca. 2691–2610 Ma, the Kaapvaal Craton collided with a small exotic terrane [the Central Zone (CZ), Limpopo Belt] in the north. Although farfield tectonic effects are likely implicit in TB geodynamics, again there is no case to be made for supercontinent formation. Following an 80–200 million years (?) hiatus, with localized deformation and removal of large thicknesses of chemically precipitated sediments along the palaeo-Rand anticline, the uppermost Pretoria Group of the Transvaal Supergroup was deposited. This reflects two episodes of rifting associated with volcanism, and subsequent thermal subsidence within a sag basin setting; an association of the second such event with flood basalts supports a plume affinity. At ca. 2050 Ma the Bushveld Complex intruded the northern Kaapvaal Craton and reflects a major plume, following which Kaapvaal–CZ collided with the Zimbabwe Craton, when for the first time, strong evidence exists for a small supercontinent assembly, at ca. 2.0 Ga. We postulate that the long-lived evidence in favour of active mantle (cf. plume) influences with subordinate and localized tectonic shortening, implicit within the review of ca. 3.1–2.05 Ga geological history of the Kaapvaal Craton, might reflect the influence of earlier Precambrian mantle-dominated thermal systems, at least for this craton.University of Pretoria and the National Research Foundation of South Africa.http://www.tandfonline.com/loi/tigr20nf201