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

Carbon isotope fluctuations in Precambrian carbonate sequences of several localities in Brazil

Carbon isotope fluctuations in Precambrian sedimentary carbonates between 2.8 Ga and 0.60 Ga in Brazil are examined in this study. The carbonate facies of the BIF of the 2.8 Ga-old Carajás Formation, state of Pará in northern Brazil, has rather homogeneous delta13C (-5 o/ooPDB), compatible with carbonatization of a silicate protolith by a CO2-rich fluid from mantle degassing. The Paleoproterozoic Gandarela Formation, state of Minas Gerais, displays a narrow delta13C variation (-1.5 to +0.5 o/oo) compatible with carbon isotope signatures of carbonates deposited around 2.4 Ga worldwide. The Fecho do Funil Formation has probably recorded the Lomagundi delta13C positive anomaly (+6.4 to +7.1 o/ooPDB). The magnesite-bearing carbonates of the Orós mobile belt, state of Ceará, exhibit carbon isotope fluctuation within the range for carbonates deposited at 1.8 Ga. The C-isotope record of the Frecheirinha Formation, northwestern state of Ceará, shows negative delta13C values in its lower portion (-2 o/oo) and positive values up section (+1 to +3 o/oo), which suggests this sequence is a cap carbonate deposited after a glacial event around 0.95 Ga. The Jacoca and Acauã sedimentary carbonate Formations, state of Sergipe, NE Brazil, show carbon isotope fluctuations very similar to each other (average around -5 o/oo), compatible with a deposition around 0.76 Ga. The younger Olho D'Água carbonate Formation, however, also in the state of Sergipe, displays negative delta13C values at the lower portion of the Formation, changing dramatically up section to positive values as high as +10 o/oo, a characteristic compatible with a Sturtian cap carbonate deposited around 0.69 Ga. On the light of the C isotope data discussed in this study, it seems that delta13C fluctuations in Paleoproterozoic carbonates in Brazil are within the range found globally for metasedimentary carbonates of this age. Carbon isotope data proved to be very useful in establishing relative chronology of Neoproterozoic carbonate formations for which precise radiometric ages are not available

Carbon isotope fluctuations in Precambrian carbonate sequences of several localities in Brazil

Carbon isotope fluctuations in Precambrian sedimentary carbonates between 2.8 Ga and 0.60 Ga in Brazil are examined in this study. The carbonate facies of the BIF of the 2.8 Ga-old Carajás Formation, state of Pará in northern Brazil, has rather homogeneous delta13C (-5 o/ooPDB), compatible with carbonatization of a silicate protolith by a CO2-rich fluid from mantle degassing. The Paleoproterozoic Gandarela Formation, state of Minas Gerais, displays a narrow delta13C variation (-1.5 to +0.5 o/oo) compatible with carbon isotope signatures of carbonates deposited around 2.4 Ga worldwide. The Fecho do Funil Formation has probably recorded the Lomagundi delta13C positive anomaly (+6.4 to +7.1 o/ooPDB). The magnesite-bearing carbonates of the Orós mobile belt, state of Ceará, exhibit carbon isotope fluctuation within the range for carbonates deposited at 1.8 Ga. The C-isotope record of the Frecheirinha Formation, northwestern state of Ceará, shows negative delta13C values in its lower portion (-2 o/oo) and positive values up section (+1 to +3 o/oo), which suggests this sequence is a cap carbonate deposited after a glacial event around 0.95 Ga. The Jacoca and Acauã sedimentary carbonate Formations, state of Sergipe, NE Brazil, show carbon isotope fluctuations very similar to each other (average around -5 o/oo), compatible with a deposition around 0.76 Ga. The younger Olho D'Água carbonate Formation, however, also in the state of Sergipe, displays negative delta13C values at the lower portion of the Formation, changing dramatically up section to positive values as high as +10 o/oo, a characteristic compatible with a Sturtian cap carbonate deposited around 0.69 Ga. On the light of the C isotope data discussed in this study, it seems that delta13C fluctuations in Paleoproterozoic carbonates in Brazil are within the range found globally for metasedimentary carbonates of this age. Carbon isotope data proved to be very useful in establishing relative chronology of Neoproterozoic carbonate formations for which precise radiometric ages are not available