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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Sodium dodecyl sulphate-treated nanohydroxyapatite as an efficient shale stabilizer for water-based drilling fluids

Drilling water-sensitive shale formations often leads to wellbore instability, resulting in drilling problems because of the clay's high-water affinity. To solve this problem, different nanoparticles (NPs), such as nanosilica, have been used to formulate water-based muds with potassium chloride (KCl-WBM). Nevertheless, the unmatched pore size of shale pores when using nanosilica fails to completely prevent shale swelling and dispersion. This study discusses the effects of KCl-WBM with sodium dodecyl sulphate-treated nanohydroxyapatite (nHAp/SDS) on shale swelling inhibition through various laboratory techniques. These techniques encompass the linear swell meter (LSM), the dynamic linear swell meter (DLSM), hot-rolling dispersion, suspension stability, and pore structure characterization of shale. The rheological and filtration characteristics of nHAp/SDS and compatibility tests were also studied, and the results were compared with those of nanosilica and KCl-WBM. At all concentrations, the performance of the nHAp/SDS test fluids surpassed that of nanosilica. When compared with KCl-WBM system at 10 cP and 25 °C, the nHAp/SDS and nanosilica concentrations increased the plastic viscosity by 20–90 % and 10–70 %, respectively. The inhibitory effect of nHAp/SDS surpasses that of conventional KCl-WBM and inorganic nanosilica. By adding 2.0 wt% nHAp/SDS to KCl-WBM, the shale swelling decreased from 10.1 to 4.7 % (a 53.4 % reduction). Nanosilica also reduced the swelling to 6.1 % (a 39.6 % reduction) during the LSM test at 25 °C. Under the DLSM test conditions, the shale swelling increased due to the activation of the clay platelet site at an increased temperature of 80 °C. For instance, between 25 and 80 °C, the DLSM test revealed that the shale plug height expanded from 6.1 to 9.8 % for 2.0 wt% nanosilica, 4.7–7.6 % for 2.0 wt% nHAp/SDS, and 10.1–18.8 % for KCl-WBM. Furthermore, the recovery rate of hot-rolled shale plugs with KCl-WBM increased from 89.8 to 96.2 % for nHAp/SDS and 76.6 to 88.8 % for nanosilica from the initial rates of 52.1–63.3 % between 65 and 120 °C. The contact angle results showed that nHAp/SDS is hydrophobic, reducing shale-water attraction. Moreover, the 12 nm nanosilica matches nanopore sizes to partially block shale pores. This research found that nHAp/SDS has the potential to improve wellbore stability