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

Size-resolved dust and aerosol contaminants associated with copper and lead smelting emissions : implications for emission management and human health

Mining operations, including crushing, grinding, smelting, refining, and tailings management, are a significant source of airborne metal and metalloid contaminants such as As, Pb and other potentially toxic elements. In this work, we show that size-resolved concentrations of As and Pb generally follow a bimodal distribution with the majority of contaminants in the fine size fraction (< 1 μm) around mining activities that include smelting operations at various sites in Australia and Arizona. This evidence suggests that contaminated fine particles (< 1 μm) are the result of vapor condensation and coagulation from smelting operations while coarse particles are most likely the result of windblown dust from contaminated mine tailings and fugitive emissions from crushing and grinding activities. These results on the size distribution of contaminants around mining operations are reported to demonstrate the ubiquitous nature of this phenomenon so that more effective emission management and practices that minimize health risks associated with metal extraction and processing can be developed.7 page(s

Windblown Dust Deposition Forecasting and Spread of Contamination around Mine Tailings

Wind erosion, transport and deposition of windblown dust from anthropogenic sources, such as mine tailings impoundments, can have significant effects on the surrounding environment. The lack of vegetation and the vertical protrusion of the mine tailings above the neighboring terrain make the tailings susceptible to wind erosion. Modeling the erosion, transport and deposition of particulate matter from mine tailings is a challenge for many reasons, including heterogeneity of the soil surface, vegetative canopy coverage, dynamic meteorological conditions and topographic influences. In this work, a previously developed Deposition Forecasting Model (DFM) that is specifically designed to model the transport of particulate matter from mine tailings impoundments is verified using dust collection and topsoil measurements. The DFM is initialized using data from an operational Weather Research and Forecasting (WRF) model. The forecast deposition patterns are compared to dust collected by inverted-disc samplers and determined through gravimetric, chemical composition and lead isotopic analysis. The DFM is capable of predicting dust deposition patterns from the tailings impoundment to the surrounding area. The methodology and approach employed in this work can be generalized to other contaminated sites from which dust transport to the local environment can be assessed as a potential route for human exposure

Hygroscopic properties and respiratory system deposition behavior of particulate matter emitted by mining and smelting operations

This study examines size-resolved physicochemical data for particles sampled near mining and smelting operations and a background urban site in Arizona with a focus on how hygroscopic growth impacts particle deposition behavior. Particles with aerodynamic diameters between 0.056-18 μm were collected at three sites: (i) an active smelter operation in Hayden, AZ, (ii) a legacy mining site with extensive mine tailings in Iron King, AZ, and (iii) an urban site, inner-city Tucson, AZ. Mass size distributions of As and Pb exhibit bimodal profiles with a dominant peak between 0.32 and 0.56 μm and a smaller mode in the coarse range (>3 μm). The hygroscopicity profile did not exhibit the same peaks owing to dependence on other chemical constituents. Submicrometer particles were generally more hygroscopic than supermicrometer ones at all three sites with finite water-uptake ability at all sites and particle sizes examined. Model calculations at a relative humidity of 99.5% reveal significant respiratory system particle deposition enhancements at sizes with the largest concentrations of toxic contaminants. Between dry diameters of 0.32 and 0.56 μm, for instance, ICRP and MPPD models predict deposition fraction enhancements of 171%-261% and 33%-63%, respectively, at the three sites.8 page(s

Outdoor/Indoor Contaminant Transport by Atmospheric Dust and Aerosol at an Active Smelter Site

Activities associated with mining operations including smelting, ore handling, and mine tailings management have been identified as sources of dust and aerosol that may contain metal and metalloid contaminants, such as lead (Pb) and arsenic (As). Previous studies on contaminant transport have concentrated on the potential impact of these particulate emissions in outdoor environments. The purposes of this study were (i) to quantify the effect of dust and aerosol particle size on contaminant transport from outdoor-to-indoor environments and (ii) to document the changes in particle chemical composition during transport through the outdoor/indoor barrier. Outdoor and indoor particulate samples were collected at a high school equipped with mechanical air filtration systems from 2016 to 2019. The school is located near a set of mine tailings and an active copper smelter in Hayden, Arizona. Particle size segregated samples were collected using a ten-stage micro-orifice uniform deposit impactor (MOUDI). Results show that airborne fine particles (aerodynamic diameters less than 1 micron) can penetrate to the indoor environment but in a reduced amount due to mechanical filtration. Aerosol in the fine fraction particulate air concentrations was around 50% of the corresponding outdoor values, but their mass concentration of contaminants was similar to outdoor values. Indoor coarse particles (> 1 micron) comprised close to 20% of the levels found in outdoor coarse particles. These results highlight the need to consider the impact of particle diameter when assessing indoor exposure and potential health effects in communities living under the direct influence of mining and smelter activities. © 2021, The Author(s), under exclusive licence to Springer Nature Switzerland AG.12 month embargo; published: 22 May 2021This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]