26 research outputs found
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
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Issues involved with non-characterized control of methanotrophic bacteria
Methane-utilizing bacteria, methanotrophs, have application as biocatalysts in the commodity chemical production, waste treatment and environmental remediation industries. Methanotrophs have the ability to oxidize many chemical compounds into more desired products, such as the production of propylene oxide. Methanotrophs can also degrade toxic compounds such as trichloroethylene. However, there are many physical, chemical and biological problems associated with the continuous oxidation of chemicals. These include, low mass transfer of methane, oxygen and propylene; toxicity of substrates and degradation products, and competition between the growth substrate, i.e., methane and chemical feed stock, e.g., propylene for the biocatalyst. To supervise methanotrophic bioprocesses, an intelligent control system must accommodate any biological limitations, e.g., toxicity, and mitigate the impact of the physical and chemical limitations, e.g., mass transfer of methane and the solubility of propylene. The intelligent control system must have the capability to assess the current conditions and metabolic state of the bacteria; recognize and diagnose instrument faults; and select and maintain sets of parameters that will result in high production and growth
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Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation
Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, ïżœLeptospirillumïżœ, ïżœFerromicrobiumïżœ, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery
Alcohol Consumption Does not Impede Recovery from Mild to Moderate Traumatic Brain Injury
A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.Diabetes mellitus: pathophysiological changes and therap
Measurement of the charged-current electron (anti-)neutrino inclusive cross-sections at the T2K off-axis near detector ND280
The electron (anti-)neutrino component of the T2K neutrino beam constitutes the largest background in the measurement of electron (anti-)neutrino appearance at the far detector. The electron neutrino scattering is measured directly with the T2K off-axis near detector, ND280. The selection of the electron (anti-)neutrino events in the plastic scintillator target from both neutrino and anti-neutrino mode beams is discussed in this paper. The flux integrated single differential charged-current inclusive electron (anti-)neutrino cross-sections, dÏ/dp and dÏ/d cos(Ξ), and the total cross-sections in a limited phase-space in momentum and scattering angle (p > 300 MeV/c and Ξ †45°) are measured using a binned maximum likelihood fit and compared to the neutrino Monte Carlo generator predictions, resulting in good agreement