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

Rheological Properties and Reverse Micelles Conditions of PEO-PPO-PEO Pluronic F68: Effects of Temperature and Solvent Mixtures

The rheological properties of Pluronic F68 were dissolved in various water/organic liquid mixtures over a wide range of temperatures, all at a concentration of 20 mg/mL. We have considered the following binary mixtures: Pluronic F68/water, F68/p-xylene, and F68/phenol. Various conformational transitions were detected and interpreted. We have also shown that these mixtures retain a Newtonian behavior independently of temperature and conformational changes. For ternary F68/p-xylene/water, F68/phenol/water, and F68/water/phenol mixtures, the behaviour of the solution is intimately related to the temperature and the amount of water and organic solvent added

Thermo-fluidic significance of non Newtonian fluid with hybrid nanostructures

The main purpose of this investigation is to analyze the flow and heat transfer behavior of a non Newtonian fluid (Oldroyd B fluid) with hybrid nanostructure subject to externally inclined magnetic field. Cattaneo Christov heat flux model is incorporated in the energy equation. Non linear thermal radiation and viscous dissipation mechanisms are considered. Shooting technique is implemented to accomplish the numerical solution. The outcomes of the numerical computations are discussed with the aid of relevant graphs. The performed study reveals that rise in magnetic field strength shows opposite behavior to fluid velocity and temperature. Thermal relaxation time factor controls the rate of heat transportation. Rise in curvature parameter accelerates the fluid flow while that of angle of inclination of magnetic field imparts the reverse effect

Applications of activation energy along with thermal and exponential space-based heat source in bioconvection assessment of magnetized third grade nanofluid over stretched cylinder/sheet

This research presents the bioconvection flow of third grade nanofluid confined by a stretched cylinder in presence of thermal radiation, heat absorption/generation phenomenon, activation energy and exponential space-based heat source. The famous Buongiorno nanofluid is used applications to access the Brownian motion and thermophoresis effects. The problem is formulated in terms of partial differential equations by using the fundamental laws. The dimensionless form of problem is obtained equations by using suitable transformation. Later on, the numerical outcomes for the couple of discretized system are obtained by employing the powerful numerical shooting algorithm. Since this investigation is based on some theoretical flow assumptions, therefore each physical parameter specified some constant range like 0.1≤β1≤1.2,0.4≤β2≤1.2,0.1≤β3≤1.2, 0.2≤Re≤0.8, 0.1≤λ≤1.4, 0.1≤M≤1.2, 0.1≤Nr≤1.2, 0.1≤Nc≤1.3, 0.0≤Rd≤0.8, 2.0≤Pr≤5.0, 0.1≤Nb≤0.25, 0.1≤Nt≤0.4,1.5≤θw≤1.8, 1.2≤Le≤2.4, 0.1≤E≤0.4, 1.2≤Lb≤2.4, 0.1≤Pe≤1.2, 0.1≤δ1≤0.6, 0.1≤λ1≤0.4,. 0.1≤λ2≤0.4, 0.2≤λ3≤0.5. The physical significance of prominent parameters versus subjective flow profiles are graphically underlined with physical justifications. It is observed that presence of exponential space-based heat source and heat source parameter is more useful to improve the nanofluid temperature. An increment in nanofluid concentration is observed with solutal Biot number and activation energy parameter. Moreover, the microorganisms profile decline with bioconvection Lewis number while reverse trend is observed for microorganism stratification Biot number

Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains

Bayesian Skyline Plots for Demographic Reconstruction using NS5B sequences.

<p>A) subtype 2c, B) subtype 2k; X-axis: Date in Years; Y-axis: Estimated effective number of infections; Bold Line: Mean Effective Number of viral population. Upper and lower Lines: Upper and Lower HPD95% (High Population Density) of Effective Number of viral population.</p

The timeline of HCV subtype 2c introduction in Tunisia.

<p>The timeline of HCV subtype 2c introduction in Tunisia.</p

Phylogenetic analysis of isolates from Subtype 2k.

<p>Phylogenetic analyses were performed using the Maximum Composite Likelihood method included in the MEGA package (version 5.1). The reliability of the phylogenetic constructions was estimated by bootstrap analysis with 1000 pseudo replicate data sets. The tree is based on the analysis of a 222-nucleotide long fragment in the NS5B region (nucleotides 8346 to 8568 according to the H77-1a prototype strain, AF009606). It includes the 11 studied Tunisian sequences (in red) and 39 HCV-2k field sequences from other countries (in black). All the sequences were indicated by their Accession Numbers followed by the country code and the collection date. The country codes according to the standard abbreviation are: France (FRA), Martinique (MTQ), Canada (CAN), Russia (RUS), United Kingdom (GBR), Uzbekistan (UZB), Azerbaijan (AZE), Morocco (MAR), Iran (IRN) and Moldova (MDA).</p