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

Electrical and Structural properties of Copper Oxide (CuO) Thin Films on Plastic Substrate Deposited by Spray Pyrolysis Technique

 In this paper, copper oxide (CuO) thin films were deposited on polyimide plastic substrates by spray pyrolysistechnique at different temperatures from 250 to 300°C. All the deposited films were characterized by X-ray diffraction (XRD) technique, ultraviolet (UV)-visible spectrophotometer, and hall effect measurements for the investigation of structural, optical, and electrical properties. The effects of substrate temperature onthe structural, optical, and electrical properties of the films were studied. The XRD results revealed that all the CuO films have a facecentered cubic structure. The crystallite grain size was calculated using Scherrer formula and it was found that at the substrate temperature of 300°C, the CuO film presented maximum crystallitegrain size of about 81.2 nm. The root mean square (RMS) roughness of the films was measured by scanning tunneling microscopy. RMS was increased with the rise of temperature. The optical transmission measurements by UV-visible spectrophotometer were used to determine the energy gap of the CuO films. Results showed thatthe optical energy gap has decreased with increasing the substrate temperature. Hall effect measurements showed that all the films are of p-type conductivity. Depending on the substrate temperature, hall measurement showed that the electrical resistivity and carrier concentration are varied from 77.4 Ω cm to 52.7 Ω cm and from 6.3 x1015 cm-3 to  10.1 x1015 cm-3., respectively

Homozygous mutation in the ADH6 gene, involved in alcohol metabolism, associated with a multisystem disorder, analogous to the fetal alcohol syndrome

Introduction: In humans, there is considerable individual variability in ethanol metabolism, and these differences have been partially attributed to genetic variability at the ADH locus at 4q22-23, where seven genes are found. They encode ADH enzymes with different kinetic and structural properties that represent the first step in a series of reactions involved in the metabolism and elimination of alcohol from the body. The objective of the study was to identify the potential genetic cause in a patient with congenital metabolic encephalopathy of unknown etiology, and having similarities to fetal alcohol syndrome. Case: We described a patient of Moroccan origin who suffered from a multisystem disorder compatible with congenital metabolic encephalopathy. The main clinical characteristics observed in the patient were psychomotor retardation, facial dysmorphism, microcephaly, and hematologic and endocrine abnormalities. Whole exome sequencing identified a homozygous missense mutation c.133G > A (p.Gly45Arg) in ADH6, a gene implicated in alcohol metabolism and previously not associated with human disease. The variant segregates well with the disease in the family, affects a highly conserved amino acid and was predicted to be damaging. Bioinformatics analysis revealed that the Gly45Arg substitution may affect the structure and function of the ADH6 protein. No other potential causal gene under an autosomal recessive inheritance model was found. Discussion: The patient presented with a congenital metabolic encephalopathy, and having similarities to fetal alcohol syndrome due to prenatal alcohol exposure. The only potential causing variant was identified in the ADH6, belonging to the Class V ADH which is a predominantly fetal alcohol dehydrogenase. In addition, he presented vacuolated lymphocytes, anemia and abnormalities of endocrine function, all have been reported to be related to an abnormal alcohol metabolism. Conclusion: We identified a novel variant in ADH6, involved in the metabolism of alcohol, in a patient with a hereditary alcohol metabolism encephalopathy syndrome