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

Molecular screening of gastric Helicobacter pullorum recovered from different avian species in Egypt

Helicobacter pullorum ( H. pullorum) is a bacterium that colonizes the intestines of poultry and causes gastroenteritis. Because these species are known as human and/or animal pathogens, identification of H. pullorum is becoming increasingly necessary. The bacterium has been linked to colitis and hepatitis in humans after being transmitted by infected meat consumption. Misdiagnosis of other enteric zoonotic pathogens such as Campylobacter and other Helicobacter species makes the diagnosis of H. pullorum extremely difficult. This study focused on the molecular detection of H. pullorum from the stomach (proventriculus and gizzard) of different avian species as new target organs for detection and transmission between avian species. Proventriculus and gizzards were obtained from 40 freshly dead chickens and resident wild birds (n=40). Diarrhea was found in the farms that were surveyed. DNA was extracted from all collected samples to conduct PCR amplification. The samples were screened for Helicobacter genus-specific 16s using C97 and C05 primers. To confirm the existence of H. pullorum, the positive samples were sequenced. H. pullorum was recorded in two out of 40 chicken samples. In addition, H. pullorum was recorded in one out of 40 resident wild birds. The 16S rRNA gene sequence for Helicobacter genus-specific in poultry and wild birds showed a 100% homology. In conclusion, broiler chickens and resident wild birds are possible reservoirs for H. pullorum, according to this report, and possibly act as a source of infection for humans via the food supply

Screening for autoimmune diseases in type 1 diabetes: Low incidence of adrenal insufficiency

AbstractObjectivesPrimary Adrenocortical insufficiency (Addison's disease) is a potentially fatal condition that often develops incidentally and can be easily overlooked. Although rare in the general population, it is more common in patients with type 1 diabetes mellitus (T1D). In this study, we reviewed our experience with the occurrence of associated adrenal insufficiency (AI) in children with T1D over 15 year's period at King Khalid University Hospital (KKUH), Riyadh, Saudi ArabiaMethodsThis is a retrospective hospital based study, included children and adolescents with T1D at KKUH in the period January 1995–December 2012. All patients were serologically screened for Celiac and thyroid diseases. Adrenal function was assessed at the time of diagnosis, and annually thereafter by measuring serum cortisol and adrenal corticotrophic hormone (ACTH) using the available commercial kit. Adrenal cortex antibodies (AAA) test was done by Bioscientia laboratory, Germany, in one patient.ResultsIn a cohort of 305 children and adolescents with T1D at KKUH, only one patient was found to have AI as a part of autoimmune polyendocrine syndrome type 1. Thyroid functions were abnormal in 65 (21.3%) patients. Of these, 26 (8.5%) patients have evidence of overt hypothyroidism and 39 (12.8%) patients had subclinical hypothyroidism. In twenty-six patients (8.5%), the intestinal biopsy results were positive for CD.ConclusionThere is no international consensus on the issue of screening for AI in children with T1D. In our experience, we do not favour screening for AI in children with T1D unless there is a clear risk factor

In silico prediction of B cell epitopes and experimental validation on wheat allergens

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Comparison of IgE-binding epitopes on wheat gliadins for patients with food allergy and experimentally sensitized mice

International audienceMice models of allergy to wheat proteins have been recently developed but have not been characterized for epitope pattern. In our laboratory, mice were sensitized with total gliadins and produced IgE antibodies that recognize the different gliadin classes :α,β,γ, *1,2 and *5. The relevance of this mouse model has to be evaluated regarding IgE-binding epitopes. The aim of the study is to compare B-cell epitopes in wheat allergic patients and sensitized mice in order to find out whether IgE antibodies elicited in mice are representative of human ones