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

Mise en évidence du dopage par la Nandrolone (aspects pré-analytiques et analytiques)

AIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Vitamin D deficiency and interleukin-17 relationship in severe obstructive sleep apnea–hypopnea syndrome

Purpose: We aimed to assess Vitamin D (VD) abnormalities in patients with severe obstructive sleep apnea–hypopnea syndrome (OSAHS), to study its association with clinical and polygraphic data, and to correlate VD levels with interleukin-17 (IL-17). Methods: Ninety-two patients with severe OSAHS were consecutively enrolled between September 2014 and February 2016 and compared to age-, sex-, and body mass index (BMI)-matched controls. Anthropometric parameters and medical history were collected. The serum levels of VD and IL-17 were determined by radioimmunoassay and enzyme-linked immunosorbent assay, respectively. Results: Ninety-two severe OSAHS patients and thirty controls were enrolled in the study. All OSAHS patients had VD deficiency. The mean level of VD was at 7.9 ng/ml among OSAHS group versus 16.8 ng/ml among control group. IL-17A levels were elevated (20.3 pg/ml) in OSAHS group compared to healthy group (10.05 pg/ml). VD levels were negatively correlated with nocturia severity (r = −0.26; P = 0.01) and positively correlated with mean O2saturation (r = 0.59; P = 0.02) and lowest O2saturation (r = 0.3; P = 0.03). IL-17 levels were positively correlated with nocturia severity (r = 0.24; P = 0.03) and negatively correlated with mean O2saturation (r = −0.42; P = 0.03). A significant negative association was observed between IL-7 and VD levels (r = −0.64, P = 0.2 10−4). The magnitude of this correlation was higher for important nocturia, lower MSaO2, or higher BMI. Conclusions: VD deficiency in patients with severe OSAHS is common with a negative association between IL-17 and VD serum levels. Hypoxia could play an important role in this association. Further studies are needed to clarify this relationship