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

Serum and fecal canine α1-proteinase inhibitor concentrations reflect the severity of intestinal crypt abscesses and/or lacteal dilation in dogs

Gastrointestinal (GI) protein loss, due to lymphangiectasia or chronic inflammation, can be challenging to diagnose. This study evaluated the diagnostic accuracy of serum and fecal canine α1-proteinase inhibitor (cα1PI) concentrations to detect crypt abscesses and/or lacteal dilation in dogs. Serum and fecal cα1PI concentrations were measured in 120 dogs undergoing GI tissue biopsies, and were compared between dogs with and without crypt abscesses/lacteal dilation. Sensitivity and specificity were calculated for dichotomous outcomes. Serial serum cα1PI concentrations were also evaluated in 12 healthy corticosteroid-treated dogs. Serum cα1PI and albumin concentrations were significantly lower in dogs with crypt abscesses and/or lacteal dilation than in those without (both P <0.001), and more severe lesions were associated with lower serum cα1PI concentrations, higher 3 days-mean fecal cα1PI concentrations, and lower serum/fecal cα1PI ratios. Serum and fecal cα1PI, and their ratios, distinguished dogs with moderate or severe GI crypt abscesses/lacteal dilation from dogs with only mild or none such lesions with moderate sensitivity (56-92%) and specificity (67-81%). Serum cα1PI concentrations increased during corticosteroid administration. We conclude that serum and fecal α1PI concentrations reflect the severity of intestinal crypt abscesses/lacteal dilation in dogs. Due to its specificity for the GI tract, measurement of fecal cα1PI appears to be superior to serum cα1PI for diagnosing GI protein loss in dogs. In addition, the serum/fecal cα1PI ratio has an improved accuracy in hypoalbuminemic dogs, but serum cα1PI concentrations should be carefully interpreted in corticosteroid-treated dogs

Mapping the Distinctive Populations of Lymphatic Endothelial Cells in Different Zones of Human Lymph Nodes

<div><p>The lymphatic sinuses in human lymph nodes (LNs) are crucial to LN function yet their structure remains poorly defined. Much of our current knowledge of lymphatic sinuses derives from rodent models, however human LNs differ substantially in their sinus structure, most notably due to the presence of trabeculae and trabecular lymphatic sinuses that rodent LNs lack. Lymphatic sinuses are bounded and traversed by lymphatic endothelial cells (LECs). A better understanding of LECs in human LNs is likely to improve our understanding of the regulation of cell trafficking within LNs, now an important therapeutic target, as well as disease processes that involve lymphatic sinuses. We therefore sought to map all the LECs within human LNs using multicolor immunofluorescence microscopy to visualize the distribution of a range of putative markers. PROX1 was the only marker that uniquely identified the LECs lining and traversing all the sinuses in human LNs. In contrast, LYVE1 and STAB2 were only expressed by LECs in the paracortical and medullary sinuses in the vast majority of LNs studied, whilst the subcapsular and trabecular sinuses lacked these molecules. These data highlight the existence of at least two distinctive populations of LECs within human LNs. Of the other LEC markers, we confirmed VEGFR3 was not specific for LECs, and CD144 and CD31 stained both LECs and blood vascular endothelial cells (BECs); in contrast, CD59 and CD105 stained BECs but not LECs. We also showed that antigen-presenting cells (APCs) in the sinuses could be clearly distinguished from LECs by their expression of CD169, and their lack of expression of PROX1 and STAB2, or endothelial markers such as CD144. However, both LECs and sinus APCs were stained with DCN46, an antibody commonly used to detect CD209.</p></div

CD209 expression in lymphatic sinuses.

<p>CD169⁺ APCs also expressed CD209 (A–D). Rare CD169⁺ CD209⁻ APCs were detected in one of the LNs assessed (B: middle panel marked with asterisk). CD209⁺CD169⁻ cells in the paracortical and medullary sinuses are likely to represent LECs (C–D). Serial LN sections stained with anti-CD209 (E) and DCN46 (F) showed that far fewer cells were stained by anti-CD209 antibody than by DCN46. Blue represents DAPI staining of cell nuclei (A–B, E–F). C,capsule; S, sinus. All scale bars represent 50 µm.</p

Assessing the phenotype of the APCs and LECs in the lymphatic sinuses.

<p>Within the sinuses in the paracortex and medulla, the PROX1⁺CD169⁻ LECs expressed the lymphatic marker LYVE1. The majority of PROX1⁻CD169⁺ APCs in the paracortical and medullary sinuses lacked LYVE1 expression (A), although rare cells in these sinuses appeared to co-express CD169 and LYVE1 (B). CD169⁺ APCs in the subcapsular and trabecular sinuses lacked LYVE1 (B). LYVE1 was expressed by a subset of the DCN46⁺ cells in the medullary sinuses, which are likely to represent the LECs (C). CD169⁺STAB2⁻ APCs were closely associated with the CD169⁻STAB2⁺ LECs in the paracortical and medullary sinuses (D–E). The subcapsular and trabecular sinuses did not express STAB2 (F), although CD169⁺ APCs were present. Blue represents DAPI staining of cell nuclei (D–F). C,capsule; T, trabecula; S, sinus. Scale bars represent 50 µm (A, C–E) and 100 µm (B, F).</p

Heterogeneous expression of LYVE1 and STAB2 by endothelial cells in lymphatic sinuses of human LNs.

<p>Low magnification images demonstrated that LYVE1 expression is restricted to the paracortical and medullary sinuses whilst the other sinuses in the superficial areas lack expression of this marker (A). PROX1⁺CD31⁺ LECs of the paracortical and medullary sinuses express LYVE1 (B) and STAB2 (D), whereas the LECs in the subcapsular and trabecular sinuses are negative for LYVE1 (C) and STAB2 (E). Blue represents DAPI staining of cell nuclei (A). P, paracortex; M, medulla; C, capsule; T, trabecula; S, sinus. All scale bars represent 100 µm.</p

Contrasting phenotypes of the lymphatic endothelial cells and blood endothelial cells in human lymph nodes.

<p>Contrasting phenotypes of the lymphatic endothelial cells and blood endothelial cells in human lymph nodes.</p

DCN46+ LECs and APCs can be identified by their expression of PROX1 and CD169 respectively.

<p>A dense body of cells staining for DCN46 was detected in the paracortical and medullary sinuses, which were located by their distinctive pattern of CD144 expression (A–B). In these regions, subsets of DCN46⁺ cells were found to co-express the exclusive lymphatic endothelial cell transcription factor PROX1 (C) and the APC marker CD169 (D). Simultaneous detection of DCN46, PROX1 and CD169 confirmed that the DCN46⁺ cells in the paracortical and medullary sinuses comprised two distinct populations: DCN46⁺PROX1⁺CD169⁻ LECs and DCN46⁺PROX1⁻CD169⁺ APCs (E). Blue represents DAPI staining of cell nuclei (A). C,capsule; T, trabecula; P, paracortex; M, medulla; H,hilum; S, sinus. All scale bars 50 µm (A–E).</p

Heat shock protein 10 and signal transduction: a “capsula eburnea” of carcinogenesis?

To date, little is known either about the physical interactions of heat shock protein 10 (Hsp10) with other proteins within the cell or its involvement in signal transduction pathways. Hsp10 has been considered mainly as a partner of Hsp60 in the Hsp60/10 protein folding machine. Only recently, Hsp10 was reported to interact with proteins involved in deoxyribonucleic acid checkpoint inactivation, termination of M-phase, messenger ribonucleic acid export, import of nuclear proteins, nucleocytoplasmic transport, and pheromone signaling pathways. At the same time, Hsp10 expression can be up-regulated in cancer cells, because it accumulates as the cell transformation progresses. Recent data suggest that Hsp10 may be not only a component of the folding machine but also an active player of the cell signaling network, influencing cell cycle, nucleocytoplasmic transport, and metabolism, with putative roles in the lack of cell differentiation and in the inhibition of apoptosis. In this review, we revise the involvement of Hsp10 in signal transduction pathways and its possible role in cancer etiology