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

The Effects of the Pesticides Imidacloprid, Atrazine, and Roundup on \u3cem\u3eDaphnia Magna\u3c/em\u3e Heart Rate

The purpose of this study was to see the effect of pesticides on aquatic organisms. It was hypothesized that the pesticide that would have the largest effect on Daphnia magna heart rate was atrazine and the pesticide that would have the least effect was imidacloprid. When conducting this experiment, there were three different pesticides (imidacloprid, atrazine, and roundup) that were each used twice in different dilutions of the recommended solution. For each pesticide, there were 15 Daphnia that were tested for each dilution. These Daphnia were all fed everyday. Once the solution was made and the Daphnia were put in their petri dishes, for 4 days straight, the Daphnia’s heart rates were observed through a microscope and recorded, mortality was also recorded. It was found that for both dilutions of the Roundup treatment, most Daphnia died by the second or third day. Daphnia died the most in both dilutions of the Roundup treatment due to its toxicity. The Roundup had the largest affect (F(6, 48)=69.92 , p\u3c0.001) on Daphnia heart rates and atrazine had the least effect on Daphnia heart rates. As each treatment got less diluted, more Daphnia died. Based on the one way ANOVA (figure 6), the treatments in order of lowest to highest heart rates are roundup (1/10 of the solution recommended by the manufacturer), imidacloprid (1/10), atrazine (1/10), atrazine (1/100), imidacloprid (1/100), and lastly roundup (1/100)

An Acylated Kaempferol Glycoside from Flowers of Foeniculum vulgare and F. Dulce

An acylated kaempferol glycoside, namely kaempferol-3-O-α-L-(2,3-di-E-pcoumaroyl)-rhamnoside (1) was isolated from the flowers of Foeniculum vulgare Mill. and F. dulce DC. It is thus isolated for the first time from family Apiaceae. In addition, the different organs of both plants afforded six flavonoid glycosides - namely afzelin (kaempferol-3-O-α-L-rhamnoside) (2), quercitrin (3), isorhamnetin-3-O-β-D-glucoside (4), isoquercitrin (5), rutin (6), and miquelianin (quercetin-3-O-β-D-glucuronide) (7). Structure elucidation of the above mentioned flavonoids was achieved by UV, 1H- and 13C-NMR, 1H-1H COSY, HMQC and EI-MS

Design, ecofriendly synthesis, anticancer and antimicrobial screening of innovative Biginelli dihydropyrimidines using β-aroylpyruvates as synthons

New ecofriendly Biginelli reaction procedures have been adapted to prepare new dihydropyrimidines (DHPMs) using a multicomponent one-pot reaction. All the synthesized compounds were evaluated for their anticancer activity against 59 human cancer cell lines and evaluated for their antimicrobial activities against representatives of both Gram-positive and Gram-negative bacteria. Compound 4 showed marked wide spectrum anticancer activity towards most of the tested cancer cell lines with a percentage of growth inhibition of 29.04–71.68% against leukemia cell line (K-562 and SR), lung cancer cell line (NCI-H522), five colon cancer cell lines (HCT-116, HCT-15, HT29, KM12 and SW-620), CNS cancer cell line (SF-295 and SNB-75), melanoma cell lines (MALME-3M and M14), renal cancer cell line (CAKI-1) and breast cancer cell lines (MCF7 and MDA-MB-468). The highest observed anticancer activity was against leukemia cell lines K-562 and SR with inhibition percentages of 64.97 and 71.68%, respectively. The renal cancer cell line (UO-31) was particularly sensitive towards all the evaluated compounds. Compounds including 2b and 5c exhibited antibacterial activity against S. aureus while 2a and 5b exhibited antifungal activity against C. albicans. The results also showed that compounds 2c and 5e exhibited both antibacterial and antifungal activity against S. aureus and C. albicans respectively

A rare case of marginal zone lymphoma in a 15-year old ataxia telangiectasia patient with massive bone marrow involvement and a challenging nodal diagnosis

This is a report of a very rare case of marginal zone lymphoma in a 15-years old male with Ataxia Telangiectasia. Besides being a rare diagnosis within the pediatric age group, this case exhibited a true challenge not only from diagnostic point of view but also regarding management plans. Marginal zone lymphoma is an indolent disease in which transformation is extremely rare particularly the pediatric subtype. However, there isn't enough data regarding marginal zone lymphoma in a sitting of immunodeficiency conditions had been published so far. The case described here showed some features pointing to more aggressive disease with massive bone marrow involvement and areas of focal transformation unlike the subtle pattern of infiltration that is usually seen in cases of marginal zone lymphoma. Another interesting finding in our case is the presence of a clone of CD4/CD8 double positive T-cells of moderate size (12%) with restricted expansion of Vb1 region. The significance of this clone is uncertain as it could be a transient reactive clone or a pre-malignant one. Keywords: Ataxia telangiectasia, Marginal zone lymphoma, Low grade lymphom

Probiotic Ameliorating Effects of Altered GABA/Glutamate Signaling in a Rodent Model of Autism

Autism spectrum disorders (ASDs) comprise a heterogeneous group of pathological conditions, mainly of genetic origin, characterized by stereotyped behavior, such as marked impairment in verbal and nonverbal communication, social skills, and cognition. Excitatory/inhibitory (E/I) imbalances have been recorded as an etiological mechanism of ASD. Furthermore, GABA, the main inhibitory neurotransmitter in adult life, is known to be much lower in both patients and rodent models of ASD. We propose correcting GABA signaling as a therapeutic strategy for ASD. In this study, 40 young male western Albino rats, 3–4 weeks in age, weighing about 60–70 g, were used. The animals were randomly assigned into six experimental groups, each including eight rats. Group I served as the control group and was orally administered phosphate-buffered saline. Groups II and III served as rodent models of ASD and were orally administered a neurotoxic dose of propionic acid (PPA). The rats in the three therapeutic groups (IV, V, and IV) received the same doses of PPA, followed by 0.2 g/kg body weight of pure Bifidobacterium infantis, a probiotic mixture of ProtexinR, and pure Lactobacillus bulgaricus, respectively, for 3 weeks. Selected variables related to oxidative stress, glutamate excitotoxicity, and gut bacteria were measured in the six groups. Both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating glutamate excitotoxicity as an autistic feature developed in the PPA-induced rodent model. Their therapeutic effects mostly involved the correction of oxidative stress, restoration of depleted GABA, and up-regulation of GABA receptor gene expression. Pure Bifidobacterium was the most effective, followed by the mixture of probiotics and finally lactobacillus. In conclusion, Bifidobacteria and lactobacilli can be used independently or in combination as psychobiotics to ameliorate oxidative stress and glutamate excitotoxicity as two confirmed etiological mechanisms through the gut–brain axis

Prognostic Value of BRAF, Programmed Cell Death 1 (PD1), and PD Ligand 1 (PDL1) Protein Expression in Colon Adenocarcinoma

Patients with colorectal cancer in different stages show variable outcomes/therapeutic responses due to their distinct tumoral biomarkers and biological features. In this sense, this study aimed to explore the prognostic utility of BRAF, programmed death-1 (PD1), and its ligand (PDL1) protein signatures in colon adenocarcinoma. The selected protein markers were explored in 64 archived primary colon adenocarcinomas in relation to clinicopathological features. BRAF overexpression was found in 39% of the cases and was significantly associated with grade 3, N1, advanced Dukes stage, presence of relapse, and shorter overall survival (OS). PD1 expression in the infiltrating immune cells (IICs) exhibited significant association with T2/T3, N0/M0, early Dukes stage, and absence of relapse. PDL1 expression in IICs is significantly associated with advanced nodal stage/distant metastasis, advanced Dukes stage, and shorter OS. Meanwhile, PDL1 expression in neoplastic cells (NC) was associated with the advanced lymph node/Dukes stage. A positive combined expression pattern of PDL1 in NC/IICs was associated with poor prognostic indices. Tumor PDL1 expression can be an independent predictor of OS and DFS. The multivariate analyses revealed that short OS was independently associated with the RT side location of the tumor, PD1 expression in stromal IICs, and PDL1 expression in NC. In conclusion, overexpression of BRAF in colon adenocarcinoma is considered a poor prognostic pathological marker. In addition, PDL1 expression in NC is considered an independent prognostic factor for DFS/OS. Combined immunohistochemical assessment for BRAF and PD1/PDL1 protein expressions in colon adenocarcinoma might be beneficial for selecting patients for future targeted therapy

Evaluation of inactivated avian influenza virus and Newcastle disease virus bivalent vaccination program against newly circulated H5N8 and NDV strains

ABSTRACT: Avian influenza virus (AIV) and Newcastle disease virus (NDV) are respiratory illness syndromes that have recently been detected in vaccinated flocks and are causing major financial losses in the chicken farming industry. The objective was to evaluate the efficacy of Valley Vac H5Plus NDVg7 vaccine in protecting chickens against the H5N8 and NDV strains that have recently been circulating in comparison with the efficacy of the commercially available bivalent H5+ND7 vaccine. In contrast to the H5+ND7 vaccine, which was made of genetically distinct H5N8/2018 clade 2.3.4.4b genotype group (G5), H9N2/2016, H5N1/2017, and genetically comparable NDV genotype VII 1.1/2019 of the recently circulating challenge viruses, the Valley Vac H5Plus NDVg7 vaccine consisted of the recently isolated (RG HPAI H5N1 AIV/2015 Clade 2.2.1.2, RG HPAIV H5N8/2020 Clade 2.3.4.4b genotype group 6 (G6), and NDV genotype VII 1.1/2012) which were genetically similar to challenged strains. To determine the effectiveness of the Valley Vac H5Plus NDVg7 vaccine, a total of 70-day-old commercial chicks were divided into 7 groups of 10 birds each. Groups (G1 and G4) received Valley Vac H5Plus NDVg7 vaccine. Groups (G2 and G5) groups received commercial H5+ND7 vaccine. While groups (G3 and G6) were kept nonvaccinated, and group (G7) was kept as a nonchallenged and nonvaccinated. After 3-wk post vaccination (WPV), groups G1, G2, and G3 were challenged with A/Duck/ Egypt/SMG4/2019(H5N8) genotype G6. On the other hand, groups G4, G5, G6 were challenged with NDV/EGYPT/18629F/2018 genotype VII 1.1 with an intranasal injection of 0.1 mL. Antibody titer was calculated at the first 3 wk after vaccination, and the viral shedding titer was calculated at 3-, 5-, and 7-days post challenge. Mortality and morbidity rates were monitored daily during the experiment, and for the first 10 d after the challenge, to provide an estimate of the protection rate. The results showed that a single dosage of 0.5 mL per bird of Valley Vac H5Plus NDVg7 vaccine provides 80% protection against both H5N8 and NDV, compared to the bivalent H5+ND7 vaccine, which provided 20 and 80% protection against H5N8 and NDV, respectively. In addition, 0.5 mL per bird of Valley Vac H5Plus NDVg7 vaccine produced a greater immune response against both viruses than commercial vaccination at 1 to 3 WPV with a significant difference at 1 WPV for H5N8 and a comparatively higher immune response for NDV. Furthermore, it reduced virus shedding of H5N8 on the third, fifth, seventh, and tenth days lower than H5+ND7 vaccine with a significant difference on the third day for H5N8 and relatively lower than bivalent H5+ND7 vaccine for NDV with a significant difference on the fifth day. The Valley vaccinated group demonstrated more tissue intactness compared to the commercially vaccinated group against the H5N8 challenge, however the bivalent commercially vaccinated group showed the similar level of tissue integrity against NDV. In conclusion, Valley Vac H5Plus NDVg7  that contains the  genetically similar strain to recently circulating challenged virus (H5N8 genotype G6) provided better protection with greater immune response and decreased the amount of virus shed against H5N8 genotype G6 and showed less histopathological alteration than the commercial bivalent H5+ND7 vaccine that contain genetically distinct (H5N8 genotype G5). However the Valley Vac H5Plus NDVg7 provided the same protection with relatively high immune response and  relatively decreased the amount of virus shed and showed equal tissue integrity than the commercial bivalent H5+ND7 vaccine against NDV genotype VII 1.1 that contain the same genotype of NDV genotype VII 1.1

Antioxidant and Anti-Inflammatory Potential of Thymoquinone and Lycopene Mitigate the Chlorpyrifos-Induced Toxic Neuropathy

CPF (chlorpyrifos) is an organophosphate pesticide used in agricultural and veterinary applications. Our experiment aimed to explore the effects of thymoquinone (TQ) and/or lycopene (LP) against CPF-induced neurotoxicity. Wistar rats were categorized into seven groups: first group served as a control (corn oil only); second group, TQ (10 mg/kg); third group, LP (10 mg/kg); fourth group, CPF (10 mg/kg) and deemed as CPF toxic control; fifth group, TQ + CPF; sixth group, (LP + CPF); and seventh group, (TQ + LP + CPF). CPF intoxication inhibited acetylcholinesterase (AchE), decreased glutathione (GSH) content, and increased levels of malondialdehyde (MDA), an oxidative stress biomarker. Furthermore, CPF impaired the activity of antioxidant enzymes including superoxide dismutase (SOD) and catalase (CAT) along with enhancement of the level of inflammatory mediators such as tumor necrosis factor-α (TNF-α), interleukin (IL)-6, and IL-1β. CPF evoked apoptosis in brain tissue. TQ or LP treatment of CPF-intoxicated rats greatly improved AchE activity, oxidative state, inflammatory responses, and cell death. Co-administration of TQ and LP showed better restoration than their sole treatment. In conclusion, TQ or LP supplementation may alleviate CPF-induced neuronal injury, most likely due to TQ or LPs’ antioxidant, anti-inflammatory, and anti-apoptotic effects