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

Ultrasound appearances of liver hydatid disease

PubMed ID: 7225721The grey scale ultrasound features of liver hydatid disease have been evaluated on 65 surgically proven cysts in 38 patients. The majority of cysts showed the well-known ultrasound pattern of simple cysts. However, a minority of lesions were either multicystic or gave the appearance of a cyst within a cyst. Occasionally cysts showed a feature which we have called 'the ultrasonographic water lily sign'. Hydatid sand was also occasionally seen in the most dependent portion of hydatid cysts. We have noted that if a hydatid cyst becomes secondarily infected these typical ultrasound patterns are lost and the ultrasound diagnosis may then become more difficult

Encysted peritoneal hydatidosis, unusual ultrasonographic and clinical presentation of liver echinococcosis

PubMed ID: 7225722[No abstract available

Expansion characteristics of a nutritious extruded snack food using response surface methodology

Response surface methodology was used to analyze the effect of screw speed (220-340 rpm), feed moisture (11.0-15.0%, wet basis) and feed rate (22.0-26.0 kg/h, wet basis) on the physical properties (i.e., bulk density, expansion, porosity) of a nutritionally balanced extruded snack food. Regression equations describing the effect of each variable on the responses were obtained. Responses were most affected by changes in screw speed followed by feed moisture and feed rate (P<0.05). Expansion and porosity increased with screw speed and feed moisture whereas the opposite was observed for bulk density. Radial expansion was found to be a better index to measure the extent of expansion than the axial and overall expansions, indicated by a higher correlation coefficient. © Springer-Verlag 2004.Acknowledgements The authors would like to thank DEFRA and the partners of the LINK Eating, Food and Health Programme (EFH 11) in their support of this research

Inactivation effect of probiotic biofilms on growth of Listeria monocytogenes [Listeria monocytogenes’in gelişimi üzerine probiyotik biyofilmlerin ınaktivasyon etkisi]

Probiotic lactic acid bacteria and their biofilms have antagonistic activity against food spoilage organisms and pathogenic bacteria. Recently, researchers focused on the use of probiotic biofilms for inhibition of pathogenic bacteria. The aim of this research is to improve probiotic biofilms with optimal prebiotic concentration and to determine their inactivation effect on both planktonic cells and biofilm growth of Listeria monocytogenes. Biofilm formations were detected by using microplate method. Prebiotic ingredients were used to form biofilm with highest viable probiotic cell counts and optimal concentrations of prebiotic ingredients were determined according to the response surface method. Biofilm produced by Lactobacillus casei Shirota and Lactobacillus rhamnosus contained 9.46 and 9.66 log cfu/mL viable cell counts, respectively. Optimal prebiotic concentrations were found 3% casein peptone-0% fructo-oligosaccharides (FOS) for biofilm formation with highest viable cell counts by L. casei Shirota and 1.5% casein peptone-1.5% FOS for biofilm formation with highest viable cell counts by L. rhamnosus. Probiotic biofilms exhibited inactivation against growth of L. monocytogenes and caused a reduction of 0.66- 2.01 log cfu/mL for planktonic L. monocytogenes and 0.40-1.69 log cfu/ml for L. monocytogenes biofilm. Planktonic cells of L. monocytogenes were observed to be more susceptible to probiotic biofilms than biofilm of L. monocytogenes. Biofilm of L. rhamnosus showed higher inhibition effect on L. monocytogenes growth than L. casei Shirota. These findings showed that biofilms of probiotic Lactobacillus strains used in this study may be excellent candidate for controlling of pathogenic bacteria. © 2017, Veteriner Fakultesi Dergisi. All rights reserved

Effect of extrusion process on the antioxidant activity and total phenolics in a nutritious snack food

The effect of screw speed (220-340 rpm), moisture content of the feed (11.0-15.0%, wet base) and feed rate (22.0-26.0 kg h-1, wet base) on the total antioxidant capacity (TAA) and concentration of total phenolics (TP) in a nutritionally balanced extruded snack were investigated. Regression equations describing the effect of each variable on the responses were obtained. Results indicated that screw speed, moisture content of the feed and feed rate had an effect on the TAA values of the samples at 95% confidence interval (CI). The interaction between the three factors was also found to be significant at 95% CI for TAA values. Extrusion conditions applied in this study did not change the TP values in the samples. The TAA value of samples decreased with an increase in screw speed and decrease in moisture content. © 2005 Institute of Food Science and Technology Trust Fund

Heat shock protein 70 expression in neonatal rats after hypoxic stress

Objectives: The tissue damage due to hypoxia in newborns is to some-extent age-dependent; organs of premature babies are more vulnerable to hypoxic insult than full-term neonates. The aim of this immunohistochemical study was to investigate the role of heat shock protein 70 (HSP70), a stress-inducible protein, in developing the response to hypoxia in premature newborns. Methods: Postnatal day-7 rats (corresponding to a human fetus of 32-34 weeks' gestation) and day-12 rats (corresponding to a full-term newborn infant) (n = 7) were subjected to mild hypoxia at 33°C. Control rats (n = 7) for each group breathed room air for 4 h. After 4 h of recovery, the animals were killed, and brains, hearts and kidneys were removed for immunohistochemical staining. Results: Immunohistochemically, HSP70 expression was found to be induced in the hippocampus and myocardium after exposure to hypoxia. The level of HSP70 expression in the hippocampus after hypoxic stress was significantly higher in the 12-day rats than in the 7-day rats (p = 0.03). However, HSP70 expression in the myocardium did not show any significant difference between the two groups. In addition, no significant induction of HSP70 expression was apparent in the kidney of rats exposed to hypoxia or in any organ of the control animals. Conclusions: We conclude that diminished HSP70 expression in the hippocampus of premature newborns may play a critical role in developing the response to hypoxic stress. However, HSP70 expression in the heart and the kidney after exposure to hypoxia did not appear to be related to fetal maturity

Negativity of the electromechanical window: relation to frequent premature ventricular complexes

OBJECTIVE: The electromechanical window (EMW) was investigated as a new predictor of arrhythmia in the presence of long QT. However, the use of EMW to predict idiopathic frequent ventricular premature complexes (PVCs) in those with normal QT intervals has not been clarified. PATIENTS AND METHODS: This single-center study included consecutive patients who presented to the Cardiology Clinic with palpitations and were found to have idiopathic PVC on 24-hour Holter monitoring. Those with a PVC/24-hour frequency of 10% as group 3. The EMW was defined as the time difference (in ms) between the aortic valve closure and the end of the QT interval, measured from an ECG on the concurrent echocardiogram. RESULTS: A total of 148 patients were included in the study, 64% (n = 94) of which were female. The patients’ mean age was 50.11 ± 14.7. The groups were similar in terms of the patients’ age, BMI, and comorbidities. There was a statistically significant difference between the three groups in terms of the EMW measurements (group 1: 3.78 ± 19.6, group 2: -7 ± 30.9, group 3: -34.83 ± 55.2 ms: p 10%. An EMW value of ≤ -15 ms was associated with the frequency of 24-h PVC > 10%, with a sensitivity of 70% and a specificity of 70% (AUC 0.716, 95% CI: 0.636-0.787 p < 0.001). CONCLUSIONS: The results showed that a negative increase in the EMW may be associated with frequent idiopathic PVCs