Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

Publisher Copyright: © 2021 O'Toole Á et al.Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.Peer reviewe

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

Effects of dietary Garcinia kola supplementation and oxidative stress in isolated perfused rat hearts

Thesis submitted in fulfilment of the requirements for the degree of Master of Technology: Biomedical Technology In the Faculty of Health and Wellness Sciences At the Cape Peninsula University of Technology Supervisors: Prof. Adriaan J Esterhuyse Dr Dirk J Bester Bellville January 2014Background: Oxidative stress and chronic inflammation contributes significantly to the pathogenesis of several ischaemic heart diseases, including atherosclerotic plaque rupture and myocardial infarction. It is widely demonstrated that ischaemia, followed by reperfusion, results in alterations of the mitochondrial and endothelial function through uncontrolled cascades of events characterized by free radical release and inflammation. Recent experimental evidence shows that modulation of inflammatory and antioxidant signaling mediators may determine the host outcome following myocardial ischaemia-reperfusion injury. Investigations from the past decade indicate that food supplements may play an important role in the prevention and management of chronic inflammatory diseases. Garcinia kola seeds are flavonoid rich nut from a tropical flowering, non-timber plant of the Guttiferae family. This plant is highly valued in several African cultures for its use in herbal medicine. Recently, the majority of experimental research has linked phytochemicals found in Garcinia kola nut, to its proposed beneficial effects in treatment and management of oxidative stress related-chronic diseases. Research performed in our laboratory demonstrated that kolaviron, a prominent Garcinia kola flavonoid extract, reduces myocardial apoptosis during ischaemia-reperfusion injury. Therefore, the aim of our current study was to determine the effects of Garcinia kola supplementation on cardiac inflammatory and antioxidant signaling pathways during ischaemia-reperfusion using a Wistar rat heart model. Materials and Methods: Male wistar rats were randomly divided into two groups: a control group receiving 2ml/kg corn oil and the experimental group receiving 100mg/kg Garcinia kola dissolved in corn oil, daily for 4 weeks. After the feeding period, blood samples were collected and lymphocytic DNA damage was analyzed using the alkaline comet assay. Furthermore, rat hearts were isolated and perfused with Krebs-Henseleit buffer on a working heart perfusion apparatus to measure myocardial functional parameters. Myocardial functional recovery was measured after 15 minutes global ischaemia followed by 25 minutes reperfusion. Hearts were freeze clamped at three different time points for myocardial cytokine concentration determinations using multiplex electrochemilunescent immunoassay. Nuclear factor kappa beta (NF- kβ), p38 mitogen activated protein kinases (p38 MAPK), protein kinase B/Akt (PKB/Akt), nitro-tyrosine, inducible nitric oxide (iNOS), cyclooxygenase-2 (COX-2), poly (adenosine-di-phosphate) ribose polymerase-1 (PARP-1) and caspase-3 expression and their phosphorylated forms (where applicable) were analyzed using the Western blot technique. Results: Dietary Garcinia kola supplementation significantly improved functional recovery when compared to the control group as reflected by the improved aortic output recovery (68.47 ± 6.16% versus 44.96 ± 7.00%; p<0.05). Our biochemical results supports the hypothesis that, dietary Garcinia kola supplementation modulates different cardiac proteins in terms of expression and activation at different time points when compared to the control group. We show that, before induction of ischaemia, Garcinia kola supplementation attenuates expression of inflammatory mediators and pro-apoptotic proteins when compared to the control group. The improved functional recovery was associated with a prompt inflammatory response, activation of PKB/Akt and attenuation of protein nitrosylation after 10 minutes of reperfusion. Modulation of NF-kβ and the p38 MAPK family proteins expression could have also played a significant role in myocardial functional recovery. Conclusion: We have shown that a 4 week period of dietary Garcinia kola supplementation at 100mg/kg daily improves cardiac functional recovery following ischaemia-reperfusion injury. We propose that dietary Garcinia kola supplementation protects cardiac myocytes from ischaemia-reperfusion induced oxidative stress through the induction of a prompt inflammatory response and controlled expression and/or activation of the, NF-kβ, PKB/Akt and p38 MAPK protein signaling pathways PARP-1 and caspase. Finally, we demonstrated that dietary Garcinia kola supplementation did not induce rat lymphocytic DNA damage when compared to the control group

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501YV2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.</ns3:p