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

Site-directed mutagenesis of wheat 9 kDa lipid transfer protein (LTP)

International audienceWheat 9 kDa LTP and four mutants were produced in Escherichia coli and compared with wheat-extracted LTP. Only the Y79 mutant was affected in lipid-binding activity, confirming the position of this residue in the three-dimensionnal structure of the protein

Site-directed mutagenesis of wheat 9 kDa lipid transfer protein (LTP)

National audienc

Can intra-annual stable isotope signals in tree-ring cellulose be used to extend Fluxnet data-model analysis to larger temporal and spatial scales?

International audienc

Measurement of the Mass of the Z-Boson and the Energy Calibration of Lep

Contains fulltext : 26847___.PDF (publisher's version ) (Open Access

The EASL-Lancet Liver Commission: protecting the next generation of Europeans against liver disease complications and premature mortality

Liver diseases have become a major health threat across Europe, and the face of European hepatology is changing due to the cure of viral hepatitis C and the control of chronic viral hepatitis B, the increasingly widespread unhealthy use of alcohol, the epidemic of obesity, and undiagnosed or untreated liver disease in migrant populations. Consequently, Europe is facing a looming syndemic, in which socioeconomic and health inequities combine to adversely affect liver disease prevalence, outcomes, and opportunities to receive care. In addition, the COVID-19 pandemic has magnified pre-existing challenges to uniform implementation of policies and equity of access to care in Europe, arising from national borders and the cultural and historical heterogeneity of European societies. In following up on work from the Lancet Commission on liver disease in the UK and epidemiological studies led by the European Association for the Study of the Liver (EASL), our multidisciplinary Commission, comprising a wide range of public health, medical, and nursing specialty groups, along with patient representatives, set out to provide a snapshot of the European landscape on liver diseases and to propose a framework for the principal actions required to improve liver health in Europe. We believe that a joint European process of thinking, and construction of uniform policies and action, implementation, and evaluation can serve as a powerful mechanism to improve liver care in Europe and set the way for similar changes globally. On the basis of these data, we present ten actionable recommendations, half of which are oriented towards health-care providers and half of which focus primarily on health policy. A fundamental shift must occur, in which health promotion, prevention, proactive casefinding, early identification of progressive liver fibrosis, and early treatment of liver diseases replace the current emphasis on the management of end-stage liver disease complications. A considerable focus should be put on underserved and marginalised communities, including early diagnosis and management in children, and we provide proposals on how to better target disadvantaged communities through health promotion, prevention, and care using multilevel interventions acting on current barriers. Underlying this transformative shift is the need to enhance awareness of the preventable and treatable nature of many liver diseases. Therapeutic nihilism, which is prevalent in current clinical practice across a range of medical specialities as well as in many patients themselves, has to end. We wish to challenge medical specialty protectionism and invite a broad range of stakeholders, including primary care physicians, nurses, patients, peers, and members of relevant communities, along with medical specialists trained in obesity, diabetes, liver disease, oncology, cardiovascular disease, public health, addictions, infectious diseases, and more, to engage in integrated person-centred liver patient care across classical medical specialty boundaries. This shift includes a revision in how we converse about liver disease and speak with our patients, and a reappraisal of disease-related medical nomenclature conducted to increase awareness and reduce the social stigmatisation associated with liver disease. Reimbursement mechanisms and insurance systems must be harmonised to account for patient-centric, multimorbidity models of care across a range of medical specialties, and the World Health Assembly resolution to improve the transparency and fairness of market prices for medicines throughout Europe should be reinforced. Finally, we outline how Europe can move forward with implementation of effective policy action on taxation, food reformulation, and product labelling, advertising, and availability, similar to that implemented for tobacco, to reduce consumption of alcohol, ultraprocessed foods, and foods with added sugar, especially among young people. We should utilise the window of opportunity created by the COVID-19 pandemic to overcome fragmentation and the variability of health prevention policies and research across Europe. We argue that the liver is a window to the 21st-century health of the European population. Through our proposed syndemic approach to liver disease and social and health inequities in Europe, the liver will serve as a sentinel for improving the overall health of European populations

The EASL-Lancet Liver Commission: protecting the next generation of Europeans against liver disease complications and premature mortality

Liver diseases have become a major health threat across Europe, and the face of European hepatology is changing due to the cure of viral hepatitis C and the control of chronic viral hepatitis B, the increasingly widespread unhealthy use of alcohol, the epidemic of obesity, and undiagnosed or untreated liver disease in migrant populations. Consequently, Europe is facing a looming syndemic, in which socioeconomic and health inequities combine to adversely affect liver disease prevalence, outcomes, and opportunities to receive care. In addition, the COVID-19 pandemic has magnified pre-existing challenges to uniform implementation of policies and equity of access to care in Europe, arising from national borders and the cultural and historical heterogeneity of European societies. In following up on work from the Lancet Commission on liver disease in the UK and epidemiological studies led by the European Association for the Study of the Liver (EASL), our multidisciplinary Commission, comprising a wide range of public health, medical, and nursing specialty groups, along with patient representatives, set out to provide a snapshot of the European landscape on liver diseases and to propose a framework for the principal actions required to improve liver health in Europe. We believe that a joint European process of thinking, and construction of uniform policies and action, implementation, and evaluation can serve as a powerful mechanism to improve liver care in Europe and set the way for similar changes globally. On the basis of these data, we present ten actionable recommendations, half of which are oriented towards health-care providers and half of which focus primarily on health policy. A fundamental shift must occur, in which health promotion, prevention, proactive case- finding, early identification of progressive liver fibrosis, and early treatment of liver diseases replace the current emphasis on the management of end-stage liver disease complications. A considerable focus should be put on underserved and marginalised communities, including early diagnosis and management in children, and we provide proposals on how to better target disadvantaged communities through health promotion, prevention, and care using multilevel interventions acting on current barriers. Underlying this transformative shift is the need to enhance awareness of the preventable and treatable nature of many liver diseases. Therapeutic nihilism, which is prevalent in current clinical practice across a range of medical specialities as well as in many patients themselves, has to end. We wish to challenge medical specialty protectionism and invite a broad range of stakeholders, including primary care physicians, nurses, patients, peers, and members of relevant communities, along with medical specialists trained in obesity, diabetes, liver disease, oncology, cardiovascular disease, public health, addictions, infectious diseases, and more, to engage in integrated person-centred liver patient care across classical medical specialty boundaries. This shift includes a revision in how we converse about liver disease and speak with our patients, and a reappraisal of disease-related medical nomenclature conducted to increase awareness and reduce the social stigmatisation associated with liver disease. Reimbursement mechanisms and insurance systems must be harmonised to account for patient-centric, multimorbidity models of care across a range of medical specialties, and the World Health Assembly resolution to improve the transparency and fairness of market prices for medicines throughout Europe should be reinforced. Finally, we outline how Europe can move forward with implementation of effective policy action on taxation, food reformulation, and product labelling, advertising, and availability, similar to that implemented for tobacco, to reduce consumption of alcohol, ultra- processed foods, and foods with added sugar, especially among young people. We should utilise the window of opportunity created by the COVID-19 pandemic to overcome fragmentation and the variability of health prevention policies and research across Europe. We argue that the liver is a window to the 21st-century health of the European population. Through our proposed syndemic approach to liver disease and social and health inequities in Europe, the liver will serve as a sentinel for improving the overall health of European populations