9 research outputs found

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    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

    Drivers of land use change and carbon mapping in the savannah area of Ghana

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    Land-use and land-cover change in both forest reserves and off-reserves is a critical issue in sub Saharan Africa. Deforestation and conversion of forest land to agricultural land continue to be one of the major environmental problems in Africa, and for that matter, Ghana cannot be exceptional; and its resultant effect is the loss in the ecological integrity and the quality of forests, resulting in carbon loss and the resultant climate change effects (FAO 2016). The study area covers the Community Resource Management Areas (CREMA) of the Mole National Park in Ghana, and this study reveals that the area is well endowed with a diverse composition and structure of woodland including dense, open and riverine stretches, which – under the national definition of forest – qualifies as forest. The results reveal that there had been an annual deforestation rate of 0.11% over the period of review. It was concluded from the study that woodland had high carbon stocks with an average carbon of 80 tC/ha, the highest being 194 tC/ha and the lowest being 7 tC/ha, which was recorded in the dense woodland and grassland respectively. The fluxes within the land sector in the study area are moderate and the potential of the area to qualify for as REDD+ is very high. However, the drivers of deforestation, especially bush fires and illegal timber harvesting, are challenges that need to be addressed

    Landuse and land cover dynamics in the Volta River Basin surrounding APSD forest plantation, Ghana

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    Forest plantation is reckoned to accounts for 7% of total global forest cover and has the potential to provide 75% of the global industrial round wood supply. The study analyzed forest resource use trend, mapped out areas of high biodiversity conservation, and made recommendations to promote and sustain large-scale plantation development against the background of anthropogenic pressure on vulnerable ecosystems and biodiversity management

    Landuse and land cover dynamics in the Volta River Basin surrounding APSD forest plantation, Ghana

    No full text
    Forest plantation is reckoned to accounts for 7% of total global forest cover and has the potential to provide 75% of the global industrial round wood supply. The study analyzed forest resource use trend, mapped out areas of high biodiversity conservation, and made recommendations to promote and sustain large-scale plantation development against the background of anthropogenic pressure on vulnerable ecosystems and biodiversity management

    Geospatial assessment of land use and land cover dynamics in the mid-zone of Ghana

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    Land use and land cover (LULC) terrain in Ghana has undergone profound changes over the past years emanating mainly from anthropogenic activities, which have impacted countrywide and sub-regional environment. This study is a comprehensive analysis via integrated approach of geospatial procedures such as Remote Sensing (RS) and Geographic Information System (GIS) of past, present and future LULC from satellite imagery covering Ghana’s Ashanti regional capital (Kumasi) and surrounding districts. Multi-temporal satellite imagery data sets of four different years, 1990 (Landsat TM), 2000 (Landsat ETM+), 2010 (Alos and Disaster Monitoring Constellation-DMC) and 2020 (SENTINEL), spanning over a 30-year period were mapped. Five major LULC categories – Closed Forest, Open Forest, Agriculture, Built-up and Water – were delineated premised on the prevailing geographical settings, field study and remote sensing data. Markov Cellular Automata modelling was applied to predict the probable LULC change consequence for the next 20 years (2040). The study revealed that both Open Forest and Agriculture class categories decreased 51.98 to 38.82 and 27.48 to 20.11, respectively. Meanwhile, Built-up class increased from 4.8% to 24.8% (over 500% increment from 1990 to 2020). Rapid urbanization caused the depletion of forest cover and conversion of farmlands into human settlements. The 2040 forecast map showed an upward increment in the Built-up area up to 35.2% at the expense of other LULC class categories. This trend from the past to the forecasted future would demand that judicious LULC resolutions have to be made to keep Ghana’s forest cover, provide arable land for farming activities and alleviate the effects of climate change

    Geospatial assessment of land use and land cover dynamics in the mid-zone of Ghana

    No full text
    Land use and land cover (LULC) terrain in Ghana has undergone profound changes over the past years emanating mainly from anthropogenic activities, which have impacted countrywide and sub-regional environment. This study is a comprehensive analysis via integrated approach of geospatial procedures such as Remote Sensing (RS) and Geographic Information System (GIS) of past, present and future LULC from satellite imagery covering Ghana’s Ashanti regional capital (Kumasi) and surrounding districts. Multi-temporal satellite imagery data sets of four different years, 1990 (Landsat TM), 2000 (Landsat ETM+), 2010 (Alos and Disaster Monitoring Constellation-DMC) and 2020 (SENTINEL), spanning over a 30-year period were mapped. Five major LULC categories – Closed Forest, Open Forest, Agriculture, Built-up and Water – were delineated premised on the prevailing geographical settings, field study and remote sensing data. Markov Cellular Automata modelling was applied to predict the probable LULC change consequence for the next 20 years (2040). The study revealed that both Open Forest and Agriculture class categories decreased 51.98 to 38.82 and 27.48 to 20.11, respectively. Meanwhile, Built-up class increased from 4.8% to 24.8% (over 500% increment from 1990 to 2020). Rapid urbanization caused the depletion of forest cover and conversion of farmlands into human settlements. The 2040 forecast map showed an upward increment in the Built-up area up to 35.2% at the expense of other LULC class categories. This trend from the past to the forecasted future would demand that judicious LULC resolutions have to be made to keep Ghana’s forest cover, provide arable land for farming activities and alleviate the effects of climate change

    Adaptation of the Wound Healing Questionnaire universal-reporter outcome measure for use in global surgery trials (TALON-1 study): mixed-methods study and Rasch analysis

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    BackgroundThe Bluebelle Wound Healing Questionnaire (WHQ) is a universal-reporter outcome measure developed in the UK for remote detection of surgical-site infection after abdominal surgery. This study aimed to explore cross-cultural equivalence, acceptability, and content validity of the WHQ for use across low- and middle-income countries, and to make recommendations for its adaptation.MethodsThis was a mixed-methods study within a trial (SWAT) embedded in an international randomized trial, conducted according to best practice guidelines, and co-produced with community and patient partners (TALON-1). Structured interviews and focus groups were used to gather data regarding cross-cultural, cross-contextual equivalence of the individual items and scale, and conduct a translatability assessment. Translation was completed into five languages in accordance with Mapi recommendations. Next, data from a prospective cohort (SWAT) were interpreted using Rasch analysis to explore scaling and measurement properties of the WHQ. Finally, qualitative and quantitative data were triangulated using a modified, exploratory, instrumental design model.ResultsIn the qualitative phase, 10 structured interviews and six focus groups took place with a total of 47 investigators across six countries. Themes related to comprehension, response mapping, retrieval, and judgement were identified with rich cross-cultural insights. In the quantitative phase, an exploratory Rasch model was fitted to data from 537 patients (369 excluding extremes). Owing to the number of extreme (floor) values, the overall level of power was low. The single WHQ scale satisfied tests of unidimensionality, indicating validity of the ordinal total WHQ score. There was significant overall model misfit of five items (5, 9, 14, 15, 16) and local dependency in 11 item pairs. The person separation index was estimated as 0.48 suggesting weak discrimination between classes, whereas Cronbach's α was high at 0.86. Triangulation of qualitative data with the Rasch analysis supported recommendations for cross-cultural adaptation of the WHQ items 1 (redness), 3 (clear fluid), 7 (deep wound opening), 10 (pain), 11 (fever), 15 (antibiotics), 16 (debridement), 18 (drainage), and 19 (reoperation). Changes to three item response categories (1, not at all; 2, a little; 3, a lot) were adopted for symptom items 1 to 10, and two categories (0, no; 1, yes) for item 11 (fever).ConclusionThis study made recommendations for cross-cultural adaptation of the WHQ for use in global surgical research and practice, using co-produced mixed-methods data from three continents. Translations are now available for implementation into remote wound assessment pathways

    SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

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    Background: Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods: The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results: NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion: As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population
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