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

Hypovitaminosis D Among Patients Admitted With Hip Fracture to a Level-1 Trauma Center in the Sunny Upper Egypt

Introduction: Despite abundant sunshine, hypovitaminosis D is common in the Middle East. The aim of this study was to determine the prevalence of hypovitaminosis D and related correlates among patients with hip fracture in Assiut University Hospitals in Upper Egypt. Materials and Methods: A cross-sectional study was carried out in 133 patients with hip fracture, aged 50 years and older, admitted to Trauma Unit of Assiut University Hospitals, from January through December 2014. Patients were selected by systematic random sampling. Serum 25-hydroxy vitamin D level was measured by enzyme-linked immunosorbent assay; bone mineral density (BMD) by dual-energy X-ray absorptiometry. Weight and height measurements were used for body mass index (BMI) calculation. Results: Patients’ median age was 70 years (range: 50-99); 51.9% were females. Osteoporosis (femoral neck T score: 30 ng/mL). According to univariate analysis, vitamin D deficiency was significantly associated with obesity ( P = .012) and low T scores of the femoral neck ( P = .001), L2 ( P = .021), L3 ( P = .031), L4 ( P = .012), and the greater trochanter ( P < .001). In a multivariable logistic regression model, high BMI and low BMD of the femoral neck and greater trochanter were associated with hypovitaminosis D. Conclusion: Prevalence of hypovitaminosis D is high among patients with hip fracture and associated with low BMD and high BMI. Increasing awareness about prevention as well as detection and treatment of vitamin D deficiency is recommended

Delayed union of multifragmentary diaphyseal fractures after bridge-plate fixation

Despite recent developments in fracture treatment, cases of non-union after long bone fractures are still encountered. This work aims at evaluating the active management of delayed union after the bridge-plate fixation of multifragmentary diaphyseal fractures by a limited surgical interference. Nineteen patients were included. All had revision surgery for delayed union of multifragmentary diaphyseal fractures after bridge-plate fixation. The period between primary and revision surgery was 12–20 weeks. Increasing stability was performed by adding more screws in all cases. Interfragmentary compression was performed in 16 patients. Axial compression of the fracture was applied in two patients, while one patient had the plate exchanged for a longer one. Bone grafting was added in nine patients. Union was achieved in all patients 8–16 weeks after re-operation. This work is a message for timely surgical interference in delayed union after bridge-plate fixation by a limited surgical procedure, before complete failure of the fracture stabilisation or non-union

Valgus intertrochanteric osteotomy with single-angled 130° plate fixation for fractures and non-unions of the femoral neck

Non-union of femoral neck fractures may occur due to mechanical and biological factors. Valgus intertrochanteric osteotomy (VITO) alters hip biomechanics and enhances fracture union. The double-angled 120° plate is usually used for internal fixation of the osteotomy. It allows the osteotomy to heal with medialisation and verticalisation of the femoral shaft. This deformity causes medial ligament strain of the knee joint, genu valgum and ultimately osteoarthritis. This work presents our experience in treating vertical fractures and non-unions of the femoral neck by VITO and fixation by a single-angled 130º plate. Thirty-six patients presented with 19 recent vertical femoral neck fractures, and 17 non-unions were included. They were 26 men and ten women, and their ages averaged 37 years. Preoperative planning and VITO technique are described. Union was achieved in 35 patients (97%), and one recent fracture failed to unite (3%). Time to fracture union averaged four months in recent fractures and eight months in un-united fractures. All patients with united fractures had an almost normal configuration of the upper femur. Avascular necrosis of the femoral head was reported in five patients. Twenty-two patients (61%) were pain free, nine (25%) had hip pain on lengthy walks and the remaining five (14%) had persistent pain. Preoperative limb shortening averaged 2.5 cm, and post-operative shortening averaged 0.5 cm. We recommend VITO and fixation by a single-angled 130º plate for vertical femoral neck fractures and non-unions in relatively young adult patients

Technique and short-term results of ankle arthrodesis using anterior plating

Clinical and biomechanical trials have shown that rigid internal fixation during ankle arthrodesis leads to increased rates of union and is associated with a reduced infection rate, union time, discomfort and earlier mobilisation compared with other methods. We describe our technique of ankle arthrodesis using anterior plating with a narrow dynamic compression plate (DCP). Between 2004 and 2007, 29 patients with a mean age of 24.4 years (range 18–42) had ankle arthrodesis using an anteriorly placed narrow DCP. Twenty-two patients were post-traumatic and seven were paralytic (five after spine fracture and two after common peroneal nerve injury). Follow-up was between 12 and 18 months (average 14 months). A rate of fusion of 100% was achieved at an average of 12.2 weeks. According to the Mazur ankle score, 65.5% had excellent, 20.7% good and 13.8% fair results. Ankle arthrodesis using an anteriorly placed narrow DCP is a good method to achieve ankle fusion in many types of ankle arthropathies