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

Our experience in the diagnosis and treatment of postural orthostatic tachycardia syndrome, vasovagal syncope, and inappropriate sinus tachycardia in children

Objectives: The aim of this study was to share our experience in the diagnosis and treatment of patients who presented at our clinic with syncope, pre-syncope, dizziness, and palpitations

A 17-year experience with ALL-BFM protocol in acute lymphoblastic leukemia: Prognostic predictors and interruptions during protocol

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and despite the intense combination chemotherapy, cure rates are less than 90%. Several prognostic parameters, including nonneoplastic hematologic cell counts during induction phase, are suggested to predict outcome in ALL. We analyzed 242 ALL patients treated in our center to investigate individual prognostic parameters and the impact of delays on disease outcome. Age at diagnosis, risk groups, extramedullary involvement, t(9; 22), prednisone response, bone marrow response at days 15 and 33, day 15 platelet count, day 33 lymphocyte, monocyte, and platelet counts, treatment delay, sepsis, and omission of day 64 cyclophosphamide were valuable predictors of survival in univariate analysis. However only the age, CNS involvement, omission of cyclophosphamide, and total delay during treatment were associated with survival in multivariate analysis. Omission of second cyclophosphamide dose had no impact on survival of standard risk group patients, but adversely affected the long term survival of medium risk group (MRG) patients. The second dose might be given with the first dose on day 36 to MRG patients to prevent delays. Day 15 and 33 platelet counts are promising predictors of survival in low income countries where assessment of minimal residual disease is difficult, but this data needs further consolidation. (C) 2014 Elsevier Ltd. All rights reserved

Comparison of outcomes of children with acute lymphoblastic leukemia treated with BMF protocol across 2 decades

Acute lymphoblastic leukemia is the most common malignancy of childhood. The aim of this study is to compare the outcome of children with acute lymphoblastic leukemia treated with BFM protocol over two decades at our center. We retrospectively examined the files of 421 patients by dividing them into two groups by decade of treatment, 1995-2005 and 2006-2015. After excluding 117 patients, overall, 304 patients were included in the analysis. From the first to the second decade, the proportion of patients over 12 years of age increased from 7.1% to 16.8% (p 0.05) and the death rate during remission induction treatment decreased from 3.9% to 0.7%. The mortality rate of high-risk and standard-risk patients decreased from 62.5% to 34.5% (p 0.05), respectively. The 5-year overall survival and event-free survival rates for standard-, medium- and high-risk patients were 92.7% +/- 6.0%, 87.9% +/- 4.7%, and 54.7% +/- 13.3% and 92.5% +/- 6.3%, 83.2% +/- 5.5%, and 48.7% +/- 14.7%, respectively. For the cohort, the 5-year overall survival rate was 83.2% +/- 4.1% and the event-free survival rate was 79.9% +/- 4.7%. These results demonstrate the impact of a standard protocol, experience of staff, achieving better risk stratification on treatment success

A rare cause of sudden cardiac arrest: Catecholaminergic polymorphic ventricular tachycardia

Catecholaminergic polymorphic ventricular tachycardia is a rhythm disorder that develops due to genetic reasons in the absence of structural cardiac abnormalities. Ventricular tachycardia, ventricular fibrillation, cardiac arrest, and death may occur. Two-year-old patient presented to the Emergency Department with sudden cardiac arrest. He had syncope attacks after playing with his brother and he was followed up by the pediatric neurology and cardiology clinics. Cardiopulmonary resuscitation was performed, and he was then transferred to the Intensive Care Unit because of hypotension; dobutamine and norepinephrine treatment was started. After treatment, ventricular tachycardia, ventricular fibrillation, and cardiac arrest developed. Dobutamine and noradrenaline was stopped immediately and amiodarone was started. A genetic test revealed heterozygote missense mutation (c.9110G>A(p.Gly3037Asp)) in exon 64 of the RYR2 gene, which is compatible with catecholaminergic polymorphic ventricular tachycardia. This mutation has been reported in the literature for the first time. This case is presented with the purpose of highlighting catecholaminergic polymorphic ventricular tachycardia

A rare cause of sudden cardiac arrest: Catecholaminergic polymorphic ventricular tachycardia

Catecholaminergic polymorphic ventricular tachycardia is a rhythm disorder that develops due to genetic reasons in the absence of structural cardiac abnormalities. Ventricular tachycardia, ventricular fibrillation, cardiac arrest, and death may occur. Two-year-old patient presented to the Emergency Department with sudden cardiac arrest. He had syncope attacks after playing with his brother and he was followed up by the pediatric neurology and cardiology clinics. Cardiopulmonary resuscitation was performed, and he was then transferred to the Intensive Care Unit because of hypotension; dobutamine and norepinephrine treatment was started. After treatment, ventricular tachycardia, ventricular fibrillation, and cardiac arrest developed. Dobutamine and noradrenaline was stopped immediately and amiodarone was started. A genetic test revealed heterozygote missense mutation (c.9110G>A(p.Gly3037Asp)) in exon 64 of the RYR2 gene, which is compatible with catecholaminergic polymorphic ventricular tachycardia. This mutation has been reported in the literature for the first time. This case is presented with the purpose of highlighting catecholaminergic polymorphic ventricular tachycardia

Evaluation of cardiac functions in juvenile systemic lupus erythematosus with two-dimensional speckle tracking echocardiography

The aim of this study was to investigate subclinical systolic and diastolic dysfunction in juvenile-onset systemic lupus erythematosus (j-SLE) patients with speckle tracking echocardiography (STE) and the effects of disease activity on left ventricular (LV) regional functions. Thirty-five patients with j-SLE and 30 healthy children (control group) were evaluated between January and August 2015. STE was performed on all patients and controls. Medical records, including diagnosis criteria, age at diagnosis, and duration of disease, were evaluated. SLE disease activity was assessed using the SLE Disease Activity Index (SLEDAI). j-SLE patients had lower ejection fraction than did control subjects but still within normal range. LV end-diastolic and end-systolic dimensions were significantly larger in j-SLE patients (32.43 +/- 3.2 vs 28.3 +/- 3.1 and 21.1 +/- 1.9 vs 18.9.0 +/- 2.2, respectively; p = 0.001). There was a significant reduction in longitudinal strain of LV segments in the j-SLE patients compared with controls. J-SLE patients were further divided into subgroups. Group 1 comprised patients having SLEDAI scores > 8 at the onset of disease but who improved with therapy during follow-up. Group 2 included j-SLE patients with SLEDAI scores > 8 at diagnosis and persistently > 4 at the end of follow-up. In the LV mid-inferior and mid-inferolateral segments, STE strain measurements of group 2 were significantly lower than those of group 1 (15.9 +/- 6.4 vs 20.0 +/- 4.4, 17.9 +/- 7.2 vs 23.2 +/- 3.8; p = 0.075, p = 0.055, respectively). Simple and non-invasive STE would be helpful in predicting cardiovascular prognosis with new therapeutic medications/interventions or in objectively comparing the effects of immunosuppressive drugs in comparison with preceding STE evaluation

Evaluation of pulmonary artery pressure in patients with juvenile systemic lupus erythematosus (jSLE)

Juvenile systemic lupus erythematosus (jSLE) is a chronic multisystemic autoimmune disease. Previous studies among adults have shown impaired right ventricular (RV) function in patients with SLE. Also, these patients may develop pulmonary artery hypertension (PAH), which is one of the most threatening complications of SLE. Nevertheless, studies on PAH among jSLE patients are still rare. The aim of this study was to assess the RV function in jSLE patients by Doppler echocardiography (Echo Doppler). We also estimated pulmonary artery systolic pressure (PASP) and mean pulmonary artery pressure (mPAP) in these patients. A total of 38 jSLE patients and 40 sex- and age-matched controls were retrospectively analyzed. All patients underwent combined M-mode, cross-sectional echo, and Doppler Echo examination. The RV function was significantly impaired in jSLE patients compared to controls. PASP and mPAP were normal in 37 out of 38 patients (97.37%), however, the mean values of PASP and mPAP were significantly higher in jSLE patients compared to controls (26.90 mmHg versus 21.71 mmHg and 12.63 mmHg versus 9.89 mmHg, respectively) [p < 0.05]. Only one patient (2.6 %) had elevated mPAP (60 mmHg). The right cardiac catheterization confirmed PAH in this patient. Although PAH was detected only in one patient, there was a marked increase of PAP in our jSLE patients. Overall, PASP and mPAP were significantly higher in jSLE patients compared to healthy controls. Prospective studies with ethnically diverse cohorts could give more insight on the relevance of PAP and PHT in patients with jSLE