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

The impact of age and clinical factors in non-muscle-invasive bladder cancer treated with Bacillus Calmette Guerin therapy.

International audienceBACKGROUND: Bladder cancer is a disease of older persons, the incidence of which is expected to increase as the population ages. Prognostic factors for local recurrence for patients with non-muscle invasive bladder cancer have not been fully established. The aim of our study was to determine the influence of age on the outcomes of non muscle invasive bladder (NMIBC) cancer treated with intravesical Bacillus Calmette-Guerin (BCG) therapy. METHODS: We retrospectively reviewed the clinical and pathologic data of primary NMIBC from 112 patients who were treated with transurethral resection followed by BCG-immunotherapy. Time follow-up was 30 months. Clinicopathologic characteristics and response to BCG therapy were correlated with age using univariate and multivariate methods of analysis. RESULTS: Univariate analysis showed that age analyzed as a categorical variable was not associated with other clinicopathological characteristics. On the other hand, multivariate analysis showed that only multiplicity, stage and tumor size were independent significant prognosticators. CONCLUSIONS: The results of our study have shown that aging has no impact on the outcomes of high-risk NMIBC treated by BCG immunotherapy

The Efficacy of Intravesical Bacillus Calmette-Guerin in the Treatment of Patients with pT1 Stage Non-muscle-invasive Bladder Cancer.

Abstract Background: pT1 bladder urothelial carcinomas represent a heterogeneous group of tumors with different biologic behaviors, and identifying the subset of tumors that carries a high risk of disease recurrence and progression is therefore important. Induction and maintenance intravesical Bacillus Calmette-Guerin (BCG) has been proven to reduce tumour recurrence and progression. However, no markers are available to predict BCG response. The aim of this study is to evaluate the prognostic factors of stage in predicting recurrence after intravesical adjuvant BCG immunotherapy in patients with NMIBC. Methods: we retrospectively reviewed the clinical and pathologic data of primary NMIBC from 45 patients who were treated with transurethral resection followed by BCG-immunotherapy. Time follow-up was 30 months. The prognostic significance of clinicopathologics characteristics in determining the risk for recurrence after BCG therapy was studied with both univariate and multivariate methods of analysis. Results: univariate Cox regression analysis of clinicopathologic characteristics revealed that the rate of recurrence was statistically associated with tumor stage. Indeed, a significant concordance was noted between the EORTC s predicted risks and the actuarial recurrence rate of NMIBC at one year. On the other hand, multivariate analysis using Cox regression based on the AIC criteria and biological considerations, selected the score of recurrence as independent predictor of recurrence. Conclusion: The conventional clinicopathological factors used in EORTC model are relevant for the assessment of the outcome of pT1 stage bladder tumors treated by BCG immunotherapy. Management of pT1 bladder cancer patients remains one of the most difficult problems in urologic practice. At this time the decision to preserve the bladder or to perform a cystectomy depends on a number of clinicopathologic parameters, but none are able to sufficiently identify patients for the appropriate therapeutic modality. Additional studies using a more large scale of patients will be required to confirm our findings

The Efficiency of the EORTC Scoring System for the Prediction of Recurrence and Progression of Non-muscle-invasive Bladder Cancer Treated by Bacillus Calmette-Guerin Immunotherapy.

International audienceAbstract The authors determined the recurrence and progression at 1 year in patients with non-muscle-invasive urothelial carcinoma who underwent transurethral resection of bladder tumor (TURBT) and compared the results with the calculated risk according to the European Organization of Research and Treatment of Cancer (EORTC). Between 2002 and 2011, a total of 112 patients with NMIBC were treated with transurethral resection of bladder cancer. According to the EORTC scoring system, the patients were categorized in terms of number of tumors, tumor size, prior recurrence rate, T category, carcinoma in situ, and pathologic grade, and the scores were summed. According to the summed scores, the recurrence group and the progression group were divided into 3 subgroups: low, intermediate, and high risk, respectively. The recurrence rate and progression rate of each group were compared with the EORTC risk tables. The mean patient age was 63.9 years (range: 25-85) at diagnosis. Seventy-eight patients (68.4%) had a recurrent disease, 53 (47.3%) had a tumor larger than 3 cm in diameter, 55 (49.1%) had multiple lesions, 3 (0.26%) had carcinoma in situ, 44(39.3%) had stage T1 lesions, and 20 (17.8%) had a high-grade disease. The recurrence rates were 0, 14.2, 31.25, and 85.71% in groups with the predicted EORTC risks of 15, 24, 38, and 61%, respectively. There were 3 patients (0.2%) with progression of the diseases. The EORTC model successfully stratified recurrence and progression risks in this cohort. However, the discriminative ability of the EORTC tables decreased in these patients for progression

Tumor multiplicity is an independent prognostic factor of non-muscle-invasive bladder cancer treated with Bacillus Calmette-Guerin immunotherapy.

International audienceBACKGROUND: Bacillus Calmette-Guerin (BCG) immunotherapy is regarded as the current treatment of choice for non muscle invasive bladder cancer (NMIBC), though its efficacy is limited by high recurrence and progression rate. Identification of factor prognosticators that might be helpful in discriminating between responders and nonresponders to BCG treatment is therefore of major clinical importance. The aim of this study is to evaluate the prognostic factors of recurrence after intravesical adjuvant BCG immunotherapy in patients with NMIBC. METHODS: we retrospectively reviewed the clinical and pathologic data of primary NMIBC from 112 patients who were treated with transurethral resection followed by BCG-immunotherapy. Time follow-up was 30 months. The prognostic significance of tumor stage, grade, multiplicity, age, sex and smoking in determining the risk for recurrence after BCG therapy was studied with both univariate and multivariate methods of analysis. RESULTS: According to univariate analysis of the prognostic significance for tumor stage, grade, loci number, sex, age and smoking, the pT1 stage and multiplicity seem to be associated in a statistically significant manner with higher risk for recurrence (P = 0.009, P = 0.011, respectively). In the other hand, multivariate analysis showed that only multiplicity was an independent significant prognosticator. CONCLUSION: Significant independent predictor for recurrence was multiplicity which offers important clinical information and may be a useful tool in the selection of suitable candidates for BCG-immunotherapy

Impact of Smoking intensity on Outcomes of Patients with Non Muscle Invasive Bladder Cancer Treated by BCG Immunotherapy.

International audienceAbstract Background: Cigarette smoking is a well-known risk factor of bladder carcinogenesis. The clinical impact of smoking on bladder cancer recurrence and response to BCG immunotherapy remains unclear. We sought to investigate the effect of smoking intensity on bladder cancer response to BCG therapy, and the interactions between smoking and clinicopathological factors on bladder cancer recurrence. Methods: Clinical information was obtained from 81 smokers patients (smokers at diagnosis) with NMIBC treated with transurethral resection of the bladder tumor followed by BCG immunotherapy. The distribution of smoking intensity on patient age (≥60 years or <60 years), gender, tumor grade, tumor stage, carcinoma in situ, multiplicity and tumor size was assessed. The effect of cigarette smoking on cancer recurrence was estimated using Cox proportional hazard models and Kaplan-Meier analysis. Results: The results showed that smoking intensity was significantly associated with response to BCG immunotherapy (p = 0.010). Univariate Cox regression analysis of clinicopathologic characteristics showed that PT1 stage, tumor size more than 3 cm and smoking intensity significantly increased the risk of recurrence (respectively, p = 0.006; p = 0.008 and p = 0.012). These results were confirmed by Kaplan-Meier survival curves. In addition, multivariate analysis using Cox regression selected the model involving stage, tumor size and smoking intensity as the quasi-independent predictor of recurrence.Conclusion: These findings suggest that cigarette smoking is an independent predictor for patients with NMIBC. Although the current evidence supports a positive link between smoking intensity and the risk of recurrence on NMIBC treated by BCG immunotherapy, additional studies, are needed before definitive conclusions can be drawn

Prognostic value of Bcl-2 and Bax tumor cell expression in patients with non muscle-invasive bladder cancer receiving bacillus Calmette-Guerin immunotherapy.

International audienceApoptosis is the distinctive form of programmed cell death that complements cell proliferation in maintaining normal tissue homeostasis. The significance of constitutive apoptosis in the recurrence of Non Muscle Invasive Bladder Cancer has yet to be investigated. The aim of this study is to investigate the prognostic significance of Bax and Bcl-2 in terms of recurrence after BCG immunotherapy. Immunohistochemical analysis was performed on frozen biopsies to evaluate bcl-2 and Bax proteins expression in 28 cases of NMIBC. All patients with confirmed NMIBC were treated with intravesical BCG-immunotherapy. The follow up was performed for 26 months. The correlation between clinicopathological, immunohistochemical data and the response to BCG therapy was performed. Univariate analysis showed that, PT1 stage, High grade and Bax expression increased significantly the risk of recurrence (P = 0.015, P = 0.015 and P= 0.034 respectively). In addition, multivariate analysis selected the model involving stage, age, Bax and Bcl-2 expression as the best independent variables of recurrence. In conclusion, the expression of Bcl-2 and Bax in NMIBC could have a prognostic value in assessing the risk of recurrence after BCG immunotherapy. These findings require further investigations on larger cohort in order to ascertain new molecular markers of the response to BCG immunotherapy

Prognostic Impact of Angiogenesis in Nonmuscle Invasive Bladder Cancer as Defined by Microvessel Density after Immunohistochemical Staining for CD34.

International audienceBladder cancer is the second most common malignancy of the urogenital region. The majority of bladder cancer deaths occur as a consequence of metastatic disease. Microvessel density (MVD), a surrogate marker for angiogenesis, has been shown to be predictive of progression and poor prognosis. The aim of this study was to evaluate the predictive value and prognostic significance of angiogenesis in human non muscle invasive bladder cancer (NMIBC) treated by BCG immunotherapy. The frozen sections of 28 non muscle invasive bladder cancer specimens were stained with CD34 antibody to label the vascular endothelium using the standard streptavidin-biotin immunoperoxidase method. Angiogenic activity was measured using microvessel count determined by the expression of vascular markers CD34.The prognostic significance of tumor stage, grade, loci number, tumor size, age and CD34 expression in determining the risk for recurrence was studied with both univariate and multivariate methods of analysis. According to univariate analysis of the prognostic significance for tumor stage, grade, tumor size, loci number, age and CD34 expression, in patients with NMIBC, the pT1 stage and high grade seem to be associated in a statistically significant manner with higher risk for recurrence (P=0.004, P=0.004, respectively). In the other hand, multivariate Cox regression's analysis showed that microvessel density and multiplicity were independent predictor of recurrence after BCG immunotherapy (p=0.016, p=0.032, respectively). This study provides strong evidence that CD34 MVD is associated with recurrence after BCG immunotherapy. Independent studies, however, will be required on larger cohort to validate these findings

Relationship between toll-like receptor 2 nonsynonymous single nucleotide polymorphisms and the effectiveness of Bacille Calmette-Guérin immunotherapy in preventing recurrence of superficial bladder cancer: A prospective study

AbstractBackground: Intravesical Bacille Calmette-Guérin (BCG) immunotherapy has been used for several decades as a prophylactic approach against recurrence of superficial bladder cancer. However, its effectiveness has been both variable and unpredictable. Typically, cancer BCG-immunotherapy aims to redirect or modulate both innate and adaptive immune responses. The consequences of gene polymorphisms in several key immuno-regulatory molecules on the heterogeneity of the response to BCG-immunotherapy have been investigated.Objective: The aim of this study was to evaluate the association of toll-like receptor (TLR) 2 polymorphisms (arginine to glutamine substitution at position 753 [Arg753Gln] and arginine to tryptophan substitution at position 677 [Arg677Trp]) and the outcome of BCG-immunotherapy.Methods: This prospective study was conducted during a 3-year period from June 2006 to July 2009. Consecutive patients were recruited during a 1-year period and followed for 2 years at the Department of Urology, Charles Nicolle Hospital, Tunis, Tunisia. Patients with superficial bladder tumors at stage Ta (noninvasive papillary carcinoma) or T1 (where the tumor has grown from the layer of cells lining the bladder into the connective tissue below but has not grown into the muscle layer of the bladder) of any grade were eligible; carcinoma in situ cases were excluded. The TLR2 Arg753Gln and Arg677Trp polymorphisms were studied in peripheral blood DNA from patients treated with BCG-immunotherapy after transurethral resection.Results: A total of 112 consecutive patients were enrolled (101 men and 11 women; mean age, 63.9 years [range, 25–85 years]) and completed the 2-year followup. Polymerase chain reaction amplification followed by direct sequencing of the region containing the TLR2 single-nucleotide polymorphism (SNP) of interest did not detect Arg753Gln or Arg677Trp in any of the study participants belonging to either of 2 groups: responders (n = 67) and nonresponders (n = 45) to BCG-immunotherapy.Conclusions: No patients included in the study were found to have the 2 known TLR2 nonsynonymous SNPs, and the relative importance of these polymorphisms could not be definitely determined. However, a significant proportion of patients without these polymorphisms responded to BCG-immunotherapy, suggesting that these genetic variants are not critical in the effectiveness of this approach for preventing recurrence of the tumor