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

Trends in the placement of penile prostheses over the last 17 years in France

International audienceErectile dysfunction (ED) currently affects 152 million men worldwide and this number is likely to reach 322 million by 2025. Penile prostheses (PP) placement remains a lastresort option in cases where organic ED has not been cured by previous medications, notably intracavernosal injection and oral phosphodiesterase type-5 inhibitor. France ended 2013 with a population of 66 million inhabitants. In our study, we obtained data through the French national code registry database programme de médicalisation des systèmes d’information and from the patient-information forms filled out by the surgeon at the time of the implant. For claim purposes, this system comprehensively records information concerning every surgical procedure that is performed in a private or public hospital in France. Data were extracted for all patients who had undergone a penile implantation between 1997 and 2013

Long-term functional outcomes after artificial urinary sphincter implantation in men with stress urinary incontinence

International audienceOBJECTIVE: To evaluate long-term functional outcomes of artificial urinary sphincters (AUSs) and to determine how many men required explantation because of stress urinary incontinence (SUI) caused by sphincter deficiency after prostate surgery.PATIENTS AND METHODS: Men who had undergone placement of an AUS (American Medical Systems AMS 800®) between 1984 and 1992 to relieve SUI caused by sphincter deficiency after prostate surgery were included. Continence, defined as no need for pads, was assessed at the end of the follow-up. Kaplan-Meier survival curves estimated the survival rate of the device without needing explantation or revision.RESULTS: In all, 57 consecutive patients were included with a median (interquartile range, IQR) age of 69 (64-72) years. The median (IQR) duration of follow-up was 15 (8.25-19.75) years. At the end of follow-up, 25 patients (43.8%) still had their primary AUS. The AUS was explanted in nine men because of erosion (seven) and infection (two). Survival rates, without AUS explantation, were 87%, 87%, 80%, and 80% at 5, 10, 15, and 20 years, respectively. Survival rates, without AUS revision, were 59%, 28%, 15%, and 5% at 5, 10, 15, and 20 years, respectively. At the end of the follow-up, in intention-to-treat analysis, 77.2% of patients were continent.CONCLUSION: In the long term (>10 years) the AMS 800 can offer a high rate of continence to men with SUI caused by sphincter deficiency, with a tolerable rate of explantation and revision

Traitement de l’incontinence urinaire masculine neurologique par le sphincter urinaire artificiel AMS 800™ (Boston Scientific, Boston, États-Unis) : résultats à très long terme (> 25 ans)

International audienceObjective: The aim of the study was to report the very long-term functional outcomes of artificial urinary sphincter (AUS) in male neurological patients.Material and methods: Male neurological patients diagnosed with stress urinary incontinence due to sphincter deficiency and undergoing AUS (AMS 800®) implantation between 1985 and 1992 were enrolled. Continence, defined by no pad/condom usage, explantation and revision rates were reported.Results: Fourteen patients with a median age of 27.3 years (IQR: 27.3–40.8) were included: four had a spinal cord injury and ten a spina bifida. Prior continence surgery was reported by 6 patients (42.9 %). Artificial urinary sphincter was implanted in a peribulbar (n = 4) or periprostatic position (n = 10). Median follow-up was 18.3 years (IQR: 10.1–20.3). At last follow-up, all patients were alive. Three native devices were still in place, eight were revised (four of them were secondarily explanted) and three were explanted due to erosion or infection. The 5-, 10-, 15-, 20-year explantation-free survival rates were respectively 85.7, 62.3, 52.0, 39.0 %. The 5-, 10-, 15-, 20-year revision-free survival rates were respectively 78.6, 42.9, 28.6, 7.1 %. At last follow-up, 50 % patients were continent.Conclusion: In the very long run, AUS provided a 50 % continence rate in male neurological patients but the revision rates were important.Level of evidence: 4Objectif: Le but de cette étude était d’évaluer les résultats fonctionnels à très long terme du sphincter urinaire artificiel (SUA) implanté chez les hommes neurologiques.Matériels et méthodes: Tous les hommes neurologiques implantés avec un SUA (AMS 800®) dans notre institution entre 1985 et 1992 ont été inclus. La continence, définie par l’absence de port de protections, les taux d’explantation et de révision ont été évalués.Résultats: Au total, quatorze patients d’âge médian 27,3 ans (IQ : 27,3,5–40,8) ont été inclus : quatre étaient des blessés médullaires et dix avaient un spina bifida. Un antécédent de chirurgie de la continence était rapporté chez six patients (42,9 %). Le SUA a été implanté en position péribulbaire (n = 4) ou périprostatique (n = 10). La durée médiane de suivi était de 18,3 ans (IQR : 10,1–20,3). Tous les patients étaient vivants au terme du suivi. Trois SUA étaient natifs, huit furent révisés (dont quatre furent explantés dans un second temps) et trois explantés pour infection ou érosion. Le taux de survie sans explantation à 5, 10, 15 et 20 ans était de 85,7 %, 62,3 %, 52,0 % et 39,0 % respectivement. Le taux de survie sans révision à 5, 10, 15 et 20 ans était de 78,6, 42,9, 28,6 et 7,1 %, respectivement. Au terme du suivi, 50 % des patients étaient continents.Conclusion: À très long terme, le SUA a permis d’obtenir un taux de continence de 50 % chez les hommes neurologiques au prix d’un taux de révision important.Niveau de preuve: 4

Impact of COVID-19 pandemic on functional urology procedures in France: a prospective study

International audienc

The subclassification of papillary renal cell carcinoma does not affect oncological outcomes after nephron sparing surgery

International audienceObjectives To evaluate the oncological outcomes of papillary renal cell carcinoma (pRCC) following nephron sparing surgery (NSS) and to determine whether the subclassification type of pRCC could be a prognostic factor for recurrence, progression, and specific death. Materials and methods An international multicentre retrospective study involving 19 institutions and the French network for research on kidney cancer was conducted after IRB approval. We analyzed data of all patients with pRCC who were treated by NSS between 2004 and 2014. Results We included 486 patients. Tumors were type 1 pRCC in 369 (76 %) cases and type 2 pRCC in 117 (24 %) cases. After a mean follow-up of 35 (1–120) months, 8 (1.6 %) patients experienced a local recurrence, 12 (1.5 %) had a metastatic progression, 24 (4.9 %) died, and 7 (1.4 %) died from cancer. Patients with type I pRCC had more grade II (66.3 vs. 46.1 %; p \textless 0.001) and less grade III (20 vs. 41 %; p \textless 0.001) tumors. Three-year estimated cancer-free survival (CFS) rate for type 1 pRCC was 96.5 % and for type 2 pRCC was 95.1 % (p = 0.894), respectively. Three-year estimated cancer-specific survival rate for type 1 pRCC was 98.4 % and for type 2 pRCC was 97.3 % (p = 0.947), respectively. Tumor stage superior to pT1 was the only prognostic factor for CFS (HR 3.5; p = 0.03). Conclusion Histological subtyping of pRCC has no impact on oncologic outcomes after nephron sparing surgery. In this selected population of pRCC tumors, we found that tumor stage is the only prognostic factor for cancer-free surviva

Cannabis use as a factor of lower corpulence in hepatitis C-infected patients: results from the ANRS CO22 Hepather cohort

International audienceBackground: Patients with chronic hepatitis C virus (HCV) infection are at greater risk of developing metabolic disorders. Obesity is a major risk factor for these disorders, and therefore, managing body weight is crucial. Cannabis use, which is common in these patients, has been associated with lower corpulence in various populations. However, this relationship has not yet been studied in persons with chronic HCV infection.Methods: Using baseline data from the French ANRS CO22 Hepather cohort, we used binary logistic and multinomial logistic regression models to test for an inverse relationship between cannabis use (former/current) and (i) central obesity (i.e., large waist circumference) and (ii) overweight and obesity (i.e., elevated body mass index (BMI)) in patients from the cohort who had chronic HCV infection. We also tested for relationships between cannabis use and both waist circumference and BMI as continuous variables, using linear regression models.Results: Among the 6348 participants in the study population, 55% had central obesity, 13.7% had obesity according to their BMI, and 12.4% were current cannabis users. After multivariable adjustment, current cannabis use was associated with lower risk of central obesity (adjusted odds ratio, aOR [95% confidence interval, CI]: 0.45 [0.37-0.55]), BMI-based obesity (adjusted relative risk ratio (aRRR) [95% CI]: 0.27 [0.19-0.39]), and overweight (aRRR [95% CI]: 0.47 [0.38-0.59]). This was also true for former use, but to a lesser extent. Former and current cannabis use were inversely associated with waist circumference and BMI.Conclusions: We found that former and, to a greater extent, current cannabis use were consistently associated with smaller waist circumference, lower BMI, and lower risks of overweight, obesity, and central obesity in patients with chronic HCV infection. Longitudinal studies are needed to confirm these relationships and to assess the effect of cannabis use on corpulence and liver outcomes after HCV cure.Trial registration: ClinicalTrials.gov identifier: NCT01953458