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

Pertinence du monitorage nocturne par polygraphie ventilatoire et capnométrie trans-cutanée pour le contrôle de la qualité des réglages de la ventilation non invasive des patients en état stable au décours d une insuffisance respiratoire aiguë en soins intensifs respiratoires- (Étude Prospective)

La mise en place de la ventilation non invasive (VNI) chez des patients BPCO en état stable au décours d un épisode aiguë est controversée. L étude des bénéfices de la VNI dans cette population est en cours dans une étude multicentrique (Etude NIVOLD) qui propose d adapter les réglages de la VNI d après les résultats du monitorage nocturne en polygraphie ventilatoire et capnométrie transcutanée. Le contrôle de la qualité de la VNI est alors défini par l'association des critères suivants: 1-SatO <90% pendant moins de 10% de la durée de VNI 2-ventilation minute stable pendant au moins 75% du temps d enregistrement 3-Fuites significatives moins de 25% du temps d enregistrement 4-Tendance à la diminution de la pCO transcutanée (tc) au cours de la nuit. L objectif de notre étude prospective est de déterminer l impact de ce monitorage nocturne sur les réglages de la VNI et l évolution au cours de la nuit des échanges gazeux chez des patients BPCO. Résultats : Vingt-deux patients BPCO ont été inclus rétrospectivement et comparés à un groupe contrôle de 22 patients BPCO appariés sur l âge et le sexe. L'appareil de VNI utilisé dans le groupe témoin était la VPAP ST (monitorage par Embletta GOLD® et capnomètre Sentec® (ResMed, Australie). Des GDS ont été réalisés avant et après monitorage. Dans le groupe témoin, les réglages de la VNI étaient : IPAP 19(3), EPAP 5 (1), FR 13 (2). L oxygène était associé à la VNI dans 100% des cas. En VS avant VNI, le Ph était de 7,43 (0.04), la PaO de 8,60 (0,76) et la PaCO de 7,49 (0,9). D'après les GDS au réveil et la clinique les réglages de la VNI étaient satisfaisants dans 65% des cas- Les critères fuites, PCO tc, oxymétrie et VM étaient atteints dans 87%, 70%, 35% et 100% des cas respectivement. Seulement 26% des patients ont atteint les 4 critères réunis. Seulement 13% des patients atteignaient les critères de monitorage, l amélioration clinique et gazométrique. La diminution de PCO2 artérielle était significativement plus importante dans le groupe témoin: -28(6) % vs -3 (10)% suggérant que le monitorage de la PCO tc permet un meilleur contrôle de l hypoventilation alvéolaire. Conclusion : Dans notre population BPCO le monitorage nocturne de la PCO tc et de la saturation artérielle en oxygène permet un meilleur contrôle de l hypoventilation alvéolaire nocturne.ROUEN-BU Médecine-Pharmacie (765402102) / SudocSudocFranceF

The relationship between maximal expiratory pressure values and critical outcomes in mechanically ventilated patients: a post hoc analysis of an observational study

International audienceBackground: Little interest has been paid to expiratory muscle strength, and the impact of expiratory muscle weakness on critical outcomes is not known. Very few studies assessed the relationship between maximal expiratory pressure (MEP) and critical outcomes. The aim of this study was to investigate the relationship between MEP and critical outcomes. Methods: This work was a secondary analysis of a prospective, observational study of adult patients who required mechanical ventilation for ≥ 24 h in an 18-bed ICU. MEP was assessed before extubation after a successful, spontaneous breathing trial. The relationships between MEP and extubation failure, and short-term (30 days) mortality, were investigated. Univariate logistic regressions were computed to investigate the relationship between MEP values and critical outcomes. Two multivariate analyses, with and without maximal inspiratory pressure (MIP), both adjusted using principal component analysis, were undertaken. Unadjusted and adjusted ROC curves were computed to compare the respective ability of MEP, MIP and the combination of both measures to discriminate patients with and without extubation failure or premature death. Results: One hundred and twenty-four patients were included. Median age was 66 years (IQR 18) and median mechanical ventilation duration was 7 days (IQR 6). Extubation failure rate was 15% (18/124 patients) and the rate for 30-day mortality was 11% (14/124 patient). Higher MEP values were significantly associated with a lower risk of extubation failure in the univariate analysis [OR 0.96 95% CI (0.93–0.98)], but not with short-term mortality. MEP was independently linked with extubation failure when MIP was not included in the multivariate model, but not when it was included, despite limited collinearity between these variables. This study was not able to differentiate the respective abilities of MEP, MIP, and their combination to discriminate patients with extubation failure or premature death (adjusted AUC for the combination of MEP and MIP: 0.825 and 0.650 for extubation failure and premature death, respectively). Conclusions: MEP is related to extubation failure. But, the results did not support its use as a substitute for MIP, since the relationship between MEP and critical outcomes was no longer significant when MIP was included. The use of MIP and MEP measurements combined did not reach higher discriminative capacities for critical outcomes that MEP or MIP alone. Trial Registration This study was retrospectively registered at https://clinicaltrials.gov/ct2/show/NCT02363231?cond=NCT02363231&draw=2&rank=1 (NCT02363231) in 13 February 201