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

Influence of Concomitant Extracranial Injury on Functional and Cognitive Recovery From Mild Versus Moderateto Severe Traumatic Brain Injury.

OBJECTIVE: To determine the effect of extracranial injury (ECI) on 6-month outcome in patients with mild traumatic brain injury (TBI) versus moderate-to-severe TBI. PARTICIPANTS/SETTING: Patients with TBI (n = 135) or isolated orthopedic injury (n = 25) admitted to a UK major trauma center and healthy volunteers (n = 99). DESIGN: Case-control observational study. MAIN MEASURES: Primary outcomes: (a) Glasgow Outcome Scale Extended (GOSE), (b) depression, (c) quality of life (QOL), and (d) cognitive impairment including verbal fluency, episodic memory, short-term recognition memory, working memory, sustained attention, and attentional flexibility. RESULTS: Outcome was influenced by both TBI severity and concomitant ECI. The influence of ECI was restricted to mild TBI; GOSE, QOL, and depression outcomes were significantly poorer following moderate-to-severe TBI than after isolated mild TBI (but not relative to mild TBI plus ECI). Cognitive impairment was driven solely by TBI severity. General health, bodily pain, semantic verbal fluency, spatial recognition memory, working memory span, and attentional flexibility were unaffected by TBI severity and additional ECI. CONCLUSION: The presence of concomitant ECI ought to be considered alongside brain injury severity when characterizing the functional and neurocognitive effects of TBI, with each presenting challenges to recovery.Funding: This work was partially funded by a Medical Research Council (MRC, UK) Program Grant (Acute brain injury: heterogeneity of mechanisms, therapeutic targets and outcome effects [G9439390 ID 65883]), the European Commission under the 7th Framework Programme (FP7-270259-TBIcare), the UK National Institute of Health Research (NIHR) Biomedical Research Centre at Cambridge, the Technology Platform funding provided by the UK Department of Health and an Engineering and Physical Sciences Research Council (EPSRC, UK) Pathways to Impact award. PJH was supported by the NIHR (Research Professorship and Cambridge BRC). JPP received funding from Academy of Finland – Grant #322381, Government’s Special Financial Transfer tied to academic research in Health Sciences (Finland), the Emil Aaltonen Foundation, the Finnish Brain Foundation and the Maire Taponen Foundation. BJS receives funding from the NIHR Brain Injury MedTech Co-operative, Cambridge and the NIHR Cambridge Biomedical Research Centre (Mental Health Theme). DKM was supported by the NIHR through the NIHR Cambridge Biomedical Research Centre grant and a Senior Investigator Award. VFJN was funded by a Health Foundation/Academy of Medical Sciences Clinician Scientist Fellowship. Acknowledgements: The NIHR/Wellcome Trust Cambridge Clinical Research Facility provided nursing support to aid in the patient recruitment and data collection within the Emergency Department

Nurses' strategies for overcoming barriers to fundamental nursing care in patients with COVID-19 caused by infection with the SARS-COV-2 virus: Results from the 'COVID-NURSE' survey

Aims To identify strategies used by registered nurses and non-registered nursing care staff in overcoming barriers when providing fundamental nursing care for non-invasively ventilated inpatients with COVID-19. Design Online survey with open-ended questions to collect qualitative data. Methods In August 2020, we asked UK-based nursing staff to describe any strategies they employed to overcome barriers to delivering care in 15 fundamental nursing care categories when providing care to non-invasively ventilated patients with COVID-19. We analysed data using Framework Analysis. Results A total of 1062 nurses consented to participate in our survey. We derived four themes. 1) Communication behaviours included adapting verbal and non-verbal communication with patients, using information technology to enable patients’ significant others to communicate with staff and patients, and establishing clear information-sharing methods with other staff. 2) Organizing care required clustering interventions, carefully managing supplies, encouraging patient self-care and using ‘runners’ and interdisciplinary input. 3) Addressing patients’ well-being and values required spending time with patients, acting in loco familiae, providing access to psychological and spiritual support, obtaining information about patients’ wishes early on and providing privacy and comforting/meaningful items. 4) Management and leadership behaviours included training, timely provision of pandemic information, psychological support, team huddles and facilitating regular breaks. Conclusions Our respondents identified multiple strategies in four main areas of clinical practice. Management and leadership are crucial to both fundamental care delivery and the well-being of nurses during pandemics. Grouping strategies into these areas of action may assist nurses and leaders to prepare for pandemic nursing. Impact As these strategies are unlikely to be exclusive to the COVID-19 pandemic, their global dissemination may improve patient experience and help nurses deliver fundamental care when planning pandemic nursing. However, their effectiveness is unknown. Therefore, we are currently evaluating these strategies in a cluster randomized controlled trial

International Nosocomial Infection Control Consortiu (INICC) report, data summary of 43 countries for 2007-2012. Device-associated module

We report the results of an International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2007-December 2012 in 503 intensive care units (ICUs) in Latin America, Asia, Africa, and Europe. During the 6-year study using the Centers for Disease Control and Prevention's (CDC) U.S. National Healthcare Safety Network (NHSN) definitions for device-associated health care–associated infection (DA-HAI), we collected prospective data from 605,310 patients hospitalized in the INICC's ICUs for an aggregate of 3,338,396 days. Although device utilization in the INICC's ICUs was similar to that reported from ICUs in the U.S. in the CDC's NHSN, rates of device-associated nosocomial infection were higher in the ICUs of the INICC hospitals: the pooled rate of central line–associated bloodstream infection in the INICC's ICUs, 4.9 per 1,000 central line days, is nearly 5-fold higher than the 0.9 per 1,000 central line days reported from comparable U.S. ICUs. The overall rate of ventilator-associated pneumonia was also higher (16.8 vs 1.1 per 1,000 ventilator days) as was the rate of catheter-associated urinary tract infection (5.5 vs 1.3 per 1,000 catheter days). Frequencies of resistance of Pseudomonas isolates to amikacin (42.8% vs 10%) and imipenem (42.4% vs 26.1%) and Klebsiella pneumoniae isolates to ceftazidime (71.2% vs 28.8%) and imipenem (19.6% vs 12.8%) were also higher in the INICC's ICUs compared with the ICUs of the CDC's NHSN