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

Protein supplementation in critical illness: why, when and how?

Purpose of reviewIn critically ill patients, optimal protein provision remains a challenge given the wide range in recommended protein delivery in international guidelines and the lack of robust, high quality evidence. As patients are confronted with poor functional outcomes after admission, often attributed to muscle wasting and persisting for multiple years, there is a pressing need for optimal nutritional strategies in the ICU, particularly including protein. This review will discuss the recent literature with regard to purpose, timing and mode of protein delivery.Recent findingsRecent studies on the effect of dose and timing of protein on clinical and functional outcomes are largely observational in nature and the protein delivery considered as "high" still often only nears the lower end of current recommendations. The majority of trials observed no effect of protein supplementation on mortality, muscle strength or function, though some report attenuation of muscle volume loss, especially when combined with muscle activation. There is no strong evidence that ICU patients should receive supplementation with any specific amino acids.Though adequate protein provision is likely important, it is difficult to come to a uniform conclusion regarding dosing and timing due to conflicting results in mostly observational studies as well as different cut-off values for high, moderate and low protein intake. This topic is currently subject to large clinical trials

Long-term mortality of critically ill patients with diabetes who survive admission to the intensive care unit

Objective: Long-term outcomes of critically ill patients with diabetes are unknown. Our objectives were to evaluate the effect of diabetes on both long-term survival rates and the average number of years of life lost for patients admitted to an intensive care unit who survived to hospital discharge. Design and participants: A data linkage study evaluating all adult patients in South Australia between 2004 and 2011 who survived hospitalisation that required admission to a public hospital ICU. Main outcome measures: All patients were evaluated using hospital coding for diabetes, which was cross-referenced with registration with the Australian National Diabetes Services Scheme for a diagnosis of diabetes. This dataset was then linked to the Australian National Death Index. Longitudinal survival was assessed using Cox proportional hazards regression. Life-years lost were calculated using age- and sex-specific life-tables from the Australian Bureau of Statistics. Results: 5450 patients with diabetes and 17 023 patients without diabetes were included. Crude mortality rates were 105.5 per 1000 person-years (95% CI, 101.6-109.6 per 1000 person-years) for patients with diabetes, and 67.6 per 1000 person-years (95% CI, 65.9-69.3 per 1000 person-years) for patients without diabetes. Patients with diabetes were older and had higher illness severity scores on admission to the ICU, were more likely to die after hospital discharge (unadjusted hazard ratio [HR], 1.52 [95% CI, 1.45-1.59]; adjusted HR, 1.16 [95% CI, 1.10-1.21]; P < 0.0001) and suffered a greater number of average life-years lost. Conclusions: Our study indicates that crude mortality for ICU survivors with pre-existing diabetes is considerable after hospital discharge, and the risk of mortality is greater than for survivors without diabetes.Yasmine Ali Abdelhamid, Mark P Plummer, Mark E Finnis, Vishwanath Biradar, Shailesh Bihari, Palash Kar, Stewart Moodie, Michael Horowitz, Jonathan E Shaw, Liza K Phillips and Adam M Dean

Relationship of blood thiamine pyrophosphate to plasma phosphate and the response to enteral nutrition plus co-administration of intravenous thiamine during critical illness.

OnlinePublBackground: Hypovitamin B1 occurs frequently during critical illness but is challenging to predict or rapidly diagnose. The aim of this study was to evaluate whether plasma phosphate concentrations predict hypovitamin B1, enteral nutrition prevents hypovitamin B1 and intravenous thiamine supplementation achieves supraphysiological concentrations in critically ill patients. Methods: Thirty‐two enterally fed critically ill patients, with a plasma phosphate concentration ≤0.65 mmol/L, formed a nested cohort within a larger randomised clinical trial. Patients were assigned to receive intravenous thiamine (200 mg) twice daily, and controls were not administered intravenous thiamine. Thiamine pyrophosphate concentrations were measured at four time points (pre‐ and post‐infusion and 4‐ and 6‐h post‐infusion) on days 1 and 3 in those allocated to thiamine and once in the control group. Results: Baseline thiamine pyrophosphate concentrations were similar (intervention 88 [67, 93] vs. control 89 [62, 110] nmol/L, p = 0.49). Eight (25%) patients had hypovitamin B1 (intervention 3 vs. control 5), with two patients in the control group remaining insufficient at day 3. There was no association between baseline phosphate and thiamine pyrophosphate concentrations. Intravenous thiamine achieved supraphysiological concentrations 6 h post first infusion, with concentrations increasing to day 3. In the control group, thiamine pyrophosphate concentrations were not statistically different between baseline and day 3 (mean change: 8.6 [−6.0, 23.1] nmol/L, p = 0.25). Conclusions: Phosphate concentrations did not predict hypovitamin B1, which was observed in 25% of the participants. Enteral nutrition alone prevented the development of new hypovitamin B1. Administration of a single 200‐mg dose of intravenous thiamine achieved supraphysiological concentrations of thiamine pyrophosphate, with repeated dosing sustaining this effect.Jake T. B. Collie, Alice Jiang, Yasmine Ali Abdelhamid, Melissa Ankravs, Rinaldo Bellomo, Kathleen M. Byrne, Annabelle Clancy, Mark E. Finnis, Ronda Greaves, Brianna Tascone, Adam M. Dean

International Nosocomial Infection Control Consortium report, data summary of 50 countries for 2010-2015: Device-associated module

•We report INICC device-associated module data of 50 countries from 2010-2015.•We collected prospective data from 861,284 patients in 703 ICUs for 3,506,562 days.•DA-HAI rates and bacterial resistance were higher in the INICC ICUs than in CDC-NHSN's.•Device utilization ratio in the INICC ICUs was similar to CDC-NHSN's. Background: We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2010-December 2015 in 703 intensive care units (ICUs) in Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific. Methods: During the 6-year study period, using Centers for Disease Control and Prevention National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI), we collected prospective data from 861,284 patients hospitalized in INICC hospital ICUs for an aggregate of 3,506,562 days. Results: Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the INICC medical-surgical ICUs, the pooled rate of central line-associated bloodstream infection, 4.1 per 1,000 central line-days, was nearly 5-fold higher than the 0.8 per 1,000 central line-days reported from comparable US ICUs, the overall rate of ventilator-associated pneumonia was also higher, 13.1 versus 0.9 per 1,000 ventilator-days, as was the rate of catheter-associated urinary tract infection, 5.07 versus 1.7 per 1,000 catheter-days. From blood cultures samples, frequencies of resistance of Pseudomonas isolates to amikacin (29.87% vs 10%) and to imipenem (44.3% vs 26.1%), and of Klebsiella pneumoniae isolates to ceftazidime (73.2% vs 28.8%) and to imipenem (43.27% vs 12.8%) were also higher in the INICC ICUs compared with CDC-NHSN ICUs. Conclusions: Although DA-HAIs in INICC ICU patients continue to be higher than the rates reported in CDC-NSHN ICUs representing the developed world, we have observed a significant trend toward the reduction of DA-HAI rates in INICC ICUs as shown in each international report. It is INICC's main goal to continue facilitating education, training, and basic and cost-effective tools and resources, such as standardized forms and an online platform, to tackle this problem effectively and systematically