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

Factors associated with the length of stay in emergency departments in Southern-Ethiopia

Abstract Objectives This cross-sectional study was conducted on 399 patients at Hawassa University Comprehensive Specialized Hospital from February 15 to March 30/2018 to assess the length of stay (LOS) and its associated factors in emergency departments (EDs). Result About 91.5% patients were stayed in the EDs for greater than 24 h in different reasons. Inadequacy of beds in inpatient wards, overcrowding, absence of different laboratory test profiles and delay in radiological services were showed a significant differences in LOS greater than 24 h when compared to LOS ≤ 24 h in EDs (p < 0.05 for all). In addition, admission beds [adjusted odds ratio: 8.7 (95% CI 3.2–23.2)]; overcrowding [adjusted odds ratio: 3.6 (95% CI 1.6–8.3)]; laboratory test profiles [adjusted odds ratio: 5.1 (95% CI 1.9–14.1)], and radiology services [adjusted odds ratio: 3.7 (95% CI 1.5–9.2)] were significantly and positively associated with LOS greater than 24 h in EDs. Further, a significant proportion of patients were stayed for unnecessary extended length of time in EDs due to different factors. Therefore, the commitment of organization is crucial to provide sufficient number of admission beds, to scale-up laboratory test profiles and to decrease radiology service turn-around time in order to improve LOS in EDs

Integrated striga management (ISM) in East Africa

The parasitic weed Striga (Striga spp.) is an important constraint to crop production in Africa. Crop losses due to Striga have been severe and significant. Past research into the control of Striga has resulted in promising technologies including adapted Striga resistant crop cultivars, improved tillage and cultural practices, as well as the potential use of chemical inputs. Each of these control measures may provide significant relief to subsistence farmers confronted by severe Striga infestation. However, a more enhanced control of Striga can be achieved by combining two or more of these individual approaches synergistically. Yet, there have been limited research undertaken to evaluate the benefits of integrating multiple control options against Striga. Recently, we have established on–farm experiments in Eastern Africa to demonstrate the impact of integrated Striga management (ISM) using Striga resistant sorghum cultivars, nitrogen fertilizers, and tied-ridges as a water conservation measure. This Pilot Project started in Ethiopia and has now been extended to Eritrea and Tanzania. The program is focused on increasing the agronomic benefit of the ISM package, in promoting a functional seed production program through farmer organizations, and to enhancing the profitability of farmer’s investments in the ISM technology. In Ethiopia during the last two crop seasons, nearly 3000 one-half hectare demonstration plots have been planted to the ISM package with excellent results. Collaborators from national and regional research programs, regional Bureaus of Agriculture, and farm organizations were actively involved. Training was provided to participants promoting better understanding of Striga biology, control measures, and improved crop management practices including ISM Data collected over the two years showed drastic reduction in Striga infestation and often a ten-fold increase in sorghum yield when the ISM technology was applied. In the most severe cases, only the Striga resistant sorghum cultivar combined with improved agronomic practice gave measurable grain yield while local practices applied on to susceptible landraces often resulted in total crop failure. Encouraged by the results of these experiences, the government of Ethiopia recently proclaimed the nation-wide use of ISM in all Striga endemic areas of the country. Of 195 farmers who have taken up seed production through the pilot project, 31% successfully produced seed which met the quality standards and was sold back to the Pilot Project and to NGOs for wide distribution. A more organized and sponsored effort is needed to promote sustainability of the program nationally and to enhance profitability of the ISM package to participating farmers.

Reduction of Moniliformin During Alkaline Cooking of Corn

The incidence of moniliformin (MON) producing Fusarium spp. in selected corn (Zea mays L.) samples from Mexico and the United States and the effects of alkaline cooking and the tortilla manufacturing processes on the reduction of MON were determined. The percentage of infected kernels with Fusariumspp. ranged from 0 to 22% in eight food-grade corn samples, including six from Mexico and two from the United States. Complete (100%) reduction of MON was observed when a naturally contaminated com sample containing 1.4 µg of MON/g of corn was used in a pilot-scale alkaline cooking and tortilla manufacturing process. In a companion laboratory-scale study, using a cultured corn sample containing 17.6 µg of MON/g of corn, a 71 % reduction of the toxin was observed during the process. Alkaline cooking appeared to be an effective method for reduction of MON in corn