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

Trade‐Adjusted Concentration Ratios in the US Manufacturing Sector

Abstract This paper incorporates international trade into the four‐firm concentration ratio to get a more realistic measure of market structure in the US manufacturing sector using 1997 and 2002 NAICS data. As expected, trade‐adjusted CR4 is significantly lower than the published CR4. Moreover, the effect of international trade is higher in 2002 than in 1997, offsetting the increase in domestic concentration and leaving the US manufacturing sector in 2002 as competitive as it was in 1997. Furthermore, different tests are used to check the validity of the results. All of them confirm that trade‐adjusted CR4s are significantly lower than their published counterparts.Concentration Ratio, International Trade, Manufacturing Sector, NAICS, L11, L60,

The Market Structure of the US Economy

L10,

Can the stroke impact scale 3.0 detect cognitive impairments in patients with a recent stroke?

Purpose: The aim of this study was to identify cognitive impairments in patients with a recent stroke using Stroke Impact Scale 3.0 (SIS). Participants and Methods: A retrospective cohort study was conducted to evaluate 50 medical records in patients with a recent stroke who have completed a stroke rehabilitation programme. All data were evaluated at St. Finbarr's Hospital in Cork, Ireland. Results: A total of 41 records met the inclusion criteria, of which 53.7% were male. Regarding the risk factors, most patients complained of hypertension (85.4%), with most being diagnosed with embolic stroke (56.1%). The SIS identified numerous issues in stroke patients, such as persistent problems with memory (36.6%), concentration (29.3%), and solving everyday problems (43.9%). In addition, some patients' responses were negative regarding their emotion such as feeling sad (51.2%), not enjoying things as much as ever (39%), feeling life is not worth living (85.4%) and not smiling or laughing at least once a day (80.5%). Conclusion: The inclusion of the SIS in the stroke review clinic identified cognitive deficits that may not have otherwise been detected. By using SIS in a systematic and standardised way, deficits can be identified, and appropriate rehabilitation can be provided

How Competitive is the US Manufacturing Sector?

This paper assesses the market structure of the US manufacturing sector using a corrected four-firm concentration ratio. The correction is done to the published 1997 CR, using the North American Industry Classification System, and addresses four areas: overaggregation, underaggregation, market locality, and international trade. The paper finds the US manufacturing sector to be fairly competitive with 58.0 percent of its industries operate in competitive markets, 17.5 percent operate in loose oligopoly, 24.5 percent operate in tight oligopoly, and none operates in monopoly markets. Equally important, this research finds international trade to have an important impact on the level of competition in the manufacturing sector. Eastern Economic Journal (2009) 35, 52–70. doi:10.1057/palgrave.eej.9050043

Prevalence and risk factors of disabilities among Egyptian preschool children: a community-based population study

Abstract Background Child disability has significant implications on their well-being and healthcare systems. Aim: This survey aimed to assess the magnitude of seven types of disability among Egyptian children aged 1 < 6 years and their socio-demographic, epidemiological, and perinatal predictors. Methods A national population-based cross-sectional household survey targeting 21,316 children from eight governorates was conducted. The screening questionnaire was derived from the WHO ten-question survey tool validated for identifying seven disability categories. Results The percentage of children with at least one disability was 8.1% as follows: speech/communication (4.4%), Mobility/physical (2.5%), Seizures (2.2%), Comprehension (1.7%), Intellectual impairment (1.4%), Visual (0.3%) and Hearing (0.2%). Age was not found to affect the odds of disability except for visual disability (significantly increased with age (AOR = 1.4, 95% CI:1.1–1.7). Male sex also increased the odds of all disabilities except visual, hearing, and seizures. Convulsions after birth significantly increased the odds of disability as follows: hearing (AOR = 8.1, 95% CI: 2.2–30.5), intellectual impairment (AOR = 4.2, 95% CI: 2.5–6.9), and mobility/physical (AOR = 3.4, 95% CI: 2.3–5.0). Preterm delivery and being kept in an incubator for more than two days after birth increased the odds for visual disability (AOR = 3.7, 95% CI: 1.1–12.1 & AOR = 3.7, 95% CI: 1.7–7.9 respectively). Cyanosis increased the odds of seizures (AOR = 4.7, 95% CI: 2.2–10.3). Low birth weight also increased the odds for all disability domains except for visual and hearing. Maternal health problems during pregnancy increased the odds for all types of disability except hearing and seizures. Higher paternal education decreased the odds for all disabilities by at least 30% except for vision and hearing. Conclusion The study found a high prevalence of disability among Egyptian children aged 1–6 years. It identified a number of modifiable risk factors for disability. The practice of early screening for disability is encouraged to provide early interventions when needed

Additional file 2 of Prevalence and risk factors of disabilities among Egyptian preschool children: a community-based population study

Additional file 2: S Table 2. All data disability less than 6

Additional file 1 of Prevalence and risk factors of disabilities among Egyptian preschool children: a community-based population study

Additional file 1: S Table 1. List of the expected and targeted children according to the governorates, locality and sociodemographic status for screening of disability among children aged 1-6 years