The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Public preferences and priorities for end-of-life care in Kenya:a population-based street survey

BACKGROUND: End-of-life care needs are great in Africa due to the burden of disease. This study aimed to explore public preferences and priorities for end-of-life care in Nairobi, Kenya. METHODS: Population-based street survey of Kenyans aged ≥18; researchers approached every 10th person, alternating men and women. Structured interviews investigated quality vs. quantity of life, care priorities, preferences for information, decision-making, place of death (most and least favourite) and focus of care in a hypothetical scenario of serious illness with <1 year to live. Descriptive analysis examined variations. RESULTS: 201 individuals were interviewed (100 women) representing 17 tribes (n = 90 44.8%, Kikuyu). 56.7% (n = 114) said they would always like to be told if they had limited time left. The majority (n = 121, 61.4%) preferred quality of life over quantity i.e. extending life (n = 47, 23.9%). Keeping a positive attitude and ensuring relatives/friends were not worried were prioritised above having pain/discomfort relieved. The three most concerning problems were pain (45.8%), family burden (34.8%) and personal psychological distress (29.8%). Home was both the most (51.1% n = 98) and least (23.7% n = 44) preferred place of death. CONCLUSION: This first population-based survey on preferences and priorities for end-of-life care in Africa revealed that psycho-social domains were of greatest importance to the public, but also identified variations that require further exploration. If citizens’ preferences and priorities are to be met, the development of end-of-life care services to deliver preferences in Kenya should ensure an holistic model of palliative care responsive to individual preferences across care settings including at home

Cortical and subcortical brain structure in generalized anxiety disorder: findings from 28 research sites in the enigma-anxiety working group

The goal of this study was to compare brain structure between individuals with generalized anxiety disorder (GAD) and healthy controls. Previous studies have generated inconsistent findings, possibly due to small sample sizes, or clinical/analytic heterogeneity. To address these concerns, we combined data from 28 research sites worldwide through the ENIGMA-Anxiety Working Group, using a single, pre-registered mega-analysis. Structural magnetic resonance imaging data from children and adults (5–90 years) were processed using FreeSurfer. The main analysis included the regional and vertex-wise cortical thickness, cortical surface area, and subcortical volume as dependent variables, and GAD, age, age-squared, sex, and their interactions as independent variables. Nuisance variables included IQ, years of education, medication use, comorbidities, and global brain measures. The main analysis (1020 individuals with GAD and 2999 healthy controls) included random slopes per site and random intercepts per scanner. A secondary analysis (1112 individuals with GAD and 3282 healthy controls) included fixed slopes and random intercepts per scanner with the same variables. The main analysis showed no effect of GAD on brain structure, nor interactions involving GAD, age, or sex. The secondary analysis showed increased volume in the right ventral diencephalon in male individuals with GAD compared to male healthy controls, whereas female individuals with GAD did not differ from female healthy controls. This mega-analysis combining worldwide data showed that differences in brain structure related to GAD are small, possibly reflecting heterogeneity or those structural alterations are not a major component of its pathophysiology

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

Antibacterial and Antifungal Activity of Dombeya torrida (J.F. Gmel) and Hydnora abyssinica (A. Braun)

Background: The decoction of Dombeya torrida bark is used to treat indigestion while its roots are used for treatment of chest pains and colds. Hydnora abyssinica decoction is used as a cure for throat complaints, as an astringent in dysentery, for treatment of typhoid, anthrax, and East Coast Fever. Objectives: The present study was aimed at investigating the antibacterial and antifungal activities of D. torrida and H. abyssinica. Methodology: The D. torrida stem-bark and leaves and H. abyssinica whole plant were collected from Kiambu County and Embu County, respectively. Extraction of the plants was carried out using chloroform, methanol and water. The extracts were screened for activity against Staphylococcus aureus, Staphylococcus epididermis, Bacillus pumilus, Escherichia coli, Saccromyces cerevisiae and Candida albicans using agar diffusion assay and autobioassay. Results: Dombeya torrida bark decoction had the highest activity against S. aureus with an inhibition zone diameter of 16.91 mm. Hydnora abyssinica macerate had least activity against S. aureus with a zone diameter of 8.86 mm. Dombeya torrida bark decoction had the highest activity against S. Epididermis with a diameter of 17.05 mm with Hydnora abyssinica macerate having the least activity. Activity against E. coli was highest for D. torrida bark decoction with zone diameter of 16.56 mm. Hydnora abyssinica chloroform extract had the highest activity against B. pumilus with a zone diameter of 17.04 mm. The highest activity observed against S. cerevisiae was with D. torrida chloroform extract with a zone diameter of 17.69 mm with H. abyssinica macerate having the least activity (7.70 mm). Dombeya torrida chloroform extract was the most active extract against C. albicans with a zone diameter of 20.09 mm. Conclusion: The plants under study, D. torrida and H. abyssinica were chosen on the basis of folklore. Above results support the folklore that H. abyssinica is used as a cure for throat complaints, as an astringent in dysentery, treatment of diarrhoea and amoebic dysentery. Results of D. torrida extracts also supports its folklore use to treat chest pains and colds as many of these conditions are usually caused by bacterial infections. Keywords: antibacterial, antifungal, Dombeya torrida, Hydnora abyssinica, autobioassa

Neonatal mortality in Kenyan hospitals: a multisite, retrospective, cohort study

Background Most of the deaths among neonates in low-income and middle-income countries (LMICs) can be prevented through universal access to basic high-quality health services including essential facility-based inpatient care. However, poor routine data undermines data-informed efforts to monitor and promote improvements in the quality of newborn care across hospitals.Methods Continuously collected routine patients’ data from structured paper record forms for all admissions to newborn units (NBUs) from 16 purposively selected Kenyan public hospitals that are part of a clinical information network were analysed together with data from all paediatric admissions ages 0–13 years from 14 of these hospitals. Data are used to show the proportion of all admissions and deaths in the neonatal age group and examine morbidity and mortality patterns, stratified by birth weight, and their variation across hospitals.Findings During the 354 hospital months study period, 90 222 patients were admitted to the 14 hospitals contributing NBU and general paediatric ward data. 46% of all the admissions were neonates (aged 0–28 days), but they accounted for 66% of the deaths in the age group 0–13 years. 41 657 inborn neonates were admitted in the NBUs across the 16 hospitals during the study period. 4266/41 657 died giving a crude mortality rate of 10.2% (95% CI 9.97% to 10.55%), with 60% of these deaths occurring on the first-day of admission. Intrapartum-related complications was the single most common diagnosis among the neonates with birth weight of 2000 g or more who died. A threefold variation in mortality across hospitals was observed for birth weight categories 1000–1499 g and 1500–1999 g.Interpretation The high proportion of neonatal deaths in hospitals may reflect changing patterns of childhood mortality. Majority of newborns died of preventable causes (&gt;95%). Despite availability of high-impact low-cost interventions, hospitals have high and very variable mortality proportions after stratification by birth weight