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

Aspen Restoration Using Beaver on the Northern Yellowstone Winter Range under Reduced Ungulate Herbivory

Ungulate browsing and lack of overstory disturbance have historically prevented aspen regeneration on the Northern Yellowstone Winter Range (NYWR). Aspen clones regenerate if sprouts are produced that grow into recruitment stems (\u3e2 m tall) and replace the mature overstory. Beaver reintroduced in 1991 to Eagle Creek on the NYWR facilitated aspen restoration by removing overstory trees and increasing sprouting. However, intense ungulate browsing, primarily from the Northern Yellowstone elk herd, was preventing aspen recruitment in Eagle Creek as of 2005. Since 2005, wolf predation has contributed to a 56% decrease in this elk herd. We investigated the effects of beaver reintroduction, ungulate herbivory, and predator-mediated declines in elk numbers on aspen regeneration in Eagle Creek from 1997 to 2012. Aerial photos of Eagle Creek in 2005 and 2011 showed that the aspen overstory has not been replaced 21 years after beaver reintroduction (p \u3e 0.05). Sprouting and recruitment were investigated using 4-m radius circular plots (n = 31) established throughout Eagle Creek in 1997 and monitored annually until 2012. Beaver activity stimulated sprouting in 71% of these plots. In 2012, 77% of the plots had ≥1 recruitment stem and 75% of the paired plots associated with exclosures (n = 16) had aspen stems with an average height ≥2 m. Recent increases in aspen recruitment in Eagle Creek indicate that aspen communities are regenerating. This has likely resulted from decreased ungulate browsing pressure on aspen saplings from 2005 to 2012. These findings are consistent with the predictions of a density-mediated trophic cascade following wolf reintroduction

EGF and FGF-2 responsiveness of rat and mouse neural precursors derived from the embryonic CNS

EGF and FGF-2 induce the proliferation of embryonic neural precursors (ENPs) in vitro from a number of different species. In this study, we demonstrate that embryonic age is a crucial determinant of the number and differentiation potential of rat embryonic neural precursor cells responding to either EGF and/or FGF-2, in that (i) there is a differential response to the two growth factors (both alone and in combination) according to the gestational age of isolation and (ii) when allowed to differentiate, there are temporal changes in the ability of these cells to produce neurons. Furthermore, for cultures of all gestational ages, there is a defined pattern of senescence, with cultures expanding longest when cells are isolated earlier in gestation. The suggestion is that rat ENPs in this study consist predominantly of neural progenitor cells with limited division potential rather than self-renewing multipotential neural stem cells. In contrast, mouse ENPs appeared to expand indefinitely and thus allow for longer studies to be carried out looking at the effects of growth factor concentrations. The effect of varying the concentration of EGF was assessed using mouse ENPs

Management of oral and maxillofacial trauma during the first wave of the COVID-19 pandemic in the United Kingdom

We assess the effect of coronavirus disease 2019 (COVID-19) on UK oral and maxillofacial (OMF) trauma services and patient treatment during the first wave of the pandemic. From 1 April 2020 until 31 July 2020, OMF surgery units in the UK were invited to prospectively record all patients presenting with OMF trauma. Information included clinical presentation, mechanism of injury, how it was managed, and whether or not treatment included surgery. Participants were also asked to compare the patient’s care with the treatment that would normally have been given before the crisis. Twenty-nine units across the UK contributed with 2,229 entries. The most common aetiology was mechanical fall (39%). The most common injuries were soft tissue wounds (52%) and, for hard tissues, mandibular fractures (13%). Of 876 facial fractures, 79 patients’ treatment differed from what would have been normal pre-COVID, and 33 had their treatment deferred. Therefore the care of 112 (14%) patients was at variance with normal practice because of COVID restrictions. The pattern of OMFS injuries changed during the first COVID-19 lockdown. For the majority, best practice and delivery of quality trauma care continued despite the on-going operational challenges, and only a small proportion of patients had changes to their treatment. The lessons learnt from the first wave, combined with adequate resources and preoperative testing of patients, should allow those facial injuries in the second wave to receive best-practice care