Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

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

On permutations and permutation polytopes

An easy characterization is given of neighbors on permutation polytopes. Using this characterization it is shown that the graph of any such polytope is Hamiltonian, and that the diameter is two

More Please

More Please was the result of a collaboration with the Core company members - Moving memory, which mapped their development as a company and as developing choreographers/performance making. The show was performed at the Theatre Royal Margate and the Gulbenkian in 201

CONSEQÜÊNCIAS DA LAMINECTOMIA DORSAL DO TIPO FUNKQUIST A EM CÃES NORMAIS CONSEQUENCES OF THE FUNKQUIST A DORSAL LAMINECTOMY, IN NORMAL DOGS

O objetivo desta pesquisa foi verificar os efeitos da laminectomia dorsal do tipo Funkquist A em cães normais. A técnica realizada consistiu em abordagem dorsal à coluna vertebral; remoção (com ou sem a ajuda da elevação dos corpos vertebrais) das lâminas dorsais de T13 e L1; manutenção do ligamento supra-espinhal; colocação de gordura subcutânea como coxim supramedular; sutura da fáscia toracolombar, subcutâneo e pele; e bandagem compressiva por sete dias. Quarenta e oito horas após a cirurgia, todos os 10 cães submetidos a essa técnica exibiram perda das reações posturais e paresia de moderada a grave nos membros pélvicos. Hipoalgesia foi constatada em cinco deles. Tentando descobrir as causas, foram realizados estudos histológicos de medulas espinhais, coletadas 4 e 48 horas após a realização da laminectomia, porém com modificações como: não elevação dos corpos vertebrais durante a cirurgia e prevenção de qualquer tipo de compressão medular após a laminectomia. Analisando esses resultados, foi possível concluir que as disfunções neurológicas decorreram de lesões medulares ocasionadas possivelmente por: elevações dos corpos vertebrais durante a laminectomia, danificação de vasos espinhais, desestabilização da coluna vertebral e uma somatória de forças compressivas atuantes sobre a medula espinhal desprotegida. Na necropsia de cinco cães, acompanhados por quarenta e cinco dias, foi possível constatar: a permanência do ligamento supra-espinhal; que o enxerto de gordura não evita a penetração do tecido fibroso no canal vertebral nem sua aderência à dura- máter; notório (P< 0.01) achatamento do canal vertebral e deformação das medulas espinhais. Com base nos resultados, aconselha-se não realizar esses procedimentos cirúrgicos em cães acometidos de afeções medulares na junção toracolombar. A manutenção do ligamento supra-espinhal não perturba a realização da laminectomia, minimiza a ocorrência de defeitos estéticos na linha média dorsal e pode participar da compressão medular no pós-operatório imediato.<br>The purpose of this research was to check the effects of the Funkquist A dorsal laminectomy in normal dogs. The technique accomplished consisted in dorsal approach to the spine; removal of T13-L1 laminae with or without vertebral bodies elevation; mantainement of the supraspinous ligament; placement of subcutaneous fat as supramedulary pad; suture of thoracolumbar fascia, subcutaneous and skin; and compressive bandage for seven days. Fourty-eight hours latter all the dogs (10) submitted to this technique showed loss of the postural reactions and paraparesis classified of moderated to serious. Hypalgesia was ascertained in five of them. Trying to discover the causes, was accomplished histologic studies of spinal cord collected 4 and 48 hours after the accomplishment of the laminectomies were conducted, however with modifications as: non-elevation of the vertebral bodies during the surgery and prevention of any type of compression spinal after the laminectomie. Examining these results was possible to conclude that the neurologic dysfunctions were originated from cord lesions caused for: elevation of the vertebral bodies during the laminectomy, possible damage of spinal vessels, destabilization of the spine and a somatory of compressive forces acting upon an uncovered spinal cord. At the necropsy of five dogs realized forty - five days latter were possible to verify: the permanence of the supraspinous ligament; that the fat grafts do not avoid the penetration of the fibrous tissue into the vertebral canal neither its adherency to the dura mater; notorious (p < 0.01) flattening of the vertebral canal and deformations of the spinal cords. With support on these results, isn't advise to furfill these surgery procedure in the thoracolumbar junction of dogs. The mantainement of the supraspinatus ligament do not perturb the realization of the laminectomy, minimize the occurrence of the aesthetics defects at the dorsal midline and can participate at the immediate postoperative cord compression

'B Part of It' School Leaver study: a repeat cross-sectional study to assess the impact of increasing coverage with meningococcal B (4CMenB) vaccine on carriage of Neisseria meningitidis.

Published online September 6, 2021 OnlinePublBACKGROUND: Recombinant protein-based vaccines targeting serogroup B meningococci protect against invasive disease, but impacts on carriage are uncertain. This study assessed carriage prevalence of disease-associated meningococci from 2018-2020, as the proportion of vaccinated adolescents increased following introduction of a school-based 4CMenB immunisation program. METHODS: Eligible participants who completed high school (age 17-25) in South Australia in the previous year had an oropharyngeal swab taken and completed a risk factor questionnaire. Disease-associated meningococci (genogroups A, B, C, W, X, Y) were detected by meningococcal and genogroup-specific polymerase chain reaction. RESULTS: The final analysis included 4104 participants in 2018, 2690 in 2019, and 1338 in 2020. The proportion vaccinated with 4CMenB increased from 43% in 2018, to 78% in 2019, and 76% in 2020. Carriage prevalence of disease-associated meningococci in 2018 was 225/4104 (5.5%). There was little difference between the carriage prevalence in 2019 (134/2690, 5.0%, adjusted odds ratio [aOR] 0.82, 95% CI 0.64-1.05) and 2020 (68/1338, 5.1% aOR 0.82, 95% CI 0.57-1.17) compared to 2018. CONCLUSIONS: Increased 4CMenB uptake in adolescents was not associated with a decline in carriage of disease-associated meningococci. 4CMenB immunisation programs should focus on direct (individual) protection for groups at greatest risk of disease.Mark McMillan, Ann P. Koehler, Andrew Lawrence, Thomas R. Sullivan, Jana Bednarz, Jenny M. MacLennan ... et al