Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK

Do master narratives change among High School Students?: a characterization of how national history is represented

Master narratives frame students’ historical knowledge, possibly hindering access to more historical representations. A detailed analysis of students’ historical narratives about the origins of their own nation is presented in terms of four master narrative characteristics related to the historical subject, national identification, the main theme and the nation concept. The narratives of Argentine 8th and 11th graders were analyzed to establish whether a change toward a more complex historical account occurred. The results show that the past is mostly understood in master narrative terms but in the 11th grade narratives demonstrate a more historical understanding. Only identification appears to be fairly constant across years of history learning. The results suggest that in history education first aiming at a constructivist concept of nation and then using the concept to reflect on the national historical subject and events in the narrative might help produce historical understanding of a national past.This article was written with the support of projects EDU-2010-17725 (DGICYT, Spain) and PICT-2008-1217 (ANPCYT, Argentina), coordinated by the first author. We are grateful for that support

How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.

During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses

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

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

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Modelling and Calculation of Adaptive Devices of Automation, Control and Protection for Intellectual Electric Grid in Scilab Freeware Computer Mathematic Package

В работе исследованы возможности адаптации свободно распространяемого пакета компьютерной математики Scilab для решения специализированных вычислительных задач. Для этого в Scilab осуществлено моделирование и расчет ряда адаптивных устройств автоматики, управления и защиты для интеллектуальных электрических сетей, включая возобновляемые источники энергии. Были исследованы возможности пакета Scilab для выполнения последовательных расчетов с использованием большого числа математических функций, решения систем линейных алгебраических уравнений, анализа результата, решения задач оптимизации, построения двумерных и трехмерных графиков функций и др. Все расчетные решения, полученные для Scilab, были проанализированы в сравнении с аналогичными решениями, полученными для Mathcad. Полученные результаты подтверждают возможность использования Scilab для указанных целей и демонстрируют ряд преимуществ при применении пакета в обучении на электротехнических специальностях и проведении научных исследований

Computed Tomography Angiography for the Diagnosis of Coronary Artery Disease Among Patients Undergoing Transcatheter Aortic Valve Implantation.

Computed tomography angiography (CTA) is used to plan TAVI procedures. We investigated the performance of pre-TAVI CTA for excluding coronary artery disease (CAD). In total 127 patients were included. CTA images were analyzed for the presence of ≥ 50% (significant CAD) and ≥ 70% (severe CAD) diameter stenoses in proximal coronary arteries. Results were compared with invasive coronary angiography (ICA) at vessel and patient levels. Primary endpoint was the negative predictive value (NPV) of CTA for the presence of CAD. A total of 342 vessels were analyzable. NPV of CTA was 97.5% for significant CAD and 96.3% for severe CAD. Positive predictive value and accuracy were 44.8% and 87.1% for significant CAD and 56.3% and 94.4% for severe CAD. At patient level, NPV for significant CAD was 88.6%. Pre-TAVI CTA shows good performance for ruling out CAD and could be used as a gatekeeper for ICA in selected patients