Simultane Quantifizierung von 127I- und 129I-Spezies in Umweltproben mittels IC-ICP-MS und AMS

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SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods.Comment: V Munteanu and M Saldana contributed equally to this work A Smith and S Mangul jointly supervised this work For correspondence: [email protected]

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection,understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to getinsight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for theroutine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemicand evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets anddevelopment of therapeutic strategies. For each tool, we briefly describe its use case and how it advances researchspecifically for SARS-CoV-2.Fil: Hufsky, Franziska. Friedrich Schiller University Jena; AlemaniaFil: Lamkiewicz, Kevin. Friedrich Schiller University Jena; AlemaniaFil: Almeida, Alexandre. the Wellcome Sanger Institute; Reino UnidoFil: Aouacheria, Abdel. Centre National de la Recherche Scientifique; FranciaFil: Arighi, Cecilia. Biocuration and Literature Access at PIR; Estados UnidosFil: Bateman, Alex. European Bioinformatics Institute. Head of Protein Sequence Resources; Reino UnidoFil: Baumbach, Jan. Universitat Technical Zu Munich; AlemaniaFil: Beerenwinkel, Niko. Universitat Technical Zu Munich; AlemaniaFil: Brandt, Christian. Jena University Hospital; AlemaniaFil: Cacciabue, Marco Polo Domingo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Chuguransky, Sara Rocío. European Bioinformatics Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Drechsel, Oliver. Robert Koch-Institute; AlemaniaFil: Finn, Robert D.. Biocurator for Pfam and InterPro databases; Reino UnidoFil: Fritz, Adrian. Helmholtz Centre for Infection Research; AlemaniaFil: Fuchs, Stephan. Robert Koch-Institute; AlemaniaFil: Hattab, Georges. University Marburg; AlemaniaFil: Hauschild, Anne Christin. University Marburg; AlemaniaFil: Heider, Dominik. University Marburg; AlemaniaFil: Hoffmann, Marie. Freie Universität Berlin; AlemaniaFil: Hölzer, Martin. Friedrich Schiller University Jena; AlemaniaFil: Hoops, Stefan. University of Virginia; Estados UnidosFil: Kaderali, Lars. University Medicine Greifswald; AlemaniaFil: Kalvari, Ioanna. European Bioinformatics Institute; Reino UnidoFil: von Kleist, Max. Robert Koch-Institute; AlemaniaFil: Kmiecinski, Renó. Robert Koch-Institute; AlemaniaFil: Kühnert, Denise. Max Planck Institute for the Science of Human History; AlemaniaFil: Lasso, Gorka. Albert Einstein College of Medicine; Estados UnidosFil: Libin, Pieter. Hasselt University; BélgicaFil: List, Markus. Universitat Technical Zu Munich; AlemaniaFil: Löchel, Hannah F.. University Marburg; Alemani

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories.Peer Reviewe