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

“Slalom”: Microsurgical Cross-Over Decompression for Multilevel Degenerative Lumbar Stenosis

Objective. Selective, bilateral multisegmental microsurgical decompression of lumbar spinal canal stenosis through separate, alternating cross-over approaches. Indications. Two-segmental and multisegmental degenerative central and lateral lumbar spinal stenosis. Contraindications. None. Surgical Technique. Minimally invasive, muscle, and facet joint-sparing bilateral decompression of the lumbar spinal canal through 2 or more alternating microsurgical cross-over approaches from one side. Results. From December 2010 until December 2015 we operated on 202 patients with 2 or multisegmental stenosis (115 f; 87 m; average age 69.3 yrs, range 51–91 yrs). All patients were suffering from symptoms typical of a degenerative lumbar spinal stenosis. All patients complained about back pain; however the leg symptoms were dominant in all cases. Per decompressed segment, the average OR time was 36 min and the blood loss 45.7 cc. Patients were mobilized 6 hrs postop and hospitalization averaged 5.9 days. A total of 116/202 patients did not need submuscular drainage. 27/202 patients suffered from a complication (13.4%). Dural tears occurred in 3.5%, an epidural hematoma in 5.5%, a deep wound infection in 1.98%, and a temporary radiculopathy postop in 1.5%. Postop follow-up ranged from 12 to 24 months. There was a significant improvement of EQ 5 D, Oswestry Disability Index (ODI), VAS for Back and Leg Pain, and preoperative standing times and walking distances

Clinical and Radiological Outcome of a new Total Cervical Disc Replacement Design

Study Design: Non-randomized prospective and single center clinical trial of the ProDisc Vivo prosthesis. Objective: Investigate the clinical and radiological results of a refined cTDR - the ProDisc Vivo - with two years of follow up (FU). The incidence of implant-related complications was recorded as a secondary outcome variable. Summary of Background Data: Previous generations of the ProDisc artificial cervical disc replacement generate high primary stability due to keel-based designs with opening of the anterior cortex during the implantation and subsequent high rates of heterotopic ossifications. Methods: Clinical outcome scores included the Neck Disability Index (NDI), Visual Analogue Scale (VAS), arm and neck pain self-assessment questionnaires. The radiological outcome included the range of motion (ROM) and the occurrence of heterotopic ossifications. The incidence of implant-related complications with new implant design was recorded as a secondary outcome variable. Results: A total of 55 patients received a single level treatment with the ProDisc Vivo cTDR between C3/4 and C6/7, with a follow up rate of 78%. The clinical outcome scores improved in all parameters significantly (p = 0.0001) (NDI: 68.3 → 17.4; VAS arm: 6.3 → 1.4; VAS neck: 4.9 → 1.6). The ROM of the index-segment didn't show a significant change (p = 0.26) (7.9° → 9.2°). Heterotopic ossifications at the index segment was found as grade 0 in 58%, grade 1 in 22%, grade 2 in 10%, grade 3 (with functional impairment of the prosthesis) in 7% and grade 4 in 3% of the cases. We observed three implant-related complications (5.5%), with two implant dislocations anteriorly and one low-grade infect. Conclusion: cTDR with ProDisc Vivo demonstrated a significant and sustained improvement of all clinical outcome parameters. A less-invasive implantation mechanism with lower primary stability of the cTDR might be a reason for a higher dislocation rate compared to the keel-based previous generation ProDisc C.ISSN:0362-2436ISSN:1528-115

Relatedness of wildlife and livestock avian isolates of the nosocomial pathogen Acinetobacter baumannii to lineages spread in hospitals worldwide

The natural habitats and potential reservoirs of the nosocomial pathogen Acinetobacter baumannii are poorly defined. Here, we put forth and tested the hypothesis of avian reservoirs of A. baumannii. We screened tracheal and rectal swab samples from livestock (chicken, geese) and wild birds (white stork nestlings) and isolated A. baumannii from 3% of sampled chicken (n = 220), 8% of geese (n = 40) and 25% of white stork nestlings (n = 661). Virulence of selected avian A. baumannii isolates was comparable to that of clinical isolates in the Galleria mellonella infection model. Whole genome sequencing revealed the close relationship of an antibiotic-susceptible chicken isolate from Germany with a multidrug-resistant human clinical isolate from China and additional linkages between livestock isolates and human clinical isolates related to international clonal lineages. Moreover, we identified stork isolates related to human clinical isolates from the United States. Multilocus sequence typing disclosed further kinship between avian and human isolates. Avian isolates do not form a distinct clade within the phylogeny of A. baumannii, instead they diverge into different lineages. Further, we provide evidence that A. baumannii is constantly present in the habitats occupied by storks. Collectively, our study suggests A. baumannii could be a zoonotic organism that may disseminate into livestock

Essential Step-by-Step Techniques for Minimally Invasive Spinal Surgery

The ultimate resource for learning and mastering minimally invasive spine surgery techniques An estimated 1.5 million instrumented spinal procedures are performed every year in the US. The majority of decompressions and about 50% of fusion procedures can be performed completely or partially using minimally invasive spine surgery (MISS) techniques. The full potential of MISS techniques has yet to be realized. Essential Step-by-Step Techniques for Minimally Invasive Spinal Surgery by internationally renowned MISS neurosurgeon Roger Härtl, spine-neurosurgeon Rodrigo Navarro-Ramirez, and an impressive group of global multidisciplinary contributors is the most comprehensive and detailed textbook written to date on this topic. The foundation of the book is built on six interacting principles critical to surgical success, and MISS in particular: Target, Technology, Technique, Teaching and Training, Testing, and Talent. The text starts with an opening chapter on the definition of MISS and introduction of these principles. Fifty-six subsequent chapters provide a comprehensive discussion on how to utilize an MISS approach for a full spectrum of spinal pathologies using nuanced variations specific to the operating surgeon. To ensure readers are well versed in all aspects of MISS, these chapters include painstaking details on indications, contraindications, pathoanatomy, operating room set-up, step-by-step techniques, and postoperative management. Key Highlights Contributions from master spine surgeons across the world provide a balanced global perspective on mastering and incorporating diverse techniques into practice Invaluable clinical pearls including tips/tricks and complication avoidance High-quality images, figures, anatomic drawings, and imaging studies illustrate relevant anatomic approaches and corridors and delineate why anatomic masteryis critical to MISS Twenty-five videos enhance the ability to learn and implement MISS approaches This is a must-have resource for practicing spine surgeons interested in MISS who wish to learn the latest techniques from master surgeons and achieve optimal patient outcomes. The text and videos also provide a robust training tool for senior-level orthopaedic and neurosurgery residents and spine fellows