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      Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

      research-article
      1 , 2 , 3 , 2 , 4 , 5 , 6 , 2 , 1 , 7 , 8 , 9 , 10 , 2 , 11 , 2 , 12 , 13 , 4 , 5 , 6 , 14 , 6 , 14 , 9 , 15 , 16 , 17 , 17 , 17 , 17 , The Genotype to Phenotype Japan (G2P-Japan) Consortium, 6 , 7 , 8 , 14 , 9 , 15 , 8 , 14 , 18 , , 4 , 5 , , 1 , , 2 , 11 , 19 ,
      Nature
      Nature Publishing Group UK
      SARS-CoV-2, Viral pathogenesis

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          Abstract

          The emergence of the Omicron variant of SARS-CoV-2 is an urgent global health concern 1 . In this study, our statistical modelling suggests that Omicron has spread more rapidly than the Delta variant in several countries including South Africa. Cell culture experiments showed Omicron to be less fusogenic than Delta and than an ancestral strain of SARS-CoV-2. Although the spike (S) protein of Delta is efficiently cleaved into two subunits, which facilitates cell–cell fusion 2, 3 , the Omicron S protein was less efficiently cleaved compared to the S proteins of Delta and ancestral SARS-CoV-2. Furthermore, in a hamster model, Omicron showed decreased lung infectivity and was less pathogenic compared to Delta and ancestral SARS-CoV-2. Our multiscale investigations reveal the virological characteristics of Omicron, including rapid growth in the human population, lower fusogenicity and attenuated pathogenicity.

          Abstract

          In vitro studies in human cell lines and in vivo studies in a hamster model show that the SARS-CoV-2 Omicron variant is less pathogenic than both the Delta variant and an ancestral strain of SARS-CoV-2.

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          Most cited references30

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            fastp: an ultra-fast all-in-one FASTQ preprocessor

            Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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              A new coronavirus associated with human respiratory disease in China

              Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
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                Author and article information

                Contributors
                matsuk@czc.hokudai.ac.jp
                tanaka@med.hokudai.ac.jp
                fukut@pop.med.hokudai.ac.jp
                KeiSato@g.ecc.u-tokyo.ac.jp
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                1 February 2022
                1 February 2022
                2022
                : 603
                : 7902
                : 700-705
                Affiliations
                [1 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Department of Microbiology and Immunology, Graduate School of Medicine, , Hokkaido University, ; Sapporo, Japan
                [2 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, , The University of Tokyo, ; Tokyo, Japan
                [3 ]GRID grid.31432.37, ISNI 0000 0001 1092 3077, Faculty of Medicine, , Kobe University, ; Kobe, Japan
                [4 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Department of Cancer Pathology, Faculty of Medicine, , Hokkaido University, ; Sapporo, Japan
                [5 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), , Hokkaido University, ; Sapporo, Japan
                [6 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Division of Molecular Pathobiology, International Institute for Zoonosis Control, , Hokkaido University, ; Sapporo, Japan
                [7 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Division of International Research Promotion, International Institute for Zoonosis Control, , Hokkaido University, ; Sapporo, Japan
                [8 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, One Health Research Center, , Hokkaido University, ; Sapporo, Japan
                [9 ]GRID grid.274841.c, ISNI 0000 0001 0660 6749, Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, , Kumamoto University, ; Kumamoto, Japan
                [10 ]GRID grid.33003.33, ISNI 0000 0000 9889 5690, Department of Clinical Pathology, Faculty of Medicine, , Suez Canal University, ; Ismailia, Egypt
                [11 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, Graduate School of Medicine, , The University of Tokyo, ; Tokyo, Japan
                [12 ]GRID grid.258799.8, ISNI 0000 0004 0372 2033, Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, , Kyoto University, ; Kyoto, Japan
                [13 ]GRID grid.258799.8, ISNI 0000 0004 0372 2033, Graduate School of Pharmaceutical Sciences, , Kyoto University, ; Kyoto, Japan
                [14 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, International Collaboration Unit, International Institute for Zoonosis Control, , Hokkaido University, ; Sapporo, Japan
                [15 ]GRID grid.257022.0, ISNI 0000 0000 8711 3200, Institute of Biomedical and Health Sciences, , Hiroshima University, ; Hiroshima, Japan
                [16 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Institute for Genetic Medicine, , Hokkaido University, ; Sapporo, Japan
                [17 ]GRID grid.417096.d, Tokyo Metropolitan Institute of Public Health, ; Tokyo, Japan
                [18 ]GRID grid.39158.36, ISNI 0000 0001 2173 7691, Division of Risk Analysis and Management, International Institute for Zoonosis Control, , Hokkaido University, ; Sapporo, Japan
                [19 ]GRID grid.419082.6, ISNI 0000 0004 1754 9200, CREST, Japan Science and Technology Agency, ; Saitama, Japan
                [20 ]GRID grid.410795.e, ISNI 0000 0001 2220 1880, National Institute of Infectious Diseases, ; Tokyo, Japan
                [21 ]GRID grid.265061.6, ISNI 0000 0001 1516 6626, Tokai University, ; Isehara, Japan
                [22 ]GRID grid.136304.3, ISNI 0000 0004 0370 1101, Chiba University, ; Chiba, Japan
                [23 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, The University of Tokyo, ; Kashiwa, Japan
                [24 ]GRID grid.258799.8, ISNI 0000 0004 0372 2033, Kyoto University, ; Kyoto, Japan
                [25 ]GRID grid.274841.c, ISNI 0000 0001 0660 6749, Kumamoto University, ; Kumamoto, Japan
                [26 ]GRID grid.410849.0, ISNI 0000 0001 0657 3887, University of Miyazaki, ; Miyazaki, Japan
                Author information
                http://orcid.org/0000-0001-6145-395X
                http://orcid.org/0000-0003-0440-8321
                http://orcid.org/0000-0001-9163-1665
                http://orcid.org/0000-0001-5400-5905
                http://orcid.org/0000-0001-9910-3912
                http://orcid.org/0000-0003-1607-2175
                http://orcid.org/0000-0002-0062-2753
                http://orcid.org/0000-0002-2572-6786
                http://orcid.org/0000-0001-8069-9250
                http://orcid.org/0000-0003-0541-706X
                http://orcid.org/0000-0003-2569-2755
                http://orcid.org/0000-0003-2869-9450
                http://orcid.org/0000-0003-3765-8482
                http://orcid.org/0000-0002-4205-6526
                http://orcid.org/0000-0001-6470-3301
                http://orcid.org/0000-0001-5471-8331
                Article
                4462
                10.1038/s41586-022-04462-1
                8942852
                35104835
                d837c0f8-31a0-44a4-a66b-a9fed9090a71
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 December 2021
                : 25 January 2022
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                sars-cov-2,viral pathogenesis
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                sars-cov-2, viral pathogenesis

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