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      Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

      1 , 2 , 3 , 1 , 1 , 2 , 4 , 2 , 3 , 1 , 5 , 6 , 2 , 4 , 1 , 7 , 8 , 2 , 4 , 2 , 4 , 2 , 4 , 9 , 2 , 4 , 10 , 2 , 4 , 2 , 4 , 11 , 11 , 3 , 12 , 12 , 13 , 14 , 2 , 4 , 2 , 4 , 2 , 4 , 15 , 16 , 16 , 16 , 16 , 16 , 17 , 1 , 1 , 13 , 18 , 18 , 18 , 18 , 18 , 19 , 20 , 21 , 22 , 23 , 13 , 13 , 1 , 1 , 1 , 13 , 24 , 24 , 25 , 8 , 26 , 27 , 13 , 1 , 3 , 28 , 29 , 7 , 5 , 30 , 5 , 31 , 3 , 32 , 13 , 1 , 33 , 2 , 4
      Science
      American Association for the Advancement of Science (AAAS)

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          Abstract

          Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

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          Most cited references72

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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              Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

              A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2, SARS-CoV-2) caused an outbreak in Wuhan city, Hubei province, China, starting from December 2019 that quickly spread nationwide and to other countries around the world1-3. Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor4. Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses1-3,5. The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.
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                Author and article information

                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                April 14 2021
                : eabh2644
                Affiliations
                [1 ]MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, UK.
                [2 ]Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
                [3 ]Department of Zoology, University of Oxford, UK.
                [4 ]Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
                [5 ]Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.
                [6 ]Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.
                [7 ]Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
                [8 ]Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
                [9 ]Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil.
                [10 ]Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil.
                [11 ]Institute for Applied Economic Research–Ipea, Brasília, Brazil.
                [12 ]DB Diagnósticos do Brasil, São Paulo, Brazil.
                [13 ]Department of Mathematics, Imperial College London, UK.
                [14 ]Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
                [15 ]Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil.
                [16 ]Instituto Hermes Pardini, Brazil.
                [17 ]Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
                [18 ]CDL Laboratório Santos e Vidal, Manaus, Brazil.
                [19 ]Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
                [20 ]Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil.
                [21 ]Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.
                [22 ]Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
                [23 ]Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA.
                [24 ]Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil.
                [25 ]Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA.
                [26 ]Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
                [27 ]Mathematical Sciences, University of Southampton, Southampton, UK.
                [28 ]Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
                [29 ]Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
                [30 ]Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.
                [31 ]Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.
                [32 ]Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK.
                [33 ]Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark.
                Article
                10.1126/science.abh2644
                30fa922a-4304-4953-a9cc-ddfef24fbf7e
                © 2021
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