Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil

Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis

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Proteolytic Activation of SARS-CoV-2 Spike at the S1/S2 Boundary: Potential Role of Proteases beyond Furin

(2021) Tiffany Tang et al.   ACS Infectious Diseases

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

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

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High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19

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Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species

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Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

(2021) Delphine Planas et al.   NATURE

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

(2021) Felipe Gomes Naveca et al.   NATURE MEDICINE

Estimating epidemiologic dynamics from cross-sectional viral load distributions

(2021) James A. Hay et al.   SCIENCE

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

(2021) Bo Meng et al.   Cell Reports

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein

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Proteases and variants: context matters for SARS-CoV-2 entry assays

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

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Design, Synthesis, and Characterization of Macrocyclic Inhibitors of the Proprotein Convertase Furin

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

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ModelFinder: fast model selection for accurate phylogenetic estimates

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Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

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Cluster of Oseltamivir-Resistant 2009 Pandemic Influenza A (H1N1) Virus Infections on a Hospital Ward among Immunocompromised Patients—North Carolina, 2009

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RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

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Bayesian analysis of elapsed times in continuous-time Markov chains

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Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry

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Many-core algorithms for statistical phylogenetics

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Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology