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Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

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Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

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Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

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Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

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SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

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Serum Neutralizing Activity Elicited by mRNA-1273 Vaccine — Preliminary Report

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Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

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N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

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SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

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SARS-CoV-2 one year on: evidence for ongoing viral adaptation

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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

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Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant

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

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Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants

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Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

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Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

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Activation and evasion of type I interferon responses by SARS-CoV-2

(2020) Xiaobo Lei et al.   Nature Communications

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

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Spike mutation D614G alters SARS-CoV-2 fitness

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SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling

(2020) Lisa Miorin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

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Evasion of Type I Interferon by SARS-CoV-2

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Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

(2020) Lizhou Zhang et al.   Nature Communications

National and International Dimensions of HIV-1 Sequence Clusters in a Northern California Clinical Cohort

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

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HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens

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Gene-Wide Identification of Episodic Selection

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On the Validity of Evolutionary Models with Site-Specific Parameters

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FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

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Detecting Individual Sites Subject to Episodic Diversifying Selection

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Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate

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