Delta-Omicron recombinant escapes therapeutic antibody neutralization

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

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Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

(2022) Philippe Colson et al.   JOURNAL OF MEDICAL VIROLOGY

Recombination between SARS-CoV-2 Omicron BA.1 and BA.2 variants identified in a traveller from Nepal at the airport quarantine facility in Japan

(2022) Tsuyoshi Sekizuka et al.   JOURNAL OF TRAVEL MEDICINE

Resistance Mutations in SARS-CoV-2 Delta Variant after Sotrovimab Use

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Neutralization of the SARS-CoV-2 Deltacron and BA.3 Variants

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Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

(2022) Rebecca J. Rockett et al.   Nature Communications

Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies

(2022) Takuya Tada et al.   EBioMedicine

Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant

(2022) Emma Birnie et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Potential intervariant and intravariant recombination of Delta and Omicron variants

(2022) Lulan Wang et al.   JOURNAL OF MEDICAL VIROLOGY

Resistance of SARS-CoV-2 Omicron BA.1 and BA.2 Variants to Vaccine-Elicited Sera and Therapeutic Monoclonal Antibodies

(2022) Hao Zhou et al.   Viruses-Basel

Evolution of Anti-SARS-CoV-2 Therapeutic Antibodies

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SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

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Whole Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina-MiSeq ARTIC Protocol

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SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

(2021) Tyler N. Starr et al.   NATURE

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole et al.   Virus Evolution

Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion

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Early Treatment for Covid-19 with SARS-CoV-2 Neutralizing Antibody Sotrovimab

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Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants

(2021) Sebastian Weigang et al.   Nature Communications

Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera

(2021) Takuya Tada et al.   iScience

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells

(2020) Shutoku Matsuyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2

(2020) Zhenglin Zhu et al.   Scientific Reports

An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2

(2020) Takuya Tada et al.   Cell Reports

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

Nextstrain: real-time tracking of pathogen evolution

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SWISS-MODEL: homology modelling of protein structures and complexes

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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

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Sambamba: fast processing of NGS alignment formats

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Recombination Accelerates Adaptation on a Large-Scale Empirical Fitness Landscape in HIV-1

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Quantification of Reverse Transcriptase Activity by Real-Time PCR as a Fast and Accurate Method for Titration of HIV, Lenti- and Retroviral Vectors

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Why do RNA viruses recombine?

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Bayesian Phylogeography Finds Its Roots

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Database indexing for production MegaBLAST searches

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