2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic?

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

(2021) Tyler N. Starr et al.   SCIENCE

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

(2021) Houriiyah Tegally et al.   NATURE

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Nicholas G. Davies et al.   SCIENCE

SARS-CoV-2 within-host diversity and transmission

(2021) Katrina A. Lythgoe et al.   SCIENCE

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

(2021) Thomas P. Peacock et al.   JOURNAL OF GENERAL VIROLOGY

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

(2021) Erik Volz et al.   NATURE

Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

(2021) Shabir A. Madhi et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2021) Nuno R. Faria et al.   SCIENCE

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

(2021) Andrew L. Valesano et al.   PLoS Pathogens

A human coronavirus evolves antigenically to escape antibody immunity

(2021) Rachel T. Eguia et al.   PLoS Pathogens

The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets

(2021) Thomas P. Peacock et al.   Nature Microbiology

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

(2021) Sarah P. Otto et al.   CURRENT BIOLOGY

We shouldn’t worry when a virus mutates during disease outbreaks

(2020) Nathan D. Grubaugh et al.   Nature Microbiology

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

(2020) B. Coutard et al.   ANTIVIRAL RESEARCH

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

(2020) Markus Hoffmann et al.   MOLECULAR CELL

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

(2020) Tyler N. Starr et al.   CELL

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation

(2020) William J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The phylogenomics of evolving virus virulence

(2018) Jemma L. Geoghegan et al.   NATURE REVIEWS GENETICS

Individual immune selection pressure has limited impact on seasonal influenza virus evolution

(2018) Alvin X. Han et al.   Nature Ecology & Evolution

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype

(2017) Peter J. Kerr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel evolution of influenza across multiple spatiotemporal scales

(2017) Katherine S Xue et al.   eLife

Mechanisms of viral mutation

(2016) Rafael Sanjuán et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

(2014) I. Monne et al.   JOURNAL OF VIROLOGY

Global reemergence of enterovirus D68 as an important pathogen for acute respiratory infections

(2014) Tadatsugu Imamura et al.   REVIEWS IN MEDICAL VIROLOGY

Quantifying the Fitness Advantage of Polymerase Substitutions in Influenza A/H7N9 Viruses during Adaptation to Humans

(2013) Judith M. Fonville et al.   PLoS One

Origins of HIV and the AIDS Pandemic

(2013) P. M. Sharp et al.   Cold Spring Harbor Perspectives in Medicine

Prolonged Influenza Virus Shedding and Emergence of Antiviral Resistance in Immunocompromised Patients and Ferrets

(2013) Erhard van der Vries et al.   PLoS Pathogens

Infectious bronchitis virus variants: a review of the history, current situation and control measures

(2011) J. J. (Sjaak) de Wit et al.   AVIAN PATHOLOGY