HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

(2021) Kathy Leung et al.   Eurosurveillance

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

(2021) Bryan A. Johnson et al.   NATURE

Lead SARS-CoV-2 Candidate Vaccines: Expectations from Phase III Trials and Recommendations Post-Vaccine Approval

(2021) Ebenezer Tumban   Viruses-Basel

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines

(2021) Xiaoying Shen et al.   Cell Host & Microbe

Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK

(2021) Oliver T.R. Toovey et al.   JOURNAL OF INFECTION

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

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

(2021) Constantinos Kurt Wibmer et al.   NATURE MEDICINE

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

(2021) Kevin R. McCarthy et al.   SCIENCE

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

(2021) Matthew McCallum et al.   CELL

The SARS-CoV-2 Spike variant D614G favors an open conformational state

(2021) Rachael A. Mansbach et al.   Science Advances

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape

(2020) Nicholas C. Wu et al.   Nature Communications

Discovery of O-Linked Carbohydrate on HIV-1 Envelope and Its Role in Shielding against One Category of Broadly Neutralizing Antibodies

(2020) Zachary A. Silver et al.   Cell Reports

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Vaccines and Broadly Neutralizing Antibodies for HIV-1 Prevention

(2020) Kathryn E. Stephenson et al.   Annual Review of Immunology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

Temporal dynamics in viral shedding and transmissibility of COVID-19

(2020) Xi He et al.   NATURE MEDICINE

Site-specific glycan analysis of the SARS-CoV-2 spike

(2020) Yasunori Watanabe et al.   SCIENCE

Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

(2020) Yasunori Watanabe et al.   Nature Communications

Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

(2020) Salvatore Di Giorgio et al.   Science Advances

Emergence of SARS-CoV-2 through recombination and strong purifying selection

(2020) Xiaojun Li et al.   Science Advances

A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping

(2020) Maria Romano et al.   Cells

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

(2020) Qianqian Li et al.   CELL

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

(2020) Bette Korber et al.   CELL

Coronavirus RNA proofreading: molecular basis and therapeutic targeting

(2020) Fran Robson et al.   MOLECULAR CELL

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

(2020) Antoni G. Wrobel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2

(2020) Xiangyang Chi et al.   SCIENCE

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Transmission of SARS-CoV-2: A Review of Viral, Host, and Environmental Factors

(2020) Eric A. Meyerowitz et al.   ANNALS OF INTERNAL MEDICINE

Prolonged SARS-CoV-2 replication in an immunocompromised patient

(2020) Ji Hoon Baang et al.   JOURNAL OF INFECTIOUS DISEASES

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

Visualization of the HIV-1 Env glycan shield across scales

(2020) Zachary T. Berndsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Victoria A. Avanzato et al.   CELL

D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization

(2020) Drew Weissman et al.   Cell Host & Microbe

Correlates of protection against SARS-CoV-2 in rhesus macaques

(2020) Katherine McMahan et al.   NATURE

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

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

Coronavirus genomes carry the signatures of their habitats

(2020) Yulong Wei et al.   PLoS One

Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth

(2020) Ryan S. Roark et al.   SCIENCE

Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail

(2020) Srirupa Chakraborty et al.   iScience

The Incorporation of Host Proteins into the External HIV-1 Envelope

(2019) Jonathan Burnie et al.   Viruses-Basel

HIV subtype diversity worldwide

(2019) Nicholas Bbosa et al.   Current Opinion in HIV and AIDS

Broadly Neutralizing Antibodies against HIV: Back to Blood

(2019) Amir Dashti et al.   TRENDS IN MOLECULAR MEDICINE

Exploitation of glycosylation in enveloped virus pathobiology

(2019) Yasunori Watanabe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men who have Sex with Men

(2019) Erik Billings et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Variation in Intra-individual Lentiviral Evolution Rates: a Systematic Review of Human, Nonhuman Primate, and Felid Species

(2019) Emma Krakoff et al.   JOURNAL OF VIROLOGY

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

(2019) Christine A. Bricault et al.   Cell Host & Microbe

Multiple roles for HIV broadly neutralizing antibodies

(2019) Barton F. Haynes et al.   Science Translational Medicine

T cell-based strategies for HIV-1 vaccines

(2019) Bette Korber et al.   Human Vaccines & Immunotherapeutics

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

(2018) Hongshuo Song et al.   Nature Communications

Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

(2018) Joris Hemelaar et al.   LANCET INFECTIOUS DISEASES

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

Polyvalent vaccine approaches to combat HIV-1 diversity

(2017) Bette Korber et al.   IMMUNOLOGICAL REVIEWS

Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies

(2017) Mattia Bonsignori et al.   Science Translational Medicine

Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody

(2016) Mattia Bonsignori et al.   CELL

TNT version 1.5, including a full implementation of phylogenetic morphometrics

(2016) Pablo A. Goloboff et al.   CLADISTICS

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

(2016) Alexandra C Walls et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop

(2016) Haoqing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

(2016) Shuo Su et al.   TRENDS IN MICROBIOLOGY

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

(2016) Alexandra C Walls et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Composition and Antigenic Effects of Individual Glycan Sites of a Trimeric HIV-1 Envelope Glycoprotein

(2016) Anna-Janina Behrens et al.   Cell Reports

Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein

(2016) Jianhui Tian et al.   PLoS Computational Biology

Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization

(2016) Cecilia Rademeyer et al.   PLoS Pathogens

The increasing genetic diversity of HIV-1 in the UK, 2002–2010

(2016)   AIDS

Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies

(2015) Jinal N Bhiman et al.   NATURE MEDICINE

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env

(2015) Young Do Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

(2015) J. S. M. Sabir et al.   SCIENCE

High recombination potential of subtype A HIV-1

(2015) Olga Nikolaitchik et al.   VIROLOGY

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env

(2015) Young Do Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies

(2014) Feng Gao et al.   CELL

Impact of Clade, Geography, and Age of the Epidemic on HIV-1 Neutralization by Antibodies

(2014) P. Hraber et al.   JOURNAL OF VIROLOGY

Frequent Intra-Subtype Recombination among HIV-1 Circulating in Tanzania

(2013) Ireen E. Kiwelu et al.   PLoS One

Origins of HIV and the AIDS Pandemic

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

Eastern Chimpanzees, but Not Bonobos, Represent a Simian Immunodeficiency Virus Reservoir

(2012) Y. Li et al.   JOURNAL OF VIROLOGY

RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex

(2012) M. Bouvet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

(2012) Katharine J. Bar et al.   PLoS Pathogens

Coronaviruses

(2011) Mark R. Denison et al.   RNA Biology

Viral Evolution and Escape during Acute HIV‐1 Infection

(2010) Christian L. Boutwell et al.   JOURNAL OF INFECTIOUS DISEASES

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

The role of recombination in the emergence of a complex and dynamic HIV epidemic

(2010) Ming Zhang et al.   Retrovirology

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

(2009) R. L. Graham et al.   JOURNAL OF VIROLOGY

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

(2009) Natasha Wood et al.   PLoS Pathogens

Structures and Mechanisms of Viral Membrane Fusion Proteins: Multiple Variations on a Common Theme

(2008) Judith M. White et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

APOBEC proteins and intrinsic resistance to HIV-1 infection

(2008) M. H Malim   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES