Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2

SARS-CoV-2 variant biology: immune escape, transmission and fitness

(2023) Alessandro M. Carabelli et al.   NATURE REVIEWS MICROBIOLOGY

In vitro and in vivo suppression of SARS‐CoV‐2 replication by a modified, short, cell‐penetrating peptide targeting the C‐terminal domain of the viral spike protein

(2023) Dongbum Kim et al.   JOURNAL OF MEDICAL VIROLOGY

The evolution of SARS-CoV-2

(2023) Peter V. Markov et al.   NATURE REVIEWS MICROBIOLOGY

Rapid SARS-CoV-2 Adaptation to Available Cellular Proteases

(2022) M. Zeeshan Chaudhry et al.   JOURNAL OF VIROLOGY

Advances and gaps in SARS-CoV-2 infection models

(2022) César Muñoz-Fontela et al.   PLoS Pathogens

SARS‐CoV‐2 variants and vulnerability at the global level

(2022) Vivek P. Chavda et al.   JOURNAL OF MEDICAL VIROLOGY

Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?

(2022) Christoph Jung et al.   JOURNAL OF VIROLOGY

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

(2022) Yongbing Zhou et al.   JOURNAL OF MEDICAL VIROLOGY

Comparison of vaccination efficacy using live or ultraviolet-inactivated influenza viruses introduced by different routes in a mouse model

(2022) Kyeongbin Baek et al.   PLoS One

Choosing a cellular model to study SARS-CoV-2

(2022) Gabriel Augusto Pires De Souza et al.   Frontiers in Cellular and Infection Microbiology

Differential effect of SARS-CoV-2 infection on stress granule formation in Vero and Calu-3 cells

(2022) Dongbum Kim et al.   Frontiers in Microbiology

Spike mutations contributing to the altered entry preference of SARS-CoV-2 omicron BA.1 and BA.2

(2022) Bingjie Hu et al.   Emerging Microbes & Infections

SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis

(2022) Richard Lueking et al.   Frontiers in Genetics

SARS-CoV-2 infection and persistence in the human body and brain at autopsy

(2022) Sydney R. Stein et al.   NATURE

Effect of Previous COVID-19 Vaccination on Humoral Immunity 3 Months after SARS-CoV-2 Omicron Infection and Booster Effect of a Fourth COVID-19 Vaccination 2 Months after SARS-CoV-2 Omicron Infection

(2022) Jinsoo Kim et al.   Viruses-Basel

Production of a Monoclonal Antibody to the Nucleocapsid Protein of SARS-CoV-2 and Its Application to ELISA-Based Detection Methods with Broad Specificity by Combined Use of Detector Antibodies

(2022) Jinsoo Kim et al.   Viruses-Basel

Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial

(2022) I’ah Donovan-Banfield et al.   Nature Communications

A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients

(2022) Claudia Alteri et al.   Communications Biology

Human SARS CoV ‐2 spike protein mutations

(2021) Lalitha Guruprasad   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Differential Signaling and Virus Production in Calu-3 Cells and Vero Cells upon SARS-CoV-2 Infection

(2021) Byoung Kwon Park et al.   Biomolecules & Therapeutics

SARS-CoV-2 spike D614G change enhances replication and transmission

(2021) Bin Zhou et al.   NATURE

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms

(2021) Sarah A. Clark et al.   CELL

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell

(2021) Maritza Puray-Chavez et al.   Cell Reports

Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma

(2021) Vítor Borges et al.   mSphere

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

(2021) Haibo Wu et al.   Cell Host & Microbe

Evolution of enhanced innate immune evasion by SARS-CoV-2

(2021) Lucy G. Thorne et al.   NATURE

A humanized mouse model of chronic COVID-19

(2021) Esen Sefik et al.   NATURE BIOTECHNOLOGY

SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection

(2021) Laura Bashor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of SARS-CoV-2 N Protein-Specific Monoclonal Antibody and Its Application in an ELISA-Based Detection System and Targeting the Interaction Between the Spike C-Terminal Domain and N Protein

(2021) Dongbum Kim et al.   Frontiers in Microbiology

Serological assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), March 2020

(2020) Ranawaka APM Perera et al.   Eurosurveillance

Cell entry mechanisms of SARS-CoV-2

(2020) Jian Shang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

Characteristics of SARS-CoV-2 and COVID-19

(2020) Ben Hu et al.   NATURE REVIEWS MICROBIOLOGY

Mechanisms of SARS-CoV-2 transmission and pathogenesis

(2020) Andrew G. Harrison et al.   TRENDS IN IMMUNOLOGY

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

(2020) Erik Volz et al.   CELL

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

(2020) Victoria A. Avanzato et al.   CELL

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

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

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

(2020) Lizhou Zhang et al.   Nature Communications

A Mucin1 C-terminal Subunit-directed Monoclonal Antibody Targets Overexpressed Mucin1 in Breast Cancer

(2018) Guang Wu et al.   Theranostics

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS