High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

(2021) Ester C Sabino et al.   LANCET

SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients

(2020) Lirong Zou et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2020) Daniel Wrapp et al.   SCIENCE

Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy

(2020) M.R. Capobianchi et al.   CLINICAL MICROBIOLOGY AND INFECTION

Clinical progression of patients with COVID-19 in Shanghai, China

(2020) Jun Chen et al.   JOURNAL OF INFECTION

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

(2020) Fei Zhou et al.   LANCET

Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

(2020) Kelvin Kai-Wang To et al.   LANCET INFECTIOUS DISEASES

A human neutralizing antibody targets the receptor binding site of SARS-CoV-2

(2020) Rui Shi et al.   NATURE

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

Virological assessment of hospitalized patients with COVID-2019

(2020) Roman Wölfel et al.   NATURE

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

Contact Tracing Assessment of COVID-19 Transmission Dynamics in Taiwan and Risk at Different Exposure Periods Before and After Symptom Onset

(2020) Hao-Yuan Cheng et al.   JAMA Internal Medicine

Evolution of viral quasispecies during SARS-CoV-2 infection

(2020) A. Jary et al.   CLINICAL MICROBIOLOGY AND INFECTION

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

(2020) Timokratis Karamitros et al.   JOURNAL OF CLINICAL VIROLOGY

Viral dynamics in mild and severe cases of COVID-19

(2020) Yang Liu et al.   LANCET INFECTIOUS DISEASES

Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike

(2020) Lihong Liu et al.   NATURE

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

(2020) Bethany Dearlove et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking the COVID-19 pandemic in Australia using genomics

(2020) Torsten Seemann et al.   Nature Communications

Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes

(2020) Tongqing Zhou et al.   Cell Reports

Symmetrical arrangement of positively charged residues around the 5-fold axes of SAT type foot-and-mouth disease virus enhances cell culture of field viruses

(2020) Melanie Chitray et al.   PLoS Pathogens

Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities

(2020) Hebah A. Al Khatib et al.   Frontiers in Cellular and Infection Microbiology

Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis

(2020) Martina Rueca et al.   Microorganisms

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

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

(2020) Alexandra Popa et al.   Science Translational Medicine

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Multiple Origins of Virus Persistence during Natural Control of HIV Infection

(2016) Eli A. Boritz et al.   CELL

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA