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

Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

(2021) Lewis F. Buss et al.   SCIENCE

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

(2021) Louis du Plessis et al.   SCIENCE

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera

(2021) Daming Zhou et al.   CELL

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

(2021) Allison J. Greaney et al.   Cell Host & Microbe

S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR

(2021) Michael Kidd et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2021) Ester C Sabino et al.   LANCET

Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study

(2021) Michael Marks et al.   LANCET INFECTIOUS DISEASES

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

(2021) Houriiyah Tegally et al.   NATURE

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

(2021) Zijun Wang 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

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil

(2021) Andreza Francisco Martins et al.   Eurosurveillance

Assessment of protection against reinfection with SARS-CoV-2 among 4 million PCR-tested individuals in Denmark in 2020: a population-level observational study

(2021) Christian Holm Hansen et al.   LANCET

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

(2021) Sandile Cele et al.   NATURE

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

(2021) Erik Volz et al.   NATURE

Open access epidemiological data from the COVID-19 outbreak

(2020) Bo Xu et al.   LANCET INFECTIOUS DISEASES

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

Routes for COVID-19 importation in Brazil

(2020) Darlan Da S Candido et al.   JOURNAL OF TRAVEL MEDICINE

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking

(2020) Sarah F. McGough et al.   PLoS Computational Biology

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

(2020) Tyler N. Starr et al.   CELL

The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?

(2020) Eric Farfour et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe

(2020) Seth Flaxman et al.   NATURE

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

Modeling future spread of infections via mobile geolocation data and population dynamics. An application to COVID-19 in Brazil

(2020) Pedro S. Peixoto et al.   PLoS One

Evolution and epidemic spread of SARS-CoV-2 in Brazil

(2020) Darlan S. Candido et al.   SCIENCE

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil

(2020) William Marciel de Souza et al.   Nature Human Behaviour

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

(2020) Luca Piccoli et al.   CELL

Evaluation of three commercial assays for SARS-CoV-2 molecular detection in upper respiratory tract samples

(2020) Flora Marzia Liotti et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset

(2020) Benny Borremans et al.   eLife

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

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

(2020) Marcelo Henrique Santos Paiva et al.   Viruses-Basel

State-level tracking of COVID-19 in the United States

(2020) H. Juliette T. Unwin et al.   Nature Communications

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

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

(2016) Michael Worobey et al.   NATURE

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS