Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Variation in human mobility and its impact on the risk of future COVID-19 outbreaks in Taiwan

(2021) Meng-Chun Chang et al.   BMC PUBLIC HEALTH

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

(2021) Emma C. Thomson et al.   CELL

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

(2021) Ester C Sabino et al.   LANCET

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

(2021) Houriiyah Tegally et al.   NATURE

Insufficient social distancing may contribute to COVID-19 outbreak: The case of Ijuí city in Brazil

(2021) Thiago Gomes Heck et al.   PLoS One

Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants

(2021) Esther Viedma et al.   Microorganisms

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

Early detection of P.1 variant of SARS-CoV-2 in a cluster of cases in Salvador, Brazil

(2021) Isadora Cristina de Siqueira et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

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

(2021) Nuno R. Faria et al.   SCIENCE

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

(2021) Ronaldo da Silva Francisco Jr et al.   VIRUS RESEARCH

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

(2021) Chantal B. F. Vogels et al.   PLOS BIOLOGY

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

(2021) Felipe Gomes Naveca et al.   NATURE MEDICINE

The impact of super-spreader cities, highways, and intensive care availability in the early stages of the COVID-19 epidemic in Brazil

(2021) Miguel A. L. Nicolelis et al.   Scientific Reports

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

(2020) Yong-Zhen Zhang et al.   CELL

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

(2020) Qianqian Li et al.   CELL

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

(2020) Darlan S. Candido et al.   SCIENCE

Impact of self-imposed prevention measures and short-term government-imposed social distancing on mitigating and delaying a COVID-19 epidemic: A modelling study

(2020) Alexandra Teslya et al.   PLOS MEDICINE

Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil

(2020) Sérvio Pontes Ribeiro et al.   PeerJ

A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies

(2020) Audrey McCombs et al.   PLoS Computational Biology

Toward Understanding Molecular Bases for Biological Diversification of Human Coronaviruses: Present Status and Future Perspectives

(2020) Takaaki Koma et al.   Frontiers in Microbiology

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

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

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

SERAPHIM: studying environmental rasters and phylogenetically informed movements

(2016) Simon Dellicour et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS