Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater

(2022) Davida S. Smyth et al.   Nature Communications

‘A bloody mess’: Confusion reigns over naming of new COVID variants

(2021) Ewen Callaway   NATURE

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

(2021) Louis du Plessis et al.   SCIENCE

Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

(2021) Claudia Alteri et al.   Nature Communications

Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

(2021) Grégory Quéromès et al.   Emerging Microbes & Infections

A SARS-CoV-2 Cluster in an Acute Care Hospital

(2021) Michael Klompas et al.   ANNALS OF INTERNAL MEDICINE

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

(2021) Daming Zhou et al.   CELL

Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies

(2021) Jie Hu et al.   Cellular & Molecular Immunology

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

(2021) Carolina M. Voloch et al.   JOURNAL OF VIROLOGY

Want to track pandemic variants faster? Fix the bioinformatics bottleneck

(2021) Emma B. Hodcroft et al.   NATURE

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

(2021) Dami A. Collier et al.   NATURE

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

(2021) Houriiyah Tegally et al.   NATURE

Scientists call for fully open sharing of coronavirus genome data

(2021) Richard Van Noorden   NATURE

Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7

(2021) Pengfei Wang et al.   NATURE

SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile

(2021) Claudio Olmos et al.   PLoS One

The origin and early spread of SARS-CoV-2 in Europe

(2021) Sarah A. Nadeau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia

(2021) Andrey B. Komissarov et al.   Nature Communications

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

(2021) Nicole Pedro et al.   Microorganisms

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

(2021) Nicole L. Washington et al.   CELL

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

(2021) Erik Volz et al.   NATURE

Development of Phylodynamic Methods for Bacterial Pathogens

(2021) Danielle J. Ingle et al.   TRENDS IN MICROBIOLOGY

Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

(2021) Manon Ragonnet-Cronin et al.   Nature Communications

Infectious disease phylodynamics with occurrence data

(2021) Leo A. Featherstone et al.   Methods in Ecology and Evolution

The substitution spectra of coronavirus genomes

(2021) Diego Forni et al.   BRIEFINGS IN BIOINFORMATICS

Emergence of an early SARS-CoV-2 epidemic in the United States

(2021) Mark Zeller et al.   CELL

Untangling introductions and persistence in COVID-19 resurgence in Europe

(2021) Philippe Lemey et al.   NATURE

The lag in SARS-CoV-2 genome submissions to GISAID

(2021) Kishan Kalia et al.   NATURE BIOTECHNOLOGY

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

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

(2021) Emanuele Andreano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

(2021) Bo Meng et al.   Cell Reports

Sample size calculation for phylogenetic case linkage

(2021) Shirlee Wohl et al.   PLoS Computational Biology

Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City

(2021) Simon Dellicour et al.   PLoS Pathogens

Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand the human ACE2 receptor on binding affinity and kinetics

(2021) Michael I Barton et al.   eLife

Patterns of within-host genetic diversity in SARS-CoV-2

(2021) Gerry Tonkin-Hill et al.   eLife

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

(2021) Daniel Lule Bugembe et al.   Nature Microbiology

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

(2021) Courtney R Lane et al.   Lancet Public Health

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

(2021) Jordan Douglas et al.   Virus Evolution

Decomposing the sources of SARS-CoV-2 fitness variation in the United States

(2021) Lenora Kepler et al.   Virus Evolution

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

(2021) Sarah Cherian et al.   Microorganisms

A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

(2021) Filippo Utro et al.   BMC GENOMICS

Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2

(2021) Lorenzo Cappello et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Progress and challenges in virus genomic epidemiology

(2021) Verity Hill et al.   TRENDS IN PARASITOLOGY

Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

(2021) Maureen Rebecca Smith et al.   Nature Communications

Secondary attack rate and superspreading events for SARS-CoV-2

(2020) Yang Liu et al.   LANCET

Jointly inferring the dynamics of population size and sampling intensity from molecular sequences

(2020) K V Parag et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

(2020) Jing Lu et al.   CELL

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver et al.   CELL

Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series

(2020) Merle M Böhmer et al.   LANCET INFECTIOUS DISEASES

High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice — Skagit County, Washington, March 2020

(2020) Lea Hamner et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Phylogenetic interpretation during outbreaks requires caution

(2020) Ch. Julián Villabona-Arenas et al.   Nature Microbiology

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

(2020) Tyler N. Starr et al.   CELL

Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear

(2020) Nathan D. Grubaugh 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

On the evolutionary epidemiology of SARS-CoV-2

(2020) Troy Day et al.   CURRENT BIOLOGY

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

(2020) Erik Alm et al.   Eurosurveillance

INCREASED RISK OF SARS-CoV-2 INFECTION IN STAFF WORKING ACROSS DIFFERENT CARE HOMES ENCHANCED CoVID-19 OUTBREAK INVESTIGATIONS IN LONDON CARE HOMES

(2020) Shamez N Ladhani et al.   JOURNAL OF INFECTION

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

(2020) Luke W Meredith et al.   LANCET INFECTIOUS DISEASES

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

(2020) Reina S Sikkema et al.   LANCET INFECTIOUS DISEASES

Evidence for strong mutation bias towards, and selection against, U content in SARS-CoV-2: implications for vaccine design

(2020) Alan M Rice et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Seth Flaxman et al.   NATURE

Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak

(2020) Tsuyoshi Sekizuka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Darlan S. Candido et al.   SCIENCE

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

(2020) Xianding Deng et al.   SCIENCE

Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

(2020) Alessia Lai et al.   Viruses-Basel

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

(2020) P. Simmonds   mSphere

SARS‐CoV‐2 outbreak investigation in a German meat processing plant

(2020) Thomas Günther et al.   EMBO Molecular Medicine

Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence

(2020) Matías J. Pereson et al.   JOURNAL OF MEDICAL VIROLOGY

Uncovering two phases of early intercontinental COVID-19 transmission dynamics

(2020) Jing Yang et al.   JOURNAL OF TRAVEL MEDICINE

Genomic evidence for reinfection with SARS-CoV-2: a case study

(2020) Richard L Tillett et al.   LANCET INFECTIOUS DISEASES

Tracking COVID-19 with wastewater

(2020) David A. Larsen et al.   NATURE BIOTECHNOLOGY

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

Cryptic transmission of SARS-CoV-2 in Washington state

(2020) Trevor Bedford et al.   SCIENCE

The emergence of SARS-CoV-2 in Europe and North America

(2020) Michael Worobey et al.   SCIENCE

A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

(2020) Jalees A. Nasir et al.   Viruses-Basel

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

(2020) Philippe Lemey et al.   Nature Communications

Tracking the COVID-19 pandemic in Australia using genomics

(2020) Torsten Seemann et al.   Nature Communications

Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks — Minnesota, April–June 2020

(2020) Joanne Taylor et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

(2020) Caroline Charre et al.   Virus Evolution

Temporal signal and the phylodynamic threshold of SARS-CoV-2

(2020) Sebastian Duchene et al.   Virus Evolution

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

(2020) Erik Volz et al.   CELL

Timely Intervention and Control of a Novel Coronavirus (COVID-19) Outbreak at a Large Skilled Nursing Facility — San Francisco, California, 2020

(2020) Ellora Karmarkar et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Phylogenetic analysis of SARS-CoV-2 data is difficult

(2020) Benoit Morel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

(2020) Jacob E. Lemieux et al.   SCIENCE

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

(2020) Francesca Di Giallonardo et al.   Viruses-Basel

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

(2020) Jemma L. Geoghegan et al.   Nature Communications

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   Nature Communications

Stability of SARS-CoV-2 phylogenies

(2020) Yatish Turakhia et al.   PLoS Genetics

Does respiratory co-infection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office

(2020) Dana Weissberg et al.   Antimicrobial Resistance and Infection Control

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

(2020) Ana da Silva Filipe et al.   Nature Microbiology

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

(2020) Jennifer Giandhari et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Genomic sequencing effort for SARS-CoV-2 by country during the pandemic

(2020) Yuki Furuse   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Parallel molecular evolution and adaptation in viruses

(2019) Bernardo Gutierrez et al.   Current Opinion in Virology

Estimating Epidemic Incidence and Prevalence from Genomic Data

(2019) Timothy G Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

(2013) L M Gattepaille et al.   HEREDITY

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A

(2011) N. R. Faria et al.   JOURNAL OF GENERAL VIROLOGY