4.8 Article

Untangling introductions and persistence in COVID-19 resurgence in Europe

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Benoit Morel et al.

Summary: Inferring reliable phylogenies from virus sequence data is difficult due to the large number of sequences and low number of mutations; rooting the inferred phylogeny with external outgroups or applying novel computational methods is not credible; automatic classification of current sequences into subclasses for molecular species delimitation is also not possible due to sequences being too closely related.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

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

Louis du Plessis et al.

Summary: The study analyzed the genetic lineage structure of the early UK COVID-19 epidemic through genomic sampling, identifying that virus lineages introduced before the national lockdown tended to be larger and more dispersed. After the lockdown, lineage importation and regional diversity decreased, while lineage elimination depended on lineage size. The research emphasizes the impact of genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

SCIENCE (2021)

Article Infectious Diseases

Vaccination and non-pharmaceutical interventions for COVID-19: a mathematical modelling study

Sam Moore et al.

Summary: The study found that vaccination alone is insufficient to contain the outbreak. Even with an optimistic assumption that the vaccine can prevent 85% of infections, the reproduction number (R) is estimated to be 1.58 once all eligible adults have been offered both doses of the vaccine without non-pharmaceutical interventions (NPIs).

LANCET INFECTIOUS DISEASES (2021)

Article Multidisciplinary Sciences

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Emma B. Hodcroft et al.

Summary: A variant of SARS-CoV-2, 20E (EU1), was identified in Spain in early summer 2020 and later spread across Europe. Despite not showing increased transmissibility, the variant's success can be attributed to rising incidence in Spain, resumption of travel, and lack of effective screening and containment measures. Travel played a significant role in introducing the variant multiple times to European countries during the summer, undermining local efforts to prevent SARS-CoV-2 infection.

NATURE (2021)

Article Biochemistry & Molecular Biology

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages

Simon Dellicour et al.

Summary: Researchers have developed a rapid analytical pipeline to study the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages, focusing on the high density of available genetic data in Belgium. This methodology can be quickly applied to other countries or regions to complement epidemiological analyses and assess the impact of intervention measures on the pandemic.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction

Mandev S. Gill et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Editorial Material Medicine, General & Internal

A European roadmap out of the covid-19 pandemic Coordination between countries is crucial

Martin McKee

BMJ-BRITISH MEDICAL JOURNAL (2020)

Article Psychology, Biological

Mapping global variation in human mobility

Moritz U. G. Kraemer et al.

NATURE HUMAN BEHAVIOUR (2020)

Article Medicine, General & Internal

Impact of lockdown on COVID-19 epidemic in ile-de-France and possible exit strategies

Laura Di Domenico et al.

BMC MEDICINE (2020)

Article Microbiology

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

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

Article Multidisciplinary Sciences

Hierarchical organization of urban mobility and its connection with city livability

Aleix Bassolas et al.

NATURE COMMUNICATIONS (2019)

Proceedings Paper Computer Science, Information Systems

Facebook Disaster Maps: Aggregate Insights for Crisis Response & Recovery

Paige Maas

KDD'19: PROCEEDINGS OF THE 25TH ACM SIGKDD INTERNATIONAL CONFERENCCE ON KNOWLEDGE DISCOVERY AND DATA MINING (2019)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Article Multidisciplinary Sciences

Genomic and epidemiological monitoring of yellow fever virus transmission potential

N. R. Faria et al.

SCIENCE (2018)

Article Economics

Social Connectedness: Measurement, Determinants, and Effects

Michael Bailey et al.

JOURNAL OF ECONOMIC PERSPECTIVES (2018)

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

Editorial Material Infectious Diseases

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

Yuelong Shu et al.

EUROSURVEILLANCE (2017)

Article Multidisciplinary Sciences

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Gytis Dudas et al.

NATURE (2017)

Article Ecology

Split diversity in constrained conservation prioritization using integer linear programming

Olga Chernomor et al.

METHODS IN ECOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

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

Mandev S. Gill et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biology

Graph hierarchies for phylogeography

Gabriela B. Cybis et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)

Article Biochemical Research Methods

Bayesian Phylogeography Finds Its Roots

Philippe Lemey et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biology

Fast, accurate and simulation-free stochastic mapping

Vladimir N. Minin et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)