Publications

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2022

Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021
Martina L. Reichmuth, Emma B. Hodcroft, Julien Riou et al.
Epidemics, 41 100654. 10.1016/j.epidem.2022.100654 bibtex Fri 25 November 2022

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
Sarah A. Nadeau, Timothy G. Vaughan, Christiane Beckmann et al.
Science Translational Medicine, 0 eabn7979. 10.1126/scitranslmed.abn7979 bibtex Tue 08 November 2022

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
Christian Happi, Ifedayo Adetifa, Placide Mbala et al.
PLOS Biology, 20 e3001769. 10.1371/journal.pbio.3001769 bibtex Tue 23 August 2022

Evolution, geographic spreading, and demographic distribution of Enterovirus D68
Emma B. Hodcroft, Robert Dyrdak, Cristina Andres et al.
PLOS Pathogens, 18 e1010515. 10.1371/journal.ppat.1010515 pdf bibtex Fri 20 May 2022

2021

Nextclade: clade assignment, mutation calling and quality control for viral genomes
Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher
Journal of Open Source Software, 6 3773. 10.21105/joss.03773 bibtex Mon 15 November 2021

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Frank Konings, Mark D. Perkins, Jens H. Kuhn et al.
Nature Microbiology, 1--3. 10.1038/s41564-021-00932-w bibtex Wed 09 June 2021

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Emma B. Hodcroft, Moira Zuber, Sarah Nadeau et al.
Nature, 1--9. 10.1038/s41586-021-03677-y bibtex Mon 07 June 2021

Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe
Kimberley S.M. Benschop, Eeva K. Broberg, Emma Hodcroft et al.
Emerging Infectious Diseases, 27 1616--1626. 10.3201/eid2706.203096 bibtex Tue 01 June 2021

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Chantal B. F. Vogels, Mallery I. Breban, Isabel M. Ott et al.
PLOS Biology, 19 e3001236. 10.1371/journal.pbio.3001236 bibtex Fri 07 May 2021

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
Ana Rita Goncalves Cabecinhas, Tim Roloff, Madlen Stange et al.
Microorganisms, 9 677. 10.3390/microorganisms9040677 bibtex Thu 25 March 2021

Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
Robert Dyrdak, Emma B. Hodcroft, Martina Wahlund, Richard A. Neher and Jan Albert
Journal of Clinical Virology, 136 104754. 10.1016/j.jcv.2021.104754 bibtex Mon 01 February 2021

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
John Huddleston, James Hadfield, Thomas R. Sibley et al.
Journal of Open Source Software, 6 2906. 10.21105/joss.02906 bibtex Thu 07 January 2021

2020

Cryptic transmission of SARS-CoV-2 in Washington state
Trevor Bedford, Alexander L. Greninger, Pavitra Roychoudhury et al.
Science, 10.1126/science.abc0523 bibtex Thu 10 September 2020

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
Erik Alm, Eeva K. Broberg, Thomas Connor et al.
Eurosurveillance, 25 2001410. 10.2807/1560-7917.ES.2020.25.32.2001410 bibtex Wed 26 August 2020

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
Joseph R. Fauver, Mary E. Petrone, Emma B. Hodcroft et al.
Cell, 181 990--996.e5. 10.1016/j.cell.2020.04.021 pdf bibtex Thu 26 March 2020

COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation
Marcel Salathe, Christian L. Althaus, Richard Neher et al.
Swiss Medical Weekly, 150 10.4414/smw.2020.20225 pdf bibtex Thu 19 March 2020

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
Richard A. Neher, Robert Dyrdak, Valentin Druelle, Emma B. Hodcroft and Jan Albert
Swiss Medical Weekly, 150 10.4414/smw.2020.20224 pdf bibtex Sat 15 February 2020

Co-circulation of multiple enterovirus D68 subclades, including a novel B3 cluster, across Europe in a season of expected low prevalence, 2019/20
Sofie Elisabeth Midgley, Kimberley Benschop, Robert Dyrdak et al.
Eurosurveillance, 25 1900749. 10.2807/1560-7917.ES.2020.25.2.1900749 pdf bibtex Thu 16 January 2020

2019

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Robert Dyrdak, Monika Mastafa, Emma B. Hodcroft, Richard A. Neher and Jan Albert
Virus Evolution, 5 10.1093/ve/vez007 pdf bibtex Mon 15 April 2019

2017

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Oliver Ratmann, Emma B. Hodcroft, Michael Pickles et al.
Molecular biology and evolution, 34 185--203. 10.1093/molbev/msw217 bibtex Wed 25 January 2017

Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.
Rebecca Rose, Susanna L. Lamers, James J. Dollar et al.
AIDS research and human retroviruses, 33 211--218. 10.1089/AID.2016.0205 bibtex Wed 25 January 2017

2016

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.
Manon L. Ragonnet-Cronin, Mohaned Shilaih, Huldrych F. Gunthard et al.
Scientific reports, 6 32251. 10.1038/srep32251 bibtex Mon 25 January 2016

Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters.
Manon Ragonnet-Cronin, Samantha J. Lycett, Emma B. Hodcroft et al.
The Journal of infectious diseases, 213 1410--1418. 10.1093/infdis/jiv758 bibtex Mon 25 January 2016

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
Gonzalo Yebra, Emma B. Hodcroft, Manon L. Ragonnet-Cronin, Deenan Pillay and Andrew J. Leigh Brown
Scientific reports, 6 39489. 10.1038/srep39489 bibtex Mon 25 January 2016

2014

The contribution of viral genotype to plasma viral set-point in HIV infection.
Emma Hodcroft, Jarrod D. Hadfield, Esther Fearnhill et al.
PLoS pathogens, 10 e1004112. 10.1371/journal.ppat.1004112 bibtex Sat 25 January 2014

2013

Automated analysis of phylogenetic clusters.
Manon Ragonnet-Cronin, Emma Hodcroft, Stephane Hue et al.
BMC bioinformatics, 14 317. 10.1186/1471-2105-14-317 bibtex Fri 25 January 2013