Phylogenetic methods for genome surveillance of microbial pathogens

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

Ashleigh F Porter, Damian FJ Purcell, Benjamin P Howden, Sebastian Duchene

2023-02-03

To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-ass..

Phytest: quality control for phylogenetic analyses

Wytamma Wirth, Simon Mutch, Robert Turnbull, Sebastian Duchene

2022-10-07

MOTIVATION: The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with t..

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Mark R Davies, Sebastian Duchene, Mary Valcanis, Aaron P Jenkins, Adam Jenney, Varanisese Rosa, Andrew J Hayes, Aneley Getahun Strobel, Liam McIntyre, Jake A Lacey, Elizabeth J Klemm, Vanessa K Wong, Aalisha Sahukhan, Helen Thomson, Andrew Page, Dianna Hocking, Nancy Wang, Litia Tudravu, Eric Rafai, Gordon Dougan

2022-07-01

BACKGROUND: Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not rou..

Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis

Mona L Taouk, George Taiaroa, Shivani Pasricha, Sophie Herman, Eric PF Chow, Francesca Azzatto, Bowen Zhang, Cheryll M Sia, Sebastian Duchene, Alvin Lee, Nasra Higgins, Jacqueline Prestedge, Yi Wei Lee, Nicholas R Thomson, Bianca Graves, Ella Meumann, Manoji Gunathilake, Jane S Hocking, Catriona S Bradshaw, Mathew A Beale

2022-06-01

BACKGROUND: The incidence of syphilis has increased markedly in the past decade in high-income countries, including Australia. To ..

Real-Time and Remote MCMC Trace Inspection with Beastiary.

Wytamma Wirth, Sebastian Duchene

2022-05-03

Bayesian phylogenetics has gained substantial popularity in the last decade, with most implementations relying on Markov chain Mon..

Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology.

Sebastian Duchene, Leo Featherstone, Birgitte Freiesleben de Blasio, Edward C Holmes, Jon Bohlin, John HO Pettersson

2022-03-01

We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in ..

The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate

John H Tay, Ashleigh F Porter, Wytamma Wirth, Sebastian Duchene

2022-02-03

The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the em..

Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.

Leo A Featherstone, Joshua M Zhang, Timothy G Vaughan, Sebastian Duchene

2022-01-01

Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also e..

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.

David J Edwards, Sebastián Duchene, Bernard Pope, Kathryn E Holt

2021-12-01

Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for c..

The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution

Sebastian Duchene, Leo Featherstone, Birgitte Freiesleben de Blasio, Edward C Holmes, Jon Bohlin, John H-O Pettersson

2021-11-04

BackgroundMany countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly wi..

Development of Phylodynamic Methods for Bacterial Pathogens

Danielle J Ingle, Benjamin P Howden, Sebastian Duchene

2021-08-09

Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases..

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Danielle J Ingle, Rebecca L Ambrose, Sarah L Baines, Sebastian Duchene, Anders Goncalves da Silva, Darren YJ Lee, Miriam Jones, Mary Valcanis, George Taiaroa, Susan A Ballard, Martyn D Kirk, Benjamin P Howden, Jaclyn S Pearson, Deborah A Williamson

2021-08-09

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emer..

Infectious disease phylodynamics with occurrence data

Leo A Featherstone, Francesca Di Giallonardo, Edward C Holmes, Timothy G Vaughan, Sebastian Duchene

2021-08-01

Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance ..

The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic

Anthony Lam, Sebastian Duchene

2021-01-01

Phylodynamic inference is a pivotal tool in understanding transmission dynamics of viral outbreaks. These analyses are strongly gu..

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

Francesca Di Giallonardo, Sebastian Duchene, Ilaria Puglia, Valentina Curini, Francesca Profeta, Cesare Camma, Maurilia Marcacci, Paolo Calistri, Edward C Holmes, Alessio Lorusso

2020-12-01

Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2..

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon YW Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele

2020-11-01

Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimati..

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

Sebastian Duchene, Simon YW Ho, Ann G Carmichael, Edward C Holmes, Hendrik Poinar

2020-10-05

The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biolog..

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

Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele

2020-07-01

The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publi..

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

David A Duchene, K Jun Tong, Charles SP Foster, Sebastian Duchene, Robert Lanfear, Simon YW Ho

2020-04-01

Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees ..