Phylogenetic methods for genome surveillance of microbial pathogens
Grant number: DE190100805 | Funding period: 2019 - 2022
This project aims to develop phylogenetic approaches to harness the potential evolution of bacterial and virus pathogens data and to improve early detection of infectious outbreaks. Genome surveillance programs consist in routine sequencing of particular organisms to track their evolution over time. Such programs currently exist for important bacterial and virus pathogens. This project expects to develop computational methods to improve our understanding of pathogen outbreak emergence and infectious spread using genome data. This project will expand our knowledge base and research capability in the evolution and epidemiology of infectious agents, and aid in the prevention and control strateg..View full description
Related publications (19)
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink
Ashleigh F Porter, Damian FJ Purcell, Benjamin P Howden, Sebastian Duchene
To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-ass..
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
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
BACKGROUND: The incidence of syphilis has increased markedly in the past decade in high-income countries, including Australia. To ..
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
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
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
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
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
BackgroundMany countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly wi..
Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,,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
Salmonella enterica serovar 4,,12:i:- (Salmonella 4,,12:i:-) is a monophasic variant of Salmonella Typhimurium that has emer..
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
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
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimati..
Temporal signal and the phylodynamic threshold of SARS-CoV-2
Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele
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
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees ..