SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Publication Date
September 28, 2016
Journal
PLOS Computational Biology
Authors
Nicola De Maio, Chieh Hsi Wu & Daniel J Wilson
Volume
12
Issue
9
Pages
e1005130
DOI
https://dx.plos.org/10.1371/journal.pcbi.1005130
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005130
Web of Science
000387658600043
Scopus
84989361131
Mendeley
http://www.mendeley.com/research/scotti-efficient-reconstruction-transmission-within-outbreaks-structured-coalescent
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Mendeley | Further Information

{"title"=>"SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent", "type"=>"journal", "authors"=>[{"first_name"=>"Nicola", "last_name"=>"De Maio", "scopus_author_id"=>"36871720000"}, {"first_name"=>"Chieh Hsi", "last_name"=>"Wu", "scopus_author_id"=>"7501669553"}, {"first_name"=>"Daniel J.", "last_name"=>"Wilson", "scopus_author_id"=>"35481545900"}], "year"=>2016, "source"=>"PLoS Computational Biology", "identifiers"=>{"doi"=>"10.1371/journal.pcbi.1005130", "sgr"=>"84989361131", "pui"=>"612502402", "scopus"=>"2-s2.0-84989361131", "issn"=>"15537358", "arxiv"=>"1603.01994", "pmid"=>"27681228", "isbn"=>"1553-7358 (Electronic) 1553-734X (Linking)"}, "id"=>"71a057bb-a09f-3068-bf9a-41b382bbf572", "abstract"=>"Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our computationally efficient implementation of this model enables the inference of host-to-host transmission while accommodating within-host evolution and non-sampled hosts. SCOTTI is distributed as an open source package for the phylogenetic software BEAST2. We show that SCOTTI can generally infer transmission events even in the presence of considerable within-host variation, can account for the uncertainty associated with the possible presence of non-sampled hosts, and can efficiently use data from multiple samples of the same host, although there is some reduction in accuracy when samples are collected very close to the infection time. We illustrate the features of our approach by investigating transmission from genetic and epidemiological data in a Foot and Mouth Disease Virus (FMDV) veterinary outbreak in England and a Klebsiella pneumoniae outbreak in a Nepali neonatal unit. Transmission histories inferred with SCOTTI will be important in devising effective measures to prevent and halt transmission.", "link"=>"http://www.mendeley.com/research/scotti-efficient-reconstruction-transmission-within-outbreaks-structured-coalescent", "reader_count"=>67, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>6, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>6, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>7, "Agricultural and Biological Sciences"=>30, "Medicine and Dentistry"=>6, "Neuroscience"=>1, "Chemistry"=>1, "Computer Science"=>5, "Immunology and Microbiology"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>7}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>1, "Mexico"=>1, "United Kingdom"=>3, "Italy"=>1, "Germany"=>1}, "group_count"=>2}

Scopus | Further Information

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