LIVIVO - Search results -

Search results

Result 1 - 10 of total 172

Search options

Article ; Online: Redefining the treponemal history through pre-Columbian genomes from Brazil.

Majander, Kerttu / Pla-Díaz, Marta / du Plessis, Louis / Arora, Natasha / Filippini, Jose / Pezo-Lanfranco, Luis / Eggers, Sabine / González-Candelas, Fernando / Schuenemann, Verena J

Nature

2024 Volume 627, Issue 8002, Page(s) 182–188

Abstract: The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' ... ...

Abstract	The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions
MeSH term(s)	Humans ; Brazil/epidemiology ; Brazil/ethnology ; Europe/epidemiology ; Evolution, Molecular ; Genome, Bacterial/genetics ; History, 15th Century ; History, Ancient ; Syphilis/epidemiology ; Syphilis/history ; Syphilis/microbiology ; Syphilis/transmission ; Treponema pallidum/classification ; Treponema pallidum/genetics ; Treponema pallidum/isolation & purification ; Treponemal Infections/epidemiology ; Treponemal Infections/history ; Treponemal Infections/microbiology ; Treponemal Infections/transmission
Language	English
Publishing date	2024-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06965-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 9: Show issues
Zs.MO 244: Show issues

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: A computationally tractable birth-death model that combines phylogenetic and epidemiological data.

Zarebski, Alexander Eugene / du Plessis, Louis / Parag, Kris Varun / Pybus, Oliver George

PLoS computational biology

2022 Volume 18, Issue 2, Page(s) e1009805

Abstract: Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic ... ...

Abstract	Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.
MeSH term(s)	Computer Simulation ; Disease Outbreaks ; Genomics ; Humans ; Phylogeny ; Probability
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1009805
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences.

Parag, Kris V / du Plessis, Louis / Pybus, Oliver G

Molecular biology and evolution

2020 Volume 37, Issue 8, Page(s) 2414–2429

Abstract: Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology, and macroevolution. Popular solutions, such as the skyline and ... ...

Abstract	Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology, and macroevolution. Popular solutions, such as the skyline and skygrid methods, infer past effective population sizes from the coalescent event times of phylogenies reconstructed from sampled sequences but assume that sequence sampling times are uninformative about population size changes. Recent work has started to question this assumption by exploring how sampling time information can aid coalescent inference. Here, we develop, investigate, and implement a new skyline method, termed the epoch sampling skyline plot (ESP), to jointly estimate the dynamics of population size and sampling rate through time. The ESP is inspired by real-world data collection practices and comprises a flexible model in which the sequence sampling rate is proportional to the population size within an epoch but can change discontinuously between epochs. We show that the ESP is accurate under several realistic sampling protocols and we prove analytically that it can at least double the best precision achievable by standard approaches. We generalize the ESP to incorporate phylogenetic uncertainty in a new Bayesian package (BESP) in BEAST2. We re-examine two well-studied empirical data sets from virus epidemiology and molecular evolution and find that the BESP improves upon previous coalescent estimators and generates new, biologically useful insights into the sampling protocols underpinning these data sets. Sequence sampling times provide a rich source of information for coalescent inference that will become increasingly important as sequence collection intensifies and becomes more formalized.
MeSH term(s)	Animals ; Bison/genetics ; Humans ; Influenza A virus/genetics ; Models, Genetic ; Population Density ; Population Dynamics
Language	English
Publishing date	2020-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Validation Study
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msaa016
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2137: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Book ; Online: Understanding the Spread and Adaptation of Infectious Diseases using Genomic Sequencing Data

Du Plessis, Louis

2016

Abstract: Dissertation, ETH Zürich, 2016, No. ... ...

Abstract	Dissertation, ETH Zürich, 2016, No. 23660
Keywords	INFEKTIONSKRANKHEITEN + ANSTECKENDE KRANKHEITEN + ÜBERTRAGBARE KRANKHEITEN (MEDIZIN) ; ANSTECKUNGSARTEN + KRANKHEITSÜBERTRAGUNG + KRANKHEITSAUSBREITUNG (MEDIZIN) ; EPIDEMIOLOGIE + SEUCHEN (MEDIZIN) ; GENOMIK (MOLEKULARE GENETIK) ; EVOLUTION (BIOLOGIE)
Language	English
Publisher	Zürich
Publishing country	ch
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: A computationally tractable birth-death model that combines phylogenetic and epidemiological data.

Alexander Eugene Zarebski / Louis du Plessis / Kris Varun Parag / Oliver George Pybus

PLoS Computational Biology, Vol 18, Iss 2, p e

2022 Volume 1009805

Abstract	Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.
Keywords	Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza.

Ghafari, Mahan / du Plessis, Louis / Raghwani, Jayna / Bhatt, Samir / Xu, Bo / Pybus, Oliver G / Katzourakis, Aris

Molecular biology and evolution

2022 Volume 39, Issue 2

Abstract: High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over ... ...

Abstract	High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald-Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.
MeSH term(s)	Bayes Theorem ; COVID-19 ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza, Human/epidemiology ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2022-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msac009
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2137: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Getting to the root of epidemic spread with phylodynamic analysis of genomic data.

du Plessis, Louis / Stadler, Tanja

Trends in microbiology

2015 Volume 23, Issue 7, Page(s) 383–386

Abstract: When epidemiological and evolutionary dynamics occur on similar timescales, pathogen genomes sampled from infected hosts carry a signature of the dynamics of epidemic spread. Phylodynamic inference methods aim to extract this signature from genetic data. ...

Abstract	When epidemiological and evolutionary dynamics occur on similar timescales, pathogen genomes sampled from infected hosts carry a signature of the dynamics of epidemic spread. Phylodynamic inference methods aim to extract this signature from genetic data. We discuss the contribution of phylodynamics toward understanding the 2014 West African Ebola virus epidemic.
MeSH term(s)	Bayes Theorem ; Ebolavirus/genetics ; Evolution, Molecular ; Genome, Viral ; Genomics/methods ; Hemorrhagic Fever, Ebola/epidemiology ; Hemorrhagic Fever, Ebola/virology ; Humans ; Molecular Epidemiology ; Phylogeny
Language	English
Publishing date	2015-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2015.04.007
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3738: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Thesis ; Online: Understanding the spread and adaptation of infectious diseases using genomic sequencing data

du Plessis, Louis

2016

Keywords	EVOLUTION (BIOLOGY) ; GENOMICS (MOLECULAR GENETICS) ; GENOMIK (MOLEKULARE GENETIK) ; INFECTIOUS DISEASES + CONTAGIOUS DISEASES + COMMUNICABLE DISEASES (MEDICINE) ; EPIDEMIOLOGY + EPIDEMICS + PLAGUES (MEDICINE) ; CONTAGION MODES + INFECTION MODES + DISEASE TRANSMISSION + DISEASE PROPAGATION (MEDICINE) ; ANSTECKUNGSARTEN + KRANKHEITSÜBERTRAGUNG + KRANKHEITSAUSBREITUNG (MEDIZIN) ; EVOLUTION (BIOLOGIE) ; EPIDEMIOLOGIE + SEUCHEN (MEDIZIN) ; INFEKTIONSKRANKHEITEN + ANSTECKENDE KRANKHEITEN + ÜBERTRAGBARE KRANKHEITEN (MEDIZIN) ; info:eu-repo/classification/ddc/610 ; info:eu-repo/classification/ddc/570 ; Medical sciences ; medicine ; Life sciences
Language	English
Publisher	ETH Zürich
Publishing country	ch
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Impact of the tree prior on estimating clock rates during epidemic outbreaks.

Möller, Simon / du Plessis, Louis / Stadler, Tanja

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 16, Page(s) 4200–4205

Abstract: Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in ...

Abstract	Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in the sampling period of sequences. In particular, clock rates of epidemic outbreaks are often estimated to be higher compared with the long-term clock rate. Purifying selection has been suggested as a biological factor that contributes to this phenomenon, since it purges slightly deleterious mutations from a population over time. However, other factors such as methodological biases may also play a role and make a biological interpretation of results difficult. In this paper, we identify methodological biases originating from the choice of tree prior, that is, the model specifying epidemiological dynamics. With a simulation study we demonstrate that a misspecification of the tree prior can upwardly bias the inferred clock rate and that the interplay of the different models involved in the inference can be complex and nonintuitive. We also show that the choice of tree prior can influence the inference of clock rate on real-world Ebola virus (EBOV) datasets. While commonly used tree priors result in very high clock-rate estimates for sequences from the initial phase of the epidemic in Sierra Leone, tree priors allowing for population structure lead to estimates agreeing with the long-term rate for EBOV.
MeSH term(s)	Bayes Theorem ; Bias ; Biological Evolution ; Calibration ; Computer Simulation ; Ebolavirus/genetics ; Epidemics ; Evolution, Molecular ; Genetics, Population/methods ; Humans ; Models, Genetic ; Mutation Rate ; Phylogeny ; Sierra Leone
Language	English
Publishing date	2018-04-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1713314115
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1148: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Genomic epidemiology of

Microbial genomics

2023 Volume 9, Issue 5

Abstract: Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, ... ...

Abstract	Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619
MeSH term(s)	Animals ; Cattle ; Mycobacterium bovis/genetics ; Mustelidae/microbiology ; Northern Ireland/epidemiology ; Tuberculosis, Bovine/microbiology ; Genomics
Language	English
Publishing date	2023-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.001023
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito