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A brief history of bird flu
In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50
million people. A century later, with the advent of sequencing technology and corresponding …
million people. A century later, with the advent of sequencing technology and corresponding …
Outbreak analytics: a develo** data science for informing the response to emerging pathogens
JA Polonsky, A Baidjoe, ZN Kamvar… - … of the Royal …, 2019 - royalsocietypublishing.org
Despite continued efforts to improve health systems worldwide, emerging pathogen
epidemics remain a major public health concern. Effective response to such outbreaks relies …
epidemics remain a major public health concern. Effective response to such outbreaks relies …
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
R Bouckaert, TG Vaughan… - PLoS computational …, 2019 - journals.plos.org
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …
years with major new advances in nearly all aspects of the joint modelling of evolutionary …
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients
R León-Sampedro, J DelaFuente, C Díaz-Agero… - Nature …, 2021 - nature.com
Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern
in clinical settings worldwide. Two fundamentally different processes shape the …
in clinical settings worldwide. Two fundamentally different processes shape the …
Patterns of within-host genetic diversity in SARS-CoV-2
G Tonkin-Hill, I Martincorena, R Amato, ARJ Lawson… - elife, 2021 - elifesciences.org
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become
a major public health focus for many governments around the world. The modest mutation …
a major public health focus for many governments around the world. The modest mutation …
Gut to lung translocation and antibiotic mediated selection shape the dynamics of Pseudomonas aeruginosa in an ICU patient
RM Wheatley, JD Caballero, TE van der Schalk… - Nature …, 2022 - nature.com
Bacteria have the potential to translocate between sites in the human body, but the
dynamics and consequences of within-host bacterial migration remain poorly understood …
dynamics and consequences of within-host bacterial migration remain poorly understood …
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Genomic data are increasingly being used to understand infectious disease epidemiology.
Isolates from a given outbreak are sequenced, and the patterns of shared variation are used …
Isolates from a given outbreak are sequenced, and the patterns of shared variation are used …
Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis
Background Whole-genome sequencing (WGS) can be used in genomic epidemiology
investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted …
investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted …
[HTML][HTML] Understanding the transmission of foot-and-mouth disease virus at different scales
Highlights•FMDV is readily transmitted via direct and indirect contact between hosts.•The
role of low-probability events is difficult to recreate and model.•Sequences can be combined …
role of low-probability events is difficult to recreate and model.•Sequences can be combined …
High-resolution map** of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain
Y Xu, I Cancino-Muñoz, M Torres-Puente… - PLoS …, 2019 - journals.plos.org
Background Whole genome sequencing provides better delineation of transmission clusters
in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal …
in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal …