Phylodynamic analysis reveals disparate transmission dynamics of -complex lineages in Botswana.

Tuberculosis epidemics have traditionally been conceptualized as arising from a single uniform pathogen. However, -complex (Mtbc), the pathogen causing tuberculosis in humans, encompasses multiple lineages exhibiting genetic and phenotypic diversity that may be responsible for heterogeneity in TB transmission. We analysed a population-based dataset of 1,354 Mtbc whole-genome sequences collected over four years in Botswana, a country with high HIV and tuberculosis burden.

Using genomic epidemiology and geographic activity spaces to investigate tuberculosis outbreaks in Botswana.

Background: The integration of genomic and geospatial data into infectious disease transmission analyses typically includes residential locations and excludes other activity spaces where transmission may occur ( work, school, or social venues). The objective of this analysis was to explore residential as well as other activity spaces of tuberculosis (TB) outbreaks to identify potential geospatial 'hotspots' of transmission.

Methods: We analyzed data that included geospatial coordinates for residence and other activity spaces collected during 2012-2016 for the Kopanyo Study, a population-based study of TB transmission in Botswana.

Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data.

Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as an average number of secondary infections produced by one infectious individual per unit time.

Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data.

Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as an average number of secondary infections produced by one infectious individual per unit time.

How Trustworthy Is Your Tree? Bayesian Phylogenetic Effective Sample Size Through the Lens of Monte Carlo Error.

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as "split") probabilities and tree probabilities, and variability in the estimated summary tree.