scholarly journals Transmission trees on a known pathogen phylogeny: enumeration and sampling

2017 ◽  
Author(s):  
Matthew Hall ◽  
Caroline Colijn
Keyword(s):  
Phylogenetic Tree ◽  
Disease Transmission ◽  
R Package ◽  
Infectious Disease Transmission ◽  
New Host ◽  
Mathematical Properties ◽  
Multiple Sampling ◽  
Individual Host ◽  
Branch Lengths ◽  
Incomplete Sampling

AbstractOne approach to the reconstruction of infectious disease transmission trees from pathogen genomic data has been to use a phylogenetic tree, reconstructed from pathogen sequences, and annotate its internal nodes to provide a reconstruction of which host each lineage was in at each point in time. If only one pathogen lineage can be transmitted to a new host (i.e. the transmission bottleneck is complete), this corresponds to partitioning the nodes of the phylogeny into connected regions, each of which represents evolution in an individual host. These partitions define the possible transmission trees that are consistent with a given phylogenetic tree. However, the mathematical properties of the transmission trees given a phylogeny remain largely unexplored. Here, we describe a procedure to calculate the number of possible transmission trees for a given phylogeny, and we show how to uniformly sample from these transmission trees. The procedure is outlined for situations where one sample is available from each host and trees do not have branch lengths, and we also provide extensions for incomplete sampling, multiple sampling, and the application to time trees in a situation where limits on the period during which each host could have been infected are known. The sampling algorithm is available as an R package (STraTUS).

Travel Connectivity and Infectious Disease Transmission Risks in Oceania

2020 ◽  
Author(s):  
Angela Maria Cadavid Restrepo ◽  
Luis Furuya-Kanamori ◽  
Helen Mayfield ◽  
Eric J. Nilles ◽  
Colleen L. Lau
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Infectious Disease Transmission

The Experience of Violence Against Women Who Use Injection Drugs: An Exploratory Qualitative Study

2020 ◽  
pp. 084456212097957
Author(s):  
Cynthia Kitson ◽  
Patrick O’Byrne
Keyword(s):  
Qualitative Study ◽  
Violence Against Women ◽  
Disease Transmission ◽  
Homeless Women ◽  
Structured Interviews ◽  
Infectious Disease Transmission ◽  
Injection Drugs ◽  
Authority Figures ◽  
Canadian Context ◽  
Societal Violence

Background While literature exists about persons who use injection drugs, few studies explore the experience of women who use these substances. Furthermore, even less research specifically focuses on the lives and experiences of homeless women who use injection drugs. What literature does exist, moreover, is often dated and primarily addresses concerns about infectious disease transmission among these women; and some highlight that these women have lives fraught with violence. Purpose To update this knowledge and better understand the lives of women who use injection drugs in the Canadian context. Methods We undertook an exploratory qualitative study and we engaged in semi-structured interviews with 31 homeless women who use injection drugs in downtown Ottawa, Canada. We analyzed the data using the principles of applied thematic analysis. Results Our data identified that violence pervaded the lives of our participants and that these experiences of violence could be categorized into three main areas: early and lifelong experiences of violence; violence with authority figures (e.g., police, healthcare); and societal violence toward women who use injection drugs. Conclusions We take these findings to mean that, violence toward women is rampant in Canada (not just internationally) and that healthcare workers play a role in propagating and addressing this violence.

scholarly journals Predicting the Impact of Describing New Species on Phylogenetic Patterns

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
D C Blackburn ◽  
G Giribet ◽  
D E Soltis ◽  
E L Stanley
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Length Variation ◽  
Tree Shape ◽  
Branch Lengths ◽  
Taxonomic History ◽  
Ecological Patterns ◽  
The Impact ◽  
Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

scholarly journals SPATIAL HETEROGENEITY IN SIMPLE DETERMINISTIC SIR MODELS ASSESSED ECOLOGICALLY

2012 ◽  
Vol 54 (1-2) ◽  
pp. 23-36 ◽  
Author(s):  
E. K. WATERS ◽  
H. S. SIDHU ◽  
G. N. MERCER
Keyword(s):  
Infectious Disease ◽  
Spatial Heterogeneity ◽  
Disease Transmission ◽  
Herd Immunity ◽  
Epidemic Models ◽  
Final Size ◽  
Infectious Disease Transmission ◽  
Epidemic Dynamics ◽  
Mean Crowding ◽  
Rate Of Movement

AbstractPatchy or divided populations can be important to infectious disease transmission. We first show that Lloyd’s mean crowding index, an index of patchiness from ecology, appears as a term in simple deterministic epidemic models of the SIR type. Using these models, we demonstrate that the rate of movement between patches is crucial for epidemic dynamics. In particular, there is a relationship between epidemic final size and epidemic duration in patchy habitats: controlling inter-patch movement will reduce epidemic duration, but also final size. This suggests that a strategy of quarantining infected areas during the initial phases of a virulent epidemic might reduce epidemic duration, but leave the population vulnerable to future epidemics by inhibiting the development of herd immunity.

scholarly journals What is Communicable? Unaccounted Injuries and “Catching” Diabetes in an Illegible Epidemic

2019 ◽  
Vol 34 (4) ◽  
Author(s):  
Amy Moran-Thomas
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Disease Transmission ◽  
Communicable Disease ◽  
Treatment Access ◽  
Infectious Disease Transmission ◽  
The World ◽  
Historically Situated ◽  
Over Time ◽  
Non Communicable Disease

Long-accepted models of causality cast diseases into the binary of either “contagious” or “non-communicable,” typically with institutional resources focused primarily on interrupting infectious disease transmission. But in southern Belize, as in much of the world today, epidemic diabetes has become a leading cause of death and a notorious contributor to organ failure and amputated limbs. This ethnographic essay follows caregivers’ and families’ work to survive in-between public health categories, and asks what responses a bifurcated model of infectious versus non-communicable disease structures or incapacitates in practice. It proposes an alternative focus on diabetes as a “para-communicable” condition—materially transmitted as bodies and ecologies intimately shape each other over time, with unequal and compounding effects for historically situated groups of people. The article closes by querying how communicability relates to community, and why it matters to reframe narratives about contributing causalities in relation to struggles for treatment access.

scholarly journals Adaptive data-driven age and patch mixing in contact networks with recurrent mobility

2021 ◽  
Author(s):  
Jesse Knight ◽  
Huiting Ma ◽  
Amir Ghasemi ◽  
Mackenzie Hamilton ◽  
Kevin Brown ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Age Distribution ◽  
Age Groups ◽  
Data Driven ◽  
Infectious Disease Transmission ◽  
Mobility Data ◽  
Contact Patterns ◽  
Different Types ◽  
Mixing Patterns ◽  
Transmission Models

AbstractInfectious disease transmission models often stratify populations by age and geographic patches. Contact patterns between age groups and patches are key parameters in such models. Arenas et al. (2020) develop an approach to simulate contact patterns associated with recurrent mobility between patches, such as due to work, school, and other regular travel. Using their approach, mixing between patches is greater than mobility data alone would suggest, because individuals from patches A and B can form a contact if they meet in patch C. We build upon their approach to address three potential gaps that remain. First, our approach includes a distribution of contacts by age that is responsive to underlying age distribution of the mixing pool. Second, different age distributions by contact type are also maintained in our approach, such that changes to the numbers of different types of contacts are appropriately reflected in changes to the overall age mixing patterns. Finally, we introduce and distinguish between two mixing pools associated with each patch, with possible implications for the overall connectivity of the population: the home pool, in which contacts can only be formed with other individuals residing in the same patch; and the travel pool, in which contacts can be formed with some residents of, and any other visitors to the patch. We describe in detail the steps required to implement our approach, and present results of an example application.Graphical Abstract

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