Rolf J. F. Ypma

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Knowledge on the transmission tree of an epidemic can provide valuable insights into disease dynamics. The transmission tree can be reconstructed by analysing either detailed epidemiological data (e.g. contact tracing) or, if sufficient genetic diversity accumulates over the course of the epidemic, genetic data of the pathogen. We present a likelihood-based(More)
Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy(More)
BACKGROUND Studying day-care-associated infectious disease dynamics aids in formulating evidence-based guidelines for disease control, thereby supporting day-care centers in their continuous efforts to provide their child population with a safe and hygienic environment. The objective of this study was to estimate the (excess) infectious disease burden(More)
BACKGROUND Molecular typing is a valuable tool for gaining insight into spread of Mycobacterium tuberculosis. Typing allows for clustering of cases whose isolates share an identical genotype, revealing epidemiologic relatedness. Observed distributions of genotypic cluster sizes of tuberculosis (TB) are highly skewed. A possible explanation for this skewness(More)
Outbreaks of highly pathogenic avian influenza in poultry can cause severe economic damage and represent a public health threat. Development of efficient containment measures requires an understanding of how these influenza viruses are transmitted between farms. However, the actual mechanisms of interfarm transmission are largely unknown. Dispersal of(More)
The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools,(More)
The evolutionary rates of RNA viruses can differ from one another by several orders of magnitude. Much of this variation has been explained by differences in viral mutation rates and selective environments. However, substitution rates also vary considerably across viral populations belonging to the same species. In particular, viral lineages from epidemic(More)
Surveillance systems of contagious diseases record information on cases to monitor incidence of disease and to evaluate effectiveness of interventions. These systems focus on a well-defined population; a key question is whether observed cases are infected through local transmission within the population or whether cases are the result of importation of(More)
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