Definition: In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
Input: Background: Developing methods to reconstruct transmission histories for viral outbreaks could provide critical information to support locating sources of disease transmission. Phylogenetic methods used to measure the degree of relatedness among sequenced viral samples have proven useful in identifying potential outbreak sources. The complex nature of infectious disease, however, makes it difficult to assign a rigorously defined quantitative confidence value assessing the likelihood of a true direct transmission event using genetic data alone. Results: A new method is presented to calculate a confidence value assessing the likelihood of a transmission event using both phylogenetic inference and limited knowledge of incubation and infectious duration times. The method is applied to simulations of a foot and mouth disease (FMD) outbreak to demonstrate how the combination of both phylogenetic and epidemiology data can be used to strengthen the assessment of the likelihood of direct transmission over methods using just phylogenetic data or infection timing data alone. The method is applied to a previous FMD outbreak to identify areas where over confidence in previously inferred direct transmission may exist. Conclusion: Combining knowledge from viral evolution and epidemiology within a single integrated transmission inference framework is an important approach to assess the potential likelihood of transmission events and makes clear how specific features of a virus' spread through the course of an outbreak will directly determine the potential for confidence in inferred host transmission links. Background Developing methods to protect against RNA virus outbreaks in the face of constantly changing disease dynamics remains one of the great public health challenges of our time. One small piece of this problem involves determining the host-pathogen transmission history to identify an outbreak's origin. In recent cases such as the 2003 SARS outbreak [1, 2], H5N1 influenza [3] infection in humans and Marburgvirus [4], phylogenetic inference has been used to help identify potential outbreak sources. Typically, a collection of sequences from candidate related sources are compared to infer transmission links between the most closely related sequences. These methods have been used beyond the public health domain to provide evidence in HIV [5, 6] and other forensic investigations [7] to help infer when a suspect is involved in infecting a victim. P (δ, σ|M ) rather than P (δ|M ). This reflects the desire to estimate the probability of observing the genetic relation δ in conjunction with infection related timing values for the transmission hypothesis M . The σ parameter values are motivated by a SEIR type infection concept [22], which describes a host in one of four 5 . CC-BY-ND 4.0 International license is made available under a

Mapping a viral phylogeny onto outbreak trees to improve host transmission inference