title: Bias, accuracy, and impact of indirect genetic effects in infectious diseases.
abstract: Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not following exposure to an infectious disease. Numerous studies have shown that from this data one can infer genetic variation in individuals' underlying susceptibility. In a previous study, we showed that with an indirect genetic effect (IGE) model it is possible to capture some genetic variation in infectivity, if present, as well as in susceptibility. Infectivity is the propensity of transmitting infection upon contact with a susceptible individual. It is an important factor determining the severity of an epidemic. However, there are severe shortcomings with the Standard IGE models as they do not accommodate the dynamic nature of disease data. Here we adjust the Standard IGE model to (1) make expression of infectivity dependent on the individuals' disease status (Case Model) and (2) to include timing of infection (Case-ordered Model). The models are evaluated by comparing impact of selection, bias, and accuracy of each model using simulated binary disease data. These were generated for populations with known variation in susceptibility and infectivity thus allowing comparisons between estimated and true breeding values. Overall the Case Model provided better estimates for host genetic susceptibility and infectivity compared to the Standard Model in terms of bias, impact, and accuracy. Furthermore, these estimates were strongly influenced by epidemiological characteristics. However, surprisingly, the Case-Ordered model performed considerably worse than the Standard and the Case Models, pointing toward limitations in incorporating disease dynamics into conventional variance component estimation methodology and software used in animal breeding.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, Genetics and Genomics, University of Edinburgh Midlothian, UK.
authors.forename: Debby
authors.initials: D
authors.lastname: Lipschutz-Powell
authors.forename: J A
authors.initials: JA
authors.lastname: Woolliams
authors.forename: P
authors.initials: P
authors.lastname: Bijma
authors.forename: R
authors.initials: R
authors.lastname: Pong-Wong
authors.forename: M L
authors.initials: ML
authors.lastname: Bermingham
authors.forename: A B
authors.initials: AB
authors.lastname: Doeschl-Wilson
keywords: associative; binary; breeding; indirect genetic; infectious disease; infectivity; social interaction; super spreaders