Exploring the longitudinal dynamics of herd BVD antibody test results using model-based clustering

Abstract

Determining the Bovine Viral Diarrhoea (BVD) infection status of cattle herds is a challenge for control and eradication schemes. Given the changing dynamics of BVD virus (BVDV) antibody responses in cattle, classifying herds based on longitudinal changes in the results of BVDV antibody tests could offer a novel, complementary approach to categorising herds that is less likely than the present system to result in a herd’s status changing from year to year, as it is more likely to capture the true exposure dynamics of the farms. This paper describes the dynamics of BVDV antibody test values (measured as percentage positivity (PP)) obtained from 15,500 bovines between 2007 and 2010 from thirty nine cattle herds located in Scotland and Northern England. It explores approaches of classifying herds based on trend, magnitude and shape of their antibody PP trajectories and investigates the epidemiological similarities between farms within the same cluster. Gaussian mixture models were used for the magnitude and shape clustering. Epidemiologically meaningful clusters were obtained. Farm cluster membership depends on clustering approach used. Moderate concordance was found between the shape and magnitude clusters. These methods hold potential for application to enhance control efforts for BVD and other infectious livestock diseases.

Multi-cohort and longitudinal Bayesian clustering study of stage and subtype in Alzheimer’s disease

“…The multivariate mixture of generalized mixed effects clustering model 32 incorporates Bayesian inference to explore heterogeneity in the longitudinal brain data. We applied this model on brain volume/thickness but it has already been used in other applications 31,[33][34][35][36][37][38][39][40][41][42] . The Bayesian approach allowed the implementation of a complex hierarchical model for each cluster, where probabilistic mixture modeling (number of clusters) is combined with mixed effect modeling (number of brain regions) in one model definition.…”

A novel shape-based approach to identify gestational age-adjusted growth patterns from birth to 11 years of age

“…By removing the weight of the starting point of the trajectory (centering) we were able to focus on the shape of the trajectories and capture the variation in growth that happens in the first 24 months of life. A similar normalizing approach has been used to identify patterns of crime over time and changes in antibody levels between animals of different farms 16 , 17 . Researchers showed that when correcting by the mean value of the farm the scale of the antibody effect and the variability between farms were removed 17 .…”

“…A similar normalizing approach has been used to identify patterns of crime over time and changes in antibody levels between animals of different farms 16,17 . Researchers showed that when correcting by the mean value of the farm the scale of the antibody effect and the variability between farms were removed 17 . Similar to the change in growth we captured in the patterns in our study, clustering by shape not only provided information on the direction of change, but also other complex nonlinear patterns which may www.nature.com/scientificreports/ be influenced by changes in time.…”

Lessons learned for animal health governance from bovine viral diarrhea eradication schemes in Scotland and Ireland

“…In Scotland and Ireland, analyzes of BVD eradication schemes have focused on costs and benefits ( 46 , 47 ), modeling the optimal testing methods for achieving eradication ( 48 ) and epidemiological analyzes of the schemes ( 3 , 4 , 49 ). Reviews have been carried out on the voluntary phase of the eradication scheme in Ireland ( 50 ) and more recent analyzes of the design, progress, and challenges toward BVD eradication ( 51 ).…”