Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada

Abstract

Bovine viral diarrhea virus (BVDV) has been recognized as an important pathogen of livestock in Canada. The high mutation rate of this virus leads to a great degree of diversity between isolates resulting in the ability to infer precise evolutionary relationships. Many studies have attempted to elucidate the regional and global evolution of BVDV, but so far few have applied Bayesian methods to this end. We aimed to describe the molecular epidemiology and phylodynamics of BVDV 1a isolates in Western Canada using 5′UTR and E1–E2 sequence data, collection dates and locations. Sequences were obtained from isolates submitted to a diagnostic laboratory in Saskatoon, Canada. Path sampling and stepping stone model testing were employed to identify the model that best fit the data. We found that these Western Canadian isolates share a most recent common ancestor dated near 1909. Furthermore, the E1–E2 region shows a median substitution rate about ten times greater than the 5′UTR. It was also noted that caution should be exercised when inferring phylogenetic relationships using the 5′UTR alone, as it becomes difficult to resolve relationships within major clades. Phylogeographic and population size fluctuation estimates require more thorough sampling than was performed here to be reliable. We have found that there are significant gains to be made by utilizing a Bayesian analysis and by incorporating additional types of data beyond the sequence. These include the estimation of most common recent ancestor dates and the precise inference of transmission routes. Future work will expand upon these findings by more thoroughly sampling BVDV isolates spatially and temporally and further refining the Bayesian model employed here.