Integrating Animal Movements With Phylogeography to Model the Spread of PRRS Virus in the U.S.

Dennis N Makau*, Moh A Alkhamis, Igor A D Paploski, Cesar A Corzo, Samantha Lycett, Kimberly VanderWaal

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Viral sequence data coupled with phylodynamic models have become instrumental in investigating outbreaks of human and animal diseases, and incorporation of hypothesized drivers of pathogen spread can enhance the interpretation from phylodynamic inference. Integrating animal movement data with phylodynamics allows us to quantify the extent to which the spatial diffusion of a pathogen is influenced by animal movements and contrast the relative importance of different types of movements in shaping pathogen distribution. We combine animal movement, spatial, and environmental data in a Bayesian phylodynamic framework to explain the spatial diffusion and evolutionary trends of a rapidly spreading sub-lineage (denoted L1A) of porcine reproductive and respiratory syndrome virus (PRRSV) type 2 from 2014-17. PRRSV is the most important endemic pathogen affecting pigs in the U.S., and this particular virulent sub-lineage emerged in 2014 and continues to be the dominant lineage in the U.S. swine industry to date. Data included 984 ORF5 PRRSV L1A sequences obtained from two production systems in a swine dense production region (~ 85,000 mi2) in the U.S. between 2014 and 2017. The study area was divided into sectors for which model covariates were summarized, and animal movement data between each sector was summarized by age-class (wean: 3-4 weeks; feeder: 8-25 weeks; breeding: ≥21 weeks). We implemented a discrete-space phylogeographic generalized linear model using Bayesian evolutionary analysis by sampling trees (BEAST) to infer factors associated with variability in between-sector diffusion rates of PRRSV L1A. We found that between-sector spread was enhanced by the movement of feeder pigs, spatial adjacency of sectors, and farm density in the destination sector. The PRRSV L1A strain was introduced in the study area in early 2013, and genetic diversity and effective population size peaked in 2015 before fluctuating seasonally (peaking during summer months). Our study underscores the importance of animal movements and shows, for the first time, that movement of feeder pigs (8-25 weeks old) shaped spatial patterns of PRRSV spread much more strongly than movements of other age-classes of pigs. The inclusion of movement data into phylodynamic models as done in this analysis may enhance our ability to identify crucial pathways of disease spread that can be targeted to mitigate the spatial spread of infectious human and animal pathogens
Original languageEnglish
Article numberveab060
JournalVirus Evolution
Early online date15 Jun 2021
DOIs
Publication statusE-pub ahead of print - 15 Jun 2021

Keywords

  • Bayesian inference
  • Phylodynamics
  • PHYLOGEOGRAPHY
  • Molecular epidemiology
  • ANIMAL MOVEMENTS
  • Livestock networks

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