PMID- 34532062 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20210918 IS - 2057-1577 (Print) IS - 2057-1577 (Electronic) IS - 2057-1577 (Linking) VI - 7 IP - 2 DP - 2021 TI - Integrating animal movements with phylogeography to model the spread of PRRSV in the USA. PG - veab060 LID - 10.1093/ve/veab060 [doi] LID - veab060 AB - Viral sequence data coupled with phylodynamic models have become instrumental in investigating the outbreaks of human and animal diseases, and the incorporation of the 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 to 2017. PRRSV is the most important endemic pathogen affecting pigs in the USA, and this particular virulent sub-lineage emerged in 2014 and continues to be the dominant lineage in the US swine industry to date. Data included 984 open reading frame 5 (ORF5) PRRSV L1A sequences obtained from two production systems in a swine-dense production region ( approximately 85,000 mi(2)) in the USA between 2014 and 2017. The study area was divided into sectors for which model covariates were summarized, and animal movement data between each sector were 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 the summer months). Our study underscores the importance of animal movements and shows, for the first time, that the movement of feeder pigs (8-25 weeks old) shaped the spatial patterns of PRRSV spread much more strongly than the 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. CI - (c) The Author(s) 2021. Published by Oxford University Press. FAU - Makau, Dennis N AU - Makau DN AD - Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA. FAU - Alkhamis, Moh A AU - Alkhamis MA AD - Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait City, 24923, Safat 13110, Kuwait. FAU - Paploski, Igor A D AU - Paploski IAD AD - Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA. FAU - Corzo, Cesar A AU - Corzo CA AD - Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA. FAU - Lycett, Samantha AU - Lycett S AUID- ORCID: 0000-0003-3159-596X AD - Roslin Institute, University of Edinburgh, Edinburgh, Midlothian, EH25 9RG, UK. FAU - VanderWaal, Kimberly AU - VanderWaal K AD - Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA. LA - eng PT - Journal Article DEP - 20210715 PL - England TA - Virus Evol JT - Virus evolution JID - 101664675 PMC - PMC8438914 OTO - NOTNLM OT - Bayesian inference OT - animal movement OT - livestock networks OT - molecular epidemiology OT - phylodynamic models OT - phylogeography COIS- The authors declare no financial or commercial conflicts of interest. EDAT- 2021/09/18 06:00 MHDA- 2021/09/18 06:01 PMCR- 2021/07/15 CRDT- 2021/09/17 07:15 PHST- 2021/03/11 00:00 [received] PHST- 2021/05/22 00:00 [revised] PHST- 2021/06/14 00:00 [accepted] PHST- 2021/09/17 07:15 [entrez] PHST- 2021/09/18 06:00 [pubmed] PHST- 2021/09/18 06:01 [medline] PHST- 2021/07/15 00:00 [pmc-release] AID - veab060 [pii] AID - 10.1093/ve/veab060 [doi] PST - epublish SO - Virus Evol. 2021 Jul 15;7(2):veab060. doi: 10.1093/ve/veab060. eCollection 2021.