Untangling lineage introductions, persistence, and temporal heterogeneity of HP-PRRSV (sublineage 8.7)

Porcine reproductive and respiratory syndrome virus (PRRSV) sublineage 8.7 has been estimated as one of the most devastating and longest-circulating lineages in PRRSV, especially the emergence and prevalence of highly pathogenic PRRSV in 2006. Despite a rapid increase in sublineage 8.7 virus epidemic outbreaks in Asian countries over recent years, very little is known about the patterns of virus evolution, spread, and the spatial, demographic, and ecological factors influencing PRRSV spread. Relying on a national PRRSV surveillance project established over 20 years ago, we expanded the genomic dataset outbreak in China and deployed a series of phylogeographic extension of this dataset that enables formal testing the contribution of a range of predictor variables to the geographic spread of PRRSV. We revealed the principal role of Guangdong as a central source in Asia, with rural swine activities and provincial distance contributing to spatial spread. Independent recombination analysis of interlineage and intralineage with its temporal dynamics captured a peak wave spanning 2014 to 2016. Noted that several HP-PRRSV modified live vaccines (MLVs) were hastily approved for use on a remarkably emergency basis in China since the epidemic whereas few studies focused on its potential impact on the field spanning a long temporal vaccination, we sequenced all available three MLVs and genomic analysis suggested a key leaky period spanning 2011 to 2017, with two concurrent amino acid mutations located in ORF1a 957 and ORF2 250. Overall, our study provides a phylodynamic framework to showcase a full-scale knowledge of PRRSV sublineage 8.7 evolution, transmission dynamics, and potential leaky evidence of HP-PRRSV MLVs, providing critical insights into new MLV development under Nidovirale order.