Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus

Abstract

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009-2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact.

Keywords: PRRSV; ecology; emergence; epidemiology; evolution; multi-strain dynamics; outbreak.

FIGURE 1

Number of ORF5 sequences according to their source and how they were treated in the lineage classification process. In gray, name of software used in each step.

FIGURE 2

Phylogenetic tree of ORF5 sequences stratified according to lineages. Colors represent different lineages or sub-lineages, and differences in hues within a color represent anchor versus MSHMP sequences. Prototypes (North American – VR2332; European – Lelystad) and vaccines are highlighted using hollow blue stars and solid dark stars, respectively.

FIGURE 3

(A) Stacked bar chart of the relative frequency and (B) number of ORF5 sequences according to lineages over years and quarters.

FIGURE 4

Average scaled by branch length dN/dS for each site in PRRSV ORF5, categorized according to percentage of runs (n = 10) in which each site was identified as under positive selective pressure. Upper gray rectangles show antigenic regions (PNE – principal neutralizing epitope), lower gray rectangles show biologically significant regions (HVR – hypervariable region; TM – transmembrane region) (Delisle et al., 2012).

FIGURE 5

Infection status of farms in the study area over time (quarters and years).

FIGURE 6

We hypothesize that PRRSV evolution is partially driven by immune-mediated selective pressure. Immune-mediated pressure (either within an animal or during transmission between animals/farms) selects for escapee viral variants (inset). Over time, the selection of escapees may allow for emergence of a heterologous viral populations (i.e., strains, genetic groups, or lineages) which are able to spread within the host population. In scenarios in which some method of pre-exposure is adopted, prevalence of immunity against specific types of PRRSV is high (often artificially through vaccination or live virus inoculation) despite high population turnover, possibly favoring the occurrence of immune-mediated selection.