Evolution of porcine reproductive and respiratory syndrome virus

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the leading swine pathogens causing tremendous economic loss to the global swine industry. Since its recognition in the late 1980s, PRRSV has continued to expand in genetic diversity which poses problems for management and eradication. As a result, tracing and tracking the evolving diversity of PRRSV is critical to all stakeholders. In 2010, a phylogenetic framework was proposed to classify all type 2 PRRSV ORF5 sequences (n ≈ 8,000). Since then a further build-up of sequences (n ≈ 5,000) prompted questions on the robustness of the 2010 system in typing new sequences and what new insights on PRRSV diversity could be gauged. Phylogenetic classification of new sequences did not lead to the discovery of new evolutionary lineages but enriched the diversity of existing lineages. Importantly, lineages 1 and 9 revealed widening divergence of PRRSV isolates over time with genetic distance peaking at ≥ 10% at present. The growing genetic disparity between viruses and commercial vaccines over time was equally evident. Seven out of the nine lineages had evolutionary origins in North America while the remaining two originated from East Asia. Lineages 1, 5, 8, and 9 viruses were the dominant circulating strains in the field, accounting for > 97% of the dataset. The USA was the country most impacted from the circulation of a diverse set of viruses with isolation of strains of almost every lineage. However, Canada exhibited the greatest heterogeneity in viral diversity despite having rarely experienced foreign introductions. Asian countries also displayed significant diversity but the burden of type 2 PRRSV in Europe was limited. While intra-country diversity levels were more or less comparable across the USA, the same was highly skewed among Canadian provinces. Overall, the inferred burden of vaccine-related viruses on circulating strains was approximately 5%. To date, the majority of PRRSV diversity studies have focused on limited regions of the genome which incompletely characterize evolutionary mechanisms shaping the viral genome as a whole. A methodology of sequencing near complete-length PRRSV genomes was developed to obtain genomic sequences of a diverse set of 16 Hong Kong isolates. Genome assemblies and phylogenetic typing indicated the co-circulation of strains of both genotypes (type 1and type 2) with varying Nsp2 deletion patterns and distinct evolutionary lineages ("High Fever"-like and local endemic type). Recombination analyses revealed genomic breakpoints in structural and non-structural regions of genomes of both genotypes with evidence of many recombination events originating from common ancestors. Additionally, the high fold of coverage per nucleotide allowed the characterization of minor variants arising from the intra-strain heterogeneity. Overall, 0.56-2.83% of sites were polymorphic with respect to cognate consensus genomes. The distribution of minor variants across each genome was not uniform, indicating the influence of selective forces. The proportion of variants causing an amino acid change in their respective codons ranged between 25-67% with many predicted to be non-deleterious. Low frequency deletion variants were also detected, providing one possible mechanism for their sudden emergence as cited in previous reports.