The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage’s effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2–8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.

We report an ongoing regional outbreak of an emerging porcine reproductive and respiratory syndrome virus (PRRSV2) variant within Lineage 1C affecting 154 breeding and grow-finishing sites in the Midwestern U.S. Transmission seemed to have occurred in two waves, with the first peak of weekly cases occurring between October and December 2020 and the second starting in April 2021. Most of cases occurred within a 120 km radius. Both orf5 and whole genome sequencing results suggest that this represents the emergence of a new variant within Lineage 1C distinct from what has been previously circulating. A case-control study was conducted with 50 cases (sites affected with the newly emerged variant) and 58 controls (sites affected with other PRRSV variants) between October and December 2020. Sites that had a market vehicle that was not exclusive to the production system had 0.04 times the odds of being a case than a control. A spatial cluster (81.42 km radius) with 1.68 times higher the number of cases than controls was found. The average finishing mortality within the first 4 weeks after detection was higher amongst cases (4.50%) than controls (0.01%). The transmission of a highly similar virus between different farms carrying on trough spring rises concerns for the next high transmission season of PRRS.

In this study, we compiled 84-year worth (1934–2017) of genomic and epidemiological data of foot-and-mouth disease virus (FMDV), and performed comprehensive analyses to determine its early origin and transmission route. We found that recombination is a key feature of FMDV, and that the genomic regions coding for structural and non-structural proteins have markedly different evolutionary histories, and evolve at different rates. Despite all of these differences, analyses of both structural and non-structural protein coding regions consistently suggested that the most recent common ancestor of FMDV could be dated back to the Middle Age, ~ 200 to 300 years earlier than previously thought. The ancestors of the Euro-Asiatic and SAT strains could be dated back to the mid-seventeenth century, and to the mid-fifteenth to mid-sixteenth century, respectively. Our results implicated Mediterranean counties as an early geographical origin of FMDV before spreading to Europe and subsequently to Asia and South America.

While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995–2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants.

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to mutate, causing disruptive PRRS outbreaks in farms that lead to reproductive failure and respiratory disease-associated mortality. We present four new PRRSV type 2 variants in the United States belonging to four distinct orf5 sublineages within lineage 1.