Abstract
This study investigates the long-term evolutionary dynamics of porcine reproductive and respiratory syndrome virus (PRRSV-1) in an endemically infected and vaccinated pig herd. Over a one year and a half period, piglets from seven farrowing batches in a 300-sow PRRSV-vaccinated farm were monitored from birth to nine weeks of age by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Eighty-five PRRSV-positive samples were subjected to whole genome sequencing (Illumina Miseq), and 251 samples to open reading frame 5 (ORF5) sequencing. Farm-specific PRRSV variants' impact on anti-PRRSV antibodies was evaluated using enzyme-linked immunosorbent and neutralizing antibody assays. The replication kinetics and cytokine inhibition capabilities (IFN-α and TNF-α) of these variants were assessed in porcine alveolar macrophages. The study revealed fluctuating PRRSV-1 incidences in farrowing units and nurseries, attributed to two key evolutionary events: an escape variant emergence and a lateral introduction of a new strain. Initially, strain 1 variant α was swiftly replaced within weeks by variant 1β (99.5 per cent genomic similarity), with twenty-five amino acid mutations, primarily in nsp1α, GP2, GP3, and GP5, including an additional glycosylation site and a deletion downstream the neutralization epitope of GP5. This shift to 1β correlated with increased incidence in nurseries and higher viral loads, with sera from 1α-exposed animals showing reduced neutralization against 1β. Consistently for in vitro assays, variant 1β demonstrated enhanced replication in porcine alveolar macrophages but no difference regarding IFN-α or TNF-α responses. Later, a new strain (strain 2, 83.3 per cent similarity to strain 1) emerged and led to incidence resurgence because of the low cross reactivity with the previous antibodies. The study highlights PRRSV's rapid adaptability and challenges in controlling its spread, underscoring the necessity for more effective vaccines and eradication approaches.