Prevalence and genetic evolution of porcine reproductive and respiratory syndrome virus in commercial fattening pig farms in China

Abstract

Background: To investigate the prevalence and evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) at commercial fattening pig farms, a total of 1397 clinical samples were collected from a single fattening cycle at seven pig farms in five provinces of China from 2020 to 2021.

Results: The RT‒PCR results revealed that PRRSV was present on all seven farms, and the percentage of PRRSV-positive individuals was 17.54-53.33%. A total of 344 partial NSP2 gene sequences and 334 complete ORF5 gene sequences were obtained from the positive samples. The statistical results showed that PRRSV-2 was present on all seven commercial fattening farms, and PRRSV-1 was present on only one commercial fattening farm. A total of six PRRSV-2 subtypes were detected, and five of the seven farms had two or more PRRSV-2 subtypes. L1.8 (L1C) PRRSV was the dominant epidemic strain on five of the seven pig farms. Sequence analysis of L1.8 (L1C) PRRSV from different commercial fattening pig farms revealed that its consistency across farms varied substantially. The amino acid alignment results demonstrated that there were 131 aa discontinuous deletions in NSP2 between different L1.8 (L1C) PRRSV strains and that the GP5 mutation in L1.8 (L1C) PRRSV was mainly concentrated in the peptide signal region and T-cell epitopes. Selection pressure analysis of GP5 revealed that the use of the PRRSV MLV vaccine had no significant episodic diversifying effect on L1.8 (L1C) PRRSV.

Conclusion: PRRSV infection is common at commercial fattening pig farms in China, and the percentage of positive individuals is high. There are multiple PRRSV subtypes of infection at commercial fattening pig farms in China. L1.8 (L1C) is the main circulating PRRSV strain on commercial fattening pig farms. L1.8 (L1C) PRRSV detected at different commercial fattening pig farms exhibited substantial differences in consistency but similar molecular characteristics. The pressure on the GP5 of L1.8 (L1C) PRRSV may not be directly related to the use of the vaccines.

Fig. 1

Positive rate of PRRSV in commercial pig fattening farms. The dotted line represents the overall PRRSV-positive rate for the seven commercial farms

Fig. 2

Statistical analysis of PRRSV subtypes in seven commercial fattening pig farms. a The number of subtypes and the number of samples in each subtype. b Proportion of PRRSV subtypes. Subtypes are represented by different colours. The positive samples and percentage of L1.8 (L1C) PRRSV is shown at the top of the bar chart

Fig. 3

Molecular characteristics of NSP2 and GP5 of L1.8(L1C) PRRSV. a NSP2 deletion characteristics of L1.8(L1C) PRRSV on pig farms. The positions marked in the figure represent positions of the NSP2 amino acid sequence and refer to the position of ATCC VR2332. Purple indicates the NADC30-like PRRSV 131 aa characteristic discontinuous deletion. Additional aa deletions are indicated in sky blue, and their proportions are indicated on the right side of the sequence. b Alignment of full-length GP5 aa sequences of part-positive L1.8(L1C) PRRSV strains. Upper grey rectangles show antigenic regions (PNE—principal neutralizing epitope), and lower grey rectangles show biologically significant regions (Signal sequence; TM—transmembrane region). The rightmost digit of the aa sequence is the proportion of GP5 sequences with L1.8(L1C) molecular characteristics identical on a single farm. The aa mutation of L1.8(L1C) on a given pig farm are coloured differently than the reference strain. Positive selection sites are marked with red fivepointed stars

Fig. 4

Phylogenetic analysis based on the ORF5 gene of L1.8(L1C) PRRSV. Neighbour-joining trees based on ORF5 and bootstrap values at the nodes are based on 1000 replicates. L1.8(L1C) PRRSVS from different commercial fattening pig farms are represented in different colours