Genetic evolution of porcine reproductive and respiratory syndrome virus based on ORF5 on 7 Taiwanese pig farms

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus with high genetic variation. Open
reading frame 5 (ORF5) is the most suitable genomic region for the identification of strains that have previously
circulated on a farm. Herein, 30 ORF5 sequences from 7 Taiwanese pig farms (A, E, F, H, L, S, U) were collected from
2002 to 2014 for analysis of the within-herd genetic evolution of PRRSV analysis. VR-2332, Lelystad, and MD001
(Taiwanese prototype) were selected as reference strains. Nucleotide sequences showing an identity of less than 97%
and belonging to different clusters than last isolate from the same farm were considered to represent exotic strains. Our
results showed that the identities of these isolates to VR-2332, Lelystad, and MD001 were 84.9-88.4%, 62.1-65.3%, and
85.9-89.6%, respectively. All of these studied strains belonged to PRRSV type II and evolved separately. Two nucleotide
sequences from Farm A collected 10 years apart showed 95.5% identity but belonged to the same cluster and were
considered to be the same strain endemic to the farm. On the other 6 farms, at least 1 exotic strain was detected during
this period. We concluded that in the area, the spread and new invasions of exotic PRRSV strains at the farm level are
common events in Taiwan.