Molecular characterization of emerging variants of PRRSV in the United States: new features of the -2/-1 programmed ribosomal frameshifting signal in the nsp2 region

In this study, we characterized an emerging porcine reproductive and respiratory syndrome virus (PRRSV) isolate UIL21-0712, which is a lineage 1C variant with ORF5 restriction fragment length polymorphism (RFLP) cutting pattern of 1-4-4. The UIL21-0712 genome sequence has 85.3% nucleotide identity with the prototypic PRRSV-2 strain VR2332. The nsp2 region is the most variable, and the -2/-1 programmed ribosome frameshifting (PRF) signal therein is distinct from historical PRRSV strains. Analysis of PRRSV sequences in GenBank revealed that the majority of the emerging PRRSV variants contain substitutions that disrupt the -1 PRF stop codon to generate a nsp2N protein with a C-terminal extension. Two of the -1 PRF stop codon variant patterns were identified to be predominantly circulating in the field. They demonstrated higher growth kinetics than the other variants, suggesting that the most dominant -1 PRF stop codon variant patterns may provide enhanced growth fitness for the virus. •An emerging PRRSV RFLP1-4-4 L1C variant was isolated and characterized in cell culture.•The unique -1 PRF signal sequences express the PRRSV nsp2N protein with C-terminal extension.•The most dominant -1 PRF stop codon variants may provide enhanced growth fitness for the virus in the field.