Genetic characterization of a novel recombinant PRRSV2 from lineage 8, 1 and 3 in China with significant variation in replication efficiency and cytopathic effects

There are four major porcine reproductive and respiratory syndrome virus 2 (PRRSV2) lineages circulating in China based on classification system, including lineages 1 (NADC30‐like), 3 (QYYZ‐like), 5.1 (VR2332‐like) and 8 (JXA1‐like/CH‐1a‐Like), which leads to the potential recombination. In the present study, a novel variant of PRRSV2 strain named JS18‐3 was isolated from piglets suffering severe breathing difficulties in Jiangsu Province of China in 2018. Full‐length genome analysis indicated that JS18‐3 shared 86.5%, 87.9%, 84.2%, 82.2% and 86.4% nucleotide similarity with PRRSVs CH‐1a, JXA1, VR2332, QYYZ and NADC30, respectively. 4871–6635 of JS18‐3 shared the highest identity of 99.3% in nucleotide sequence with HP‐PRRSV representative strain JXA1 indicating ongoing evolution to HP‐PRRSV. JS18‐3 was classified into classical lineage 8 of PRRSV2 based on phylogenetic analysis of complete genome and ORF5. Genomic break points in structural (ORF3) and non‐structural (NSP2, NSP3) regions of genomes were detected in recombination analysis. JS18‐3 is a recombinant isolate from lineages 8, 1 and 3. Replication enhancement and severe cytopathic effects caused by JS18‐3 were observed in Marc‐145 cells and porcine alveolar macrophages (PAMs) as compared to JX07, a typical strain of lineage 8. Pathogenicity results indicated that piglets inoculated with JS18‐3 presented persistent fever, dyspnoea, serious microscopic lung lesions and lymph node congestion. The study suggests that lineage 8 of PRRSV2 is involved in continuing evolution by genetic recombination and mutation leading to outbreaks in vaccinated pigs in China.