Genomic characteristics of NADC30-like PRRSV SD and HLJWK108-1711
SD and HLJWK108-1711 were isolated from two diseased pig farms in Shandong (2016) and Heilongjiang Province (2017), respectively. Phylogenetic analysis showed that Chinese NADC30-like PRRSV formed a relatively independent branch and was closely related to NADC30 and XW018 (both strains isolated in the United States) based on a total of 344 whole genomes of lineage 1 (Fig. 1A). Both SD and HLJWK108-1711 were classified into branches of NADC30-like PRRSV (L1.8/L1C) (Fig. 1A). The Nsp2 proteins of SD and HLJWK108-1711 had a discontinuous 131-amino acid (aa) deletion (111 aa at position 323-433, 1 aa at position 483 and 19 aa at position 504-522) (Fig. 1B). Recombination analysis revealed that both NADC30-like PRRSVs were recombinant viruses (SD: parental virus NADC30 and minor virus ATCC VR2332-like PRRSV; HLJWK108-1711: parental virus NADC30 and minor virus JXA1-like PRRSV) (Fig. 1C). The recombination breakpoints of SD were observed at positions 7365, 7661, 12305, and 12773 (ATCC-VR2332 positions 7762, 8058, 12702 and 13170). The breakpoints separated the HLJWK108-1711 genome into ten regions, where the positions located at 521, 631, 1065, 1310, 1810, 5183, 6367, 7488, 8443(JXA1 positions 524, 634, 1068, 1313, 1813, 5490, 6674, 7795 and 8750) (Fig. 1C). However, the genomic nucleotide similarity between SD-R and HLJWK108-1711 was 89.9%, and the nucleotide similarity of the skeleton section of NADC30 was only 91.4% (Table 1). The nucleotide and amino acid similarity among different genes between SD-R and HLJWK108-1711 were 82.7-97.7% and 80.2-100%, respectively (Table 1).