Journal
VIRUSES-BASEL
Volume 10, Issue 6, Pages -Publisher
MDPI
DOI: 10.3390/v10060328
Keywords
porcine reproductive and respiratory syndrome virus; evolutionary; lineage; recombination
Categories
Funding
- Sichuan Public Welfare Scientific Research Institutes Basic Research Projects [SASA2018A01]
- Transformation Fund of Scientific and Technological Achievements of Scientific Research Institutes in Sichuan [2018YSZH0005]
- Special Finance of Sichuan [SASA2014CZYX009]
- Program for Pig Industry Technology System Innovation Team of Sichuan Province [sccxtd-004]
- Science and Technology Support Program of Sichuan [2016NYZ0042, 2016NYZ0026, 2016NZ0108, 2016NZ0006]
- Applied Basic Research Program of Science and Technology Department of Sichuan Province [2018JY0252]
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Recombination among porcine reproductive and respiratory syndrome viruses (PRRSVs) is thought to contribute to the emergence of new PRRSV variants. In this study, two newly emerged PRRSV strains, designated SCcd16 and SCya17, are isolated from lung tissues of piglets in Southwestern China. Genome comparative analysis reveals that SCcd16/SCya17 exhibit 93.1%/93.2%, 86.9%/87.0%, 85.3%/85.7%, and 83.6%/82.0% nucleotide similarity to PRRSVs JXA1, VR-2332, QYYZ and NADC30, respectively. They only exhibit 44.8%/45.1% sequence identity with LV (PRRSV-1), indicating that both emergent strains belong to the PRRSV-2 genotype. Genomic sequence alignment shows that SCcd16 and SCya17 have the same discontinuous 30-amino acid (aa) deletion in Nsp2 of the highly pathogenic Chinese PRRSV strain JXA1, when compared to strain VR-2332. Notably, SCya17 shows a unique 5-nt deletion in its 3'-UTR. Phylogenetic analysis shows that both of the isolates are classified in the QYYZ-like lineage based on ORF5 genotyping, whereas they appear to constitute an inter-lineage between JXA1-like and QYYZ-like lineages based on their genomic sequences. Furthermore, recombination analyses reveal that the two newly emerged PRRSV isolates share the same novel recombination pattern. They have both likely originated from multiple recombination events between lineage 8 (JXA1-like), lineage 1 (NADC30-like), and lineage 3 (QYYZ-like) strains that have circulated in China recently. The genomic data from SCcd16 and SCya17 indicate that there is on going evolution of PRRSV field strains through genetic recombination, leading to outbreaks in the pig populations in Southwestern China.
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