Genome-Wide Characterization of QYYZ-Like PRRSV During 2018-2021.

In the last decade, the emergence of QYYZ-like porcine reproductive and respiratory syndrome virus (PRRSV) has attracted increasing attention due to the high incidence of PRRSV mutation and recombination. However, the endemic status and genomic characteristics of the QYYZ-like strains are unclear. From 2018 to October 2021, 24 QYYZ-like PRRSV isolates were obtained from 787 PRRSV-positive clinical samples. Only one QYYZ-like positive sample was from a northern province, and the rest were from central and southern provinces. We selected 9 samples for whole-genome sequencing, revealing genome lengths of 15,008-15,316 nt. We retrieved all the available whole-genome sequences of QYYZ-like PRRSVs isolated in China from 2010 to 2021 (n = 28) from GenBank and analyzed them together with the new whole-genome sequences (n = 9). Phylogenetic tree analysis based on the ORF5 gene showed that all QYYZ-like PRRSV strains belonged to sublineage 3.5 but were clustered into three lineages (sublineage 1.8, sublineage 3.5, and sublineage 8.7) based on whole-genome sequences. Genomic sequence alignment showed that QYYZ-like strains, have characteristic amino acids insertions or deletions in the Nsp2 region (same as NADC30, JXA1 and QYYZ) and that thirteen strains also had additional amino acid deletions, mostly between 468 and 518 aa. Moreover, QYYZ-like strains (sublineage 3.5) have seven identical characteristic amino acid mutations in ORF5. Recombination analysis revealed that almost all QYYZ-like complete genome sequences (36/37) were products of recombination and mainly provided structural protein fragments (GP2-N) for the recombinant strains. Overall, QYYZ-like strains were mainly prevalent in central and southern China from 2018 to 2021, and these strains provided recombinant fragments in the PRRSV epidemic in China.

Recombination between NADC34-like and QYYZ-like strain of porcine reproductive and respiratory syndrome virus with high pathogenicity for piglets in China.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that causes huge economic losses to the swine industry worldwide. Here, a novel variant of PRRSV strain named TJnh2021 was isolated from nursery piglets with morbidity rate (75%) and mortality rate (40%) in Tianjin Province of China in 2021. Phylogenetic and molecular evolutionary analyses revealed that TJnh2021 was highly similar to NADC34-like (lineage 1.5, isolated in North America in 2014) in the ORF1ab-ORF2 and ORF6-ORF7 coding regions, as well as to QYYZ-like (lineage 3, isolated in China in 2010) in the ORF3-ORF5, suggestive of a natural recombination event. Recombination analyses revealed that recombination events occurred in two interlineage recombination events between lineages 1.5 and 3, and two breakpoints in ORF2 (nt12196) and ORF5 (nt13628) (with reference to the VR-2332 strain). Animal experiments demonstrated that TJnh2021 caused mortality rates of 40% and exhibited higher pathogenicity in piglets compared to other lineage 1.5 strains reported in China. Taken altogether, NADC34-like PRRSV has undergone genetic exchange with Chinese local PRRSV strains and recombination might be responsible for the variations in pathogenicity and highlight the importance of surveillance of this lineage in China.

Recombination in lineage 1, 3, 5 and 8 of porcine reproductive and respiratory syndrome viruses in China.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important viral swine diseases, resulting in immense economic losses in Chinese pig industry. Currently, four major lineages: lineage 1 (NADC30-like), 3 (QYYZ-like), 5.1 (VR2332-like) and 8.7 (JXA1-like) of type 2 PRRSV (North American type) have been circulating in China based on classification system, which have caused concern about the potential of virus recombination. In the present study, a novel variant of PRRSV strain named FJLIUY-2017 was isolated from abortion rate (25%) in pregnant gilts in Fujian Province in China in 2017. To further our knowledge about the novel virus strain, we characterized the complete genome of FJLIUY-2017. Comparison to PRRS sequences in GenBank confirmed the absence of close relatives (<92%), but indicated FJLIUY-2017 belonged to NADC30-like PRRSV. The full length of FJLIUY-2017 was determined to be 15017 nucleotides (nt), excluding the poly(A) tail, shared 86.2-86.6% identity with JXA1-like strains (JXA1, TJ and FJYR), 88.9-90.6% with NADC30-like PRRSVs (NADC30, FJZ03 and CHsx1401), 86.4-86.5% with VR2332-like (VR2332, RespPRRS MLV and BJ-4) and only 60.8% with LV (European type). Recombination analyses revealed genomic breakpoints in structural (ORF3, ORF4 and ORF7) and nonstructural (Nsp1, Nsp2, Nsp6, Nsp9, Nsp11 and Nsp12) regions of the genomes with evidence for recombination events between lineages 1, 3, 5.1 and 8.7. Taken altogether, the results of our study provide further confirmation that PRRSV is prone to undergo recombination events. Thus, it is critical to monitor PRRSV evolution in China and establish an effective strategy for the control of PRRS.