Genetic characterization of 11 porcine reproductive and respiratory syndrome virus isolates in South China from 2014 to 2015

Abstract

BackgroundPorcine reproductive and respiratory syndrome (PRRS) has leaded to an enormous loss per year to the swine industry, its etiology porcine reproductive and respiratory syndrome virus (PRRSV) is a highly mutated virus in pigs. To fully understand the genetic characteristics of PRRSV genome in South China, this study collected the lung samples infected with PRRSV in Guangdong and Hainan province from 2014 to 2015 and tried to isolate the PRRSV. Finally, the complete genomes of isolated strains were sequenced and analyzed.MethodsVirus isolation was performed in MARC-145 cells. The 13 fragments of PRRSV genome were amplified by RT-PCR and the complete PRRSV genome sequence was obtained by SeqMan program of DNASTAR7.0 software. Nucleotide and deduced amino acid (AA) sequences of NSP2 and ORF5 were aligned using the MegAlign program of DNASTAR7.0 software to determine sequence homology. A phylogenetic tree was constructed using MEGA5.2 software with the neighbor-joining method to analyze the evolutionary relationship.Results11 PRRSV strains were isolated in South China from 2014 to 2015. All the isolated strains clustered into subgenotype V along with the HP-PRRSV representative strains JXA1, HuN4 and JXwn06. The subgenotype V was furtherly divided into two groups. AA sequence alignment analysis indicated that all the isolated strains had 1 AA deletion and 29 AA continuous deletion at position 481 and 533-561. Notably, GDHY strain had another 120 AA continuous deletion at position 629-748. All the isolated strains had an A137S mutation in the residue A137 of GP5 which was considered to differentiate vaccine strains. All the isolated strains had a L39I mutation in the primary neutralizing epitope (PNE) of GP5. Except GDHZ had a N34T mutation, all the other isolated strains had conserved N30, N44 and N51 glycosylation sites in the four potential N-glycosylation sites (N30, N34, N44 and N51) of GP5.ConclusionsOur study showed that the prevalent strains in this region were highly pathogenic PRRS virus-like. Moreover, one new strain having another 120 amino acids continuous deletion except the discontinuous 30 (29+1) amino acids deletion in NSP2 region had emerged. Besides, the isolated strains had extensive amino acids substitutions in the putative signal, extravirion and intravirion regions of GP5. These results showed that PRRSV has undergone extensive variation in South China, providing some theoretical basis for researching effective vaccince to better controling the PRRSV in this area.

Identification of Two Porcine Reproductive and Respiratory Syndrome Virus Variants Sharing High Genomic Homology but with Distinct Virulence

“…Notably, our isolates have same additional 120 amino acid deletion at positions 628 to 747 of nsp2 . BLAST and phylogenetic analyses showed that at least 11 highly homologous viruses with the new genetic feature have been isolated in different regions of China from 2012 to 2017 [38,39,40]. These variants form a new branch within the HP-PRRSV subtype, suggesting that a new group of HP-PRRSV variants is circulating in Chinese swine herds for a long time.…”

The emergence of a highly pathogenic porcine reproductive and respiratory syndrome virus with additional 120aa deletion in Nsp2 region in Jiangxi, China

“…Table shows that variation in the region of Nsp2 that is nonessential for virus replication is the main factor contributing to genetic diversity of the PRRSV genome. Moreover, BLAST analysis showed that there were similar strains isolated in Xinjiang and Guangdong Province, but the pathogenicity of the isolated strains is not known (Xia et al., ; Yu et al., ).…”

Research progress in the development of porcine reproductive and respiratory syndrome virus as a viral vector for foreign gene expression and delivery

“…The nsp2-encoding region is highly diverse and variable in the PRRSV genome, where substitutions, deletions and insertions usually occur naturally [45] . In particular, gene deletions in the nsp2 hypervariable region often appeared in the field isolates or in vitro cultures of PRRSV, such as the representative PRRSV isolates NADC30-like, Em2007 and GDHY from China, and MN184 from the United States [46][47][48][49][50] . These isolates contain an over 30-amino acid (aa)-deletion in the nsp2 region relative to the North American prototype strain VR-2332 [46][47][48][49][50] .…”