Phylogenetic analysis and molecular characteristics of 17 porcine reproductive and respiratory syndrome virus isolates in Southern China from 2010 to 2011

Zhang, Minze; Xie, Jiexiong; Sun, Long; Cao, Zanxia; Gu, Honglang; Deng, Shulin; Chen, Yao; Cao, Zongxi; Tang, Fengfeng; Su, Shuo; Zhang, Guihong

doi:10.1016/j.micpath.2013.09.005

Cited by 8 publications

(6 citation statements)

References 21 publications

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“…Comparing the NSP2 amino acid sequence of the 11 isolated strains with the reference strains VR-2332 and CH-1a, the NSP2 region of 10 isolated strains had 30 AA discontinuous deletion, including 1 AA deletion at position 481 and 29 AA continuous deletion at position 532 to 560. The result was identical with other Chinese isolated HP-PRRSV strains since 2006 [26]. Moreover, 1 strain GDHY had an another 121 AA continuous deletion at position 630 to 750 in NSP2 region, which was completely different from the previous reports (4–7, 17, 26).…”

Section: Discussionsupporting

confidence: 75%

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

Zhao

Dong

et al. 2017

Virol J

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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.

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Section: Discussionsupporting

confidence: 75%

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

Zhao

Dong

et al. 2017

Virol J

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“…2, there were 44 JXA1-R-like strains, which included the 10 potential JXA1-R-like strains in this study and seven reported strains in China (NT1, NT2, NT3, 11NZ-GD, 11XX-GD, 11SH1-GD, and 11SH-GD) [23, 27]. These 27 Chinese strains were deposited in the GenBank database because they shared the highest nucleotide identities with JXA1-R strains (>99%) (Additional file 3: Table S3) and contained 6–11 amino acids unique to JXA1-R (Additional file 4: Figure S1).…”

Section: Resultsmentioning

confidence: 86%

“…The virulence reversion of the vaccine strain JXA1-R has been described [23, 27], but no recombination of this strain has yet been reported. Recombination analyses showed that 10 strains, which included nine strains from the present study and one isolate retrieved from the GenBank database, evolved through complicated recombination events between vaccine JXA1-R-like strains and predominant circulating strains in China.…”

Section: Discussionmentioning

confidence: 99%

“…Viral RNA purification from lung tissues and cDNA synthesis were performed as described previously [26], and PCR amplification of 14 fragments covering the PRRSV genome was performed with primers described in a previous report with minor modifications [27] (Additional file 1: Table S1). The quality of the PCR products was confirmed by electrophoresis on a 1% agarose gel and then purified using the PureLink Quick Gel Extraction Kit (Life Technologies).…”

Section: Methodsmentioning

confidence: 99%

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Emergence of mosaic recombinant strains potentially associated with vaccine JXA1-R and predominant circulating strains of porcine reproductive and respiratory syndrome virus in different provinces of China

Zhao

Han

Zhang

et al. 2017

Virol J

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BackgroundPorcine reproductive and respiratory syndrome virus (PRRSV) has caused several outbreaks in China since 2006. However, the genetic diversity of PRRSV in China has greatly increased by rapid evolution or recombination events. Modified live-attenuated vaccines are widely used to control this disease worldwide. Although the risk and inefficacy of the vaccine has been reported, the genetic diversity between epidemic field strains and vaccine strains in China has not been completely elucidated.MethodsA total of 293 clinical samples were collected from 72 pig farms in 16 provinces of China in 2015 for PRRSV detection. A total of 28 infected samples collected from 24 pig farms in nine provinces were further selected for immunohistochemical analysis and whole genome sequencing of PRRSV. Phylogenetic analysis and recombination screening were performed with the full genome sequences of the 28 strains and other 623 reference sequences of PRRSV.ResultsOf 293 clinical samples, 117 (39.93%) were positive for PRRSV by RT-PCR. Phylogenetic results showed that the 28 strains were nested into sublineage 10.5 (classic highly pathogenic [HP]-PRRSV), sublineage 10.6 (HP-PRRSV-like strains and related recombinants), sublineage 10.7 (potential vaccine JXA1-R-like strains), and lineage 9 (NADC30-like strains and recombinants of NADC30-like strains), respectively, suggesting that multiple subgenotypes of PRRSV currently circulate in China. Recombination analyses showed that nine of 28 isolates and one isolate from other laboratory were potential complicated recombinants between the vaccine JXA1-R-like strains and predominant circulating strains.ConclusionsThese results indicated an increase in recombination rates of PRRSV under current vaccination pressure and a more pressing situation for PRRSV eradication and control in China.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0735-3) contains supplementary material, which is available to authorized users.

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“…Nsp2 is the largest non-structural protein cleavage from a polyprotein (Snijder E J, et al, 1995;Zhang M, et al, 2013). Nsp2 has been recognized as the most variable region within the PRRSV genome (Allende R, et al, 1999;Yoshii M, et al, 2008;Zhou Y, et al, 2012;Wang F X, et al, 2013).…”

Section: Hp-prrsv Isolates Were the Dominant Virus Isolates During 20mentioning

confidence: 99%

Analysis of molecular variation in porcine reproductive and respiratory syndrome virus in China between 2007 and 2012

et al. 2014

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In the present study, 89 porcine reproductive and respiratory syndrome virus (PRRSV) isolates in China during 2007 to 2012 were randomly selected from the GenBank genetic sequence database. Evolutionary characteristics of these isolates were analyzed based on the sequences of non-structural protein 2 (Nsp2) and glycoprotein 5 (GP5). The genetic variations of the isolates were also compared with six representative strains. The results showed that a high degree of genetic diversity exists among the PRRSV population in China. Highly pathogenic PRRSV isolates, with a discontinuous deletion of a 30 amino acid residue in the Nsp2 region, remained the most dominant virus throughout 2007-2012 in China. Owing to the extensive use of representative vaccine strains, natural recombination events occurred between strains. Three isolates - HH08, DY, and YN-2011 - were more closely related to vaccine strains than the other isolates. Both YN-2011 and DY were the evolutionary products of recombination events between strains SP and CH-1R. The results of the present study provide useful information for the epidemiology of PRRSV as well as for vaccine development.

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Phylogenetic analysis and molecular characteristics of 17 porcine reproductive and respiratory syndrome virus isolates in Southern China from 2010 to 2011

Cited by 8 publications

References 21 publications

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

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

Emergence of mosaic recombinant strains potentially associated with vaccine JXA1-R and predominant circulating strains of porcine reproductive and respiratory syndrome virus in different provinces of China

Analysis of molecular variation in porcine reproductive and respiratory syndrome virus in China between 2007 and 2012

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