Editorial Open Access
Emergence of a Novel Subgroup Among the Isolates of North American Genotype Porcine Reproductive and Respiratory Syndrome Virus in China
Sheng-Nan Chen1, Man-Hua Tang1, Feng-Guo Wang1, Xiao-Jing Li1, Kang Wu1, Jian-Cong Ye1, Da- Xue Liang1, Man-Lin Luo1,3, Dong-Sheng He1,3, Shao-Lun Zhai2,3* and Rui-Ai Chen1,3*
1Guangdong Dahuanong Animal Health Products Co., Ltd., Xinxing 527400, China
2Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
3College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
*Corresponding author: Jan Svoboda, Institute of Molecular Genetics, Videnska 1083 Prague 6 CZ-142 20 Czech Republic, Tel: +420-224-310-238; Fax: +420-224-310-955; E-mail: svoboda@img.cas.cz
Received: May 12, 2014; Accepted: June 11, 2014; Published: July 04, 2014
Citation: Chen SN, Tang MH, Wang FG, Li XJ, Wu K, et al. (2014) Emergence of a Novel Subgroup Among the Isolates of North American Genotype Porcine Reproductive and Respiratory Syndrome Virus in China. J Virol Retrovirol 1(1), 2.
Abstract
Deng et al. published "Complete genome sequence of porcine reproductive and respiratory syndrome virus strain QY2010 reveals a novel subgroup emerging in China" and Lu et al. published "Complete genome sequence of a novel variant porcine reproductive and respiratory syndrome virus (PRRSV) strain: evidence for recombination between vaccine and wild-type PRRSV strains” in The Journal of Virology in 2012. In the above studies, two emerging PRRSV strains, QY2010 and GM2, were identified. Based on sequence analysis, both of them had similar genome characterization for classic North American (NA) genotype PRRSV, but they were different from classic NA PRRSV (Subgroup 1, 2, 3) and highly pathogenitic NA PRRSV (Subgroup 4). So, herein, QY2010 and GM2, should be divided into a new subgroup (Tentatively named as subgroup 5). The emergence of subgroup 5 made us understand more knowledge about molecular epidemiology and genetic diversity of PRRSV.

Keywords: Porcine reproductive and respiratory syndrome virus, North American genotype, Novel subgroup, China

Porcine reproductive and respiratory syndrome virus (PRRSV), a positive-strand RNA virus belonging to the family Arteriviridae, is a pathogen economically important to the world swine industries [1]. At present, according to genetical and antigenic differences, PRRSVs were divided into two genotypes, European (EU) genotype (genotype Ι) and North American (NA) genotype (genotype Π) [2, 3]. In China, since the first report in 1996, it caused huge economic losses for Chinese swine industries. It is worth mentioning that a novel PRRSV variant with 1+29 amino acid (aa) deletion brought out unprecedented losses in many geographical regions of China in 2006 [4]. To our knowledge, most Chinese isolates belong to the NA genotype and can be further classified into four subgroups based on the whole genome sequence [5, 6]. In 2011, EU PRRSV isolation and analysis was officially reported in the China mainland though partial sequences (such as B13, Ningbo42, FJ0603) of EU PRRSV isolated in mainland China was submitted to GenBank before that [7]. Up to now, both NA genotype PRRSV and EU genotype PRRSV coexisted in China, and even some novel viral strains emerged in the lastest years [7- 9].

The PRRSV isolates, QY2010 (GenBank Accession number: JQ743666) and GM2 (GenBank Accession number: JN662424), were almost simultaneously reported in a piglet with respiratory symptoms and a growing pig (10-week old) with severe respiratory problems, diarrhea, and poor growth in Guangdong province, China [8, 9]. Based on sequence analysis, both of them had almost the same genomic structure expect for ORF1b (QY2010: position from 7792 to 12174; GM2: position from 7801 to 12174). QY2010 and GM2 had much higher similarity (96.8%) than other 21 reference NA PRRSV isolates (84.0%-87.7% & 84.0%-87.9%) based on complete genome sequence. It was worth mentioning that QY2010 and GM2 had longer Nsp2 genes (3, 042 nucleotides) than other NA PRRSV isolates (varied from 2, 418 nucleotides to 2, 940 nucleotides). In Nsp2 region, they not only retained non-1+29 aa deletion for classic NA PRRSV, but also possessed 36 aa insertion in the downstream of 1+29 aa deletion region. Moreover, the phylogenetic tree was constructed based on their complete genome sequences using DNAStar 5.0 software (DNAStar Inc.). QY2010 and GM2 were clustered into the same branch (Figure 1). According to the subgroup definition in previous studies [5,6], they did not belong to four known subgroups. Therefore, herein, they should be divided into a new subgroup (Tentatively named as subgroup 5).

In summary, a novel subgroup (subgroup 5) emerged among the isolates of NA PRRSV in China. The isolate of QY2010, a member of the novel subgroup, was identified as a highly pathogenic PRRSV strain through animal experiments[8], which might be one cause of pig diseases clinically. At present questions remain such as where did they come from? How to control them? Whether did cross-protection exist with other classic vaccine strains? Up to now, we did not get more knowledge of the above issues. It is known that Nsp2 is highly variable region, notably,
Figure 1: Phylogenetic analysis of QY2010 and GM2 with other reference NA PRRSV isolates. The phylogenetic tree was constructed based on their complete genome sequences by using Clustal W method (defining unrooted trees) of DNAStar 5.0 software (DNAStar Inc.). Both QY2010 and GM2 PRRSV isolates were clustered into the same branch that belonged to North American (NA) genotype (a new subgroup 5). Note: HuN4 (GenBank No.: JQ743666), JXA1 (GenBank No.: EF112445), JXwn06 (GenBank No.: EF641008), NVDC-JS2-2011 (GenBank No.: JQ715698), YD (GenBank No.: JF748717), BJsy06 (GenBank No.: EU097707), NX06 (GenBank No.: EU097706), DC (GenBank No.: JF748718), NVDC-GD2-2011 (GenBank No.: JQ715697), HZ-31 (GenBank No.: KC445138), NJ-1106 (GenBank No.: JX880029), HK4 (GenBank No.: KF287134), HK12 (GenBank No.: KF287139), HK13 (GenBank No.: KF287140), HB-1 (GenBank No.: AY150312), HB-2 (GenBank No.: AY262352), CH-1R (GenBank No.: EU807840), BJ-4 (GenBank No.: AF331831), SD1-100 (GenBank No.: GQ914997), VR-2332 (GenBank No.: AY150564), PA8 (GenBank No.: AF176348).
both QY2010 and GM2 had longer sequences than others, which suggested that PRRSV had genetic diversity in genome level. Therefore, their emergence made us understand more knowledge about molecular epidemiology, pathogenicity and genetic diversity of PRRSV.
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