Recombination in Strains of PRRSV | CDC EID

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Volume 15, Number 12–December 2009
Dispatch
Recombination in Vaccine and Circulating Strains of Porcine Reproductive and Respiratory Syndrome Viruses
Bin Li, Liurong Fang, Zuofei Xu, Suyan Liu, Jianfeng Gao, Yunbo Jiang, Huanchun Chen, and Shaobo Xiao
Author affiliation: Huazhong Agricultural University, Wuhan, People's Republic of China

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Abstract
Em2007, a porcine reproductive and respiratory syndrome virus (PRRSV) variant with a unique 68 aa deletion in Nsp2, was recently isolated in China. Phylogenetic and molecular evolutionary analyses indicated that Em2007 is a natural recombinant between a vaccine strain of PRRSV and circulating virus. We also tested its pathogenicity in piglets.

Porcine reproductive and respiratory syndrome (PRRS) is now considered one of the most economically important diseases in countries with intensive swine industries. The causative agent, PRRS virus (PRRSV), is a member of the family Arteriviridae (1). The genome of PRRSV is ≈15 kb and encodes 9 open reading frames (ORFs). Two distinct genotypes of PRRSV share only ≈60% nucleotide identity and are represented by the North American prototype VR-2332 and the European prototype Lelystad virus (LV) (2). Sequence differences have also been found among isolates of the same genotype, particularly in the Nsp2 regions within ORF1a, and ORF5 (3). Mutation and genetic recombination play an important role in the evolution of PRRSV (4–6).

Since May 2006, porcine high fever syndrome, caused by highly pathogenic PRRSV and characterized by high fever and high death rates in pigs of all ages, has emerged in China and affected >20 million pigs (7–9). Genomic analysis showed that nearly all of the emerging highly pathogenic PRRSVs isolated from this outbreak share a unique discontinuous deletion of 30 aa in Nsp2 (7–10). However, a novel PRRSV variant, with a 68 aa deletion in Nsp2, emerged in central China in 2007. We report the unique genetic characteristics of this novel variant and its pathogenicity in piglets.

The Study
At the end of 2007, a smaller cDNA fragment than the expected size was observed from a fetal piglet when a diagnostic reverse transcription–PCR (RT-PCR) was performed to amplify the unique genetic marker of the highly pathogenic PRRSV, indicating that a novel PRRSV variant was found. This strain, designated Em2007, was subsequently isolated and the full-length genomic sequence was determined. The genome of Em2007 was 15,272 bp, including the poly(A) tail (GenBank accession no. EU262603), and shared 87.6% and 57.9% sequence identity with VR-2332 and LV, respectively, indicating that Em2007 belongs to the North American genotype. The Nsp2 gene of Em2007 was 2,736 bp and encoded 912 aa, with a unique continuous deletion of 68 aa at positions 499–566, relative to strain VR-2332 (Technical Appendix [ 2.22 MB, 3 pages]). This unique deletion is substantially different from previous PRRSV isolates with deletions in Nsp2 (3,7–11).

To establish the genetic relationships of Em2007, we constructed phylogenetic trees using the neighbor-joining method based on the full-length genome. Results showed that Em2007 formed a minor branch, which was located in the middle of 2 clusters represented by CH-1a (the first PRRSV isolated in China in 1996) and JXA1 (the highly pathogenic PRRSV isolated in China in 2006), respectively (data not shown).

We also compared the sequence identity of individual Em2007 ORFs with representative PRRSV isolates and found that all ORFs have highest identity (>92%) with CH-1R (an attenuated vaccine strain used in China), except for Nsp2 (80.2%). Because recombinations have been reported in PRRSV in previous studies (6), we speculated that Em2007 is a mosaic. To test our hypothesis, we used 3 approaches to detect possible recombination events within Em2007.

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