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Characterization of a circulating PRRSV strain by means of random PCR cloning and full genome sequencing

Jan Van Doorsselaere1*, Marc Geldhof2, Hans J Nauwynck2 and Peter L Delputte23

Author Affiliations

1 Department of Health Care and Biotechnology, KATHO Catholic University College of South-West Flanders, Wilgenstraat 32, 8800 Roeselare, Belgium

2 Department Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium

3 ProVaxs, Faculty of Medicine and Health, Ghent University, De Pintelaan 185 - 3K3, 9000 Gent, Belgium

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Virology Journal 2011, 8:160  doi:10.1186/1743-422X-8-160

Published: 10 April 2011


PRRS is a pig disease of major economic importance that causes respiratory and reproductive problems in pigs. Over the last years it has become clear that PRRSV heterogeneity is increasing. Consequently, this has a potential impact on diagnosis and strategies to counter this disease. The use of sequence-independent PCR techniques for the detection and characterization of PRRSV could be useful to bypass problems associated with the heterogeneity of this virus.

A random PCR cloning approach was tested for the characterization of PRRSV strain 07V063 of unknown genetic background that circulated on a Belgian farm. By using this approach, 7305 bp of sequence data were obtained, distributed randomly across the genome. Using RT-PCR with strain-specific primers, the full length sequence (15014 nt) was obtained. Phylogenetic relationships using ORF5 and ORF1a (NSP2) sequences showed that 07V063 was classified in type 1 subtype 1 and that 07V063 was genetically different from prototype Lelystad Virus (LV). 07V063 showed 87-93% aa identity with LV ORFs coding for structural proteins. Most variation (compared to LV) was noticed in Nsp2 (81% identity) with a deletion of 28 aa. This deletion was different from other known deletions in this ORF. In conclusion, it is shown that this random PCR cloning approach can be used for the characterization of new PRRSV strains of unknown genetic background.