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Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing

Zen H Lu1, Alexander Brown1, Alison D Wilson1, Jay G Calvert2, Monica Balasch3, Pablo Fuentes-Utrilla4, Julia Loecherbach4, Frances Turner4, Richard Talbot4, Alan L Archibald1 and Tahar Ait-Ali1*

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK

2 Zoetis Inc.,Global Biologics Research, 333 Portage St, Kalamazoo, MI 49007, USA

3 VMRD Olot Zoetis, Ctra. EU Regional Vaccines Group, Camprodon s/n Finca "La Riba", 17813 Vall de Bianya, Girona, Spain

4 Edinburgh Genomics, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK

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Virology Journal 2014, 11:42  doi:10.1186/1743-422X-11-42

Published: 4 March 2014



Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV.


We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5.


Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.

PRRSV; Microevolution; Variant spectra; Ultra-deep next generation sequencing