RECOMBINATION IN NON-SEGMENTED, POSITIVE STRAND SALMON PANCREAS DISEASE VIRUS  

Evensen, O., Petterson, E., Guo, T.-Z., Mikalsen, A.
Norwegian University of Life Sciences, PO Box Dep., N-0033 Oslo, Norway; oystein.evensen@nmbu.no

Pancreas disease (PD) is a contagious viral disease in salmonid aquaculture in Europe and North America. PD is caused by salmon pancreas disease virus also referred to as salmonid alphavirus (SAV), which belongs to the genus alphavirus within the family Togaviridae. The alphavirus genome is a single positive-strand RNA of approximately 11.7 kb in length comprising two open reading frames (ORFs). The first ORF encodes the replicase polyprotein while the second ORF encodes viral structural proteins (Figure 1). Some RNA viruses that contain segmented genomes can undergo genetic evolution by reassortment of their segments. An additional mechanism involves exchange of genetic information between non-segmented RNAs, i.e. RNA-RNA recombination. The understanding is that the RNA-dependent RNA polymerase (RdRp) switches the template strand (copy-choice mechanism) and hold on to the nascent strand, thereby generating the hybrid RNA of mixed origins. Template switching occurs usually between two "homologous" RNAs at the crossover sites. From studies of SPDV infection of salmon (Salmo salar L.) under field conditions we have shown that deleted variants of the virus is generated in infected fish but the underlying mechanisms have not been known. By reverse genetics (generation of infectious clone) of SPDV (subtype 3) we performed co-infection in vitro and now also in vivo of individually defect viral genomes of SPDV that result in generation of replication competent virus strains that can be re-isolated from internal organs of injected fish and propagated in vitro. Further to this we also find generation of variants with deletion "spots" corresponding to what was found in field isolates of SPDV. This is the first documentation of an in vivo recombination of an alphavirus - across all susceptible species - and potentially brings explanation to the host range or host plasticity of SPDV.