Assessing tropism and genetic traits of carp oedema virus isolates to enhance detection strategies

Abstract

Abstract Introduction Carp oedema virus (CEV) is a relatively understudied poxvirus. It exhibits an affinity for gill and skin epithelial cells. Investigations were conducted into selected aspects of CEV biology, with a focus on determining cell and tissue tropism of CEV, acquiring gene sequences and updating CEV tests in fish tissues. Material and Methods A total of 238 common carp tissue samples from nine aquaculture farms were analysed. The study evaluated the efficacy of intermediate detection of CEV by real-time PCR and in situ hybridisation. The genes encoding protein P4a were sequenced, analysed and aligned in a phylogenetic tree using a molecular evolution model. Results In situ hybridisation revealed the necessity to validate the Centre for Environment, Fisheries and Aquaculture Science protocols for sampling for CEV detection and to use the tissues for which the virus has the highest tropism, namely the skin and kidneys, rather than solely the gills. The level of genetic variability was determined, and it was shown that CEV mutates systematically. The creation of two distinct phylogenetic clades confirms certain strains’ description as Polish isolates. Conclusion Determining the localisation of CEV genetic material in organs and tissues is pivotal for shaping the World Organisation for Animal Health guidelines. The utility of molecular diagnostics has been demonstrated in the skin and kidney of carp, in addition to the gills, impelling their inclusion in diagnostic protocols. The clusters identified in the phylogenetic tree offer valuable insights for developing the current PCR primers. The prevalence of CEV infection in aquaculture, juxtaposed with its notably lower detection in wild fish, underscores the significance of mandatory molecular diagnostic testing for CEV in carp farming.