Genetic diversity of the carp oedema virus in France

Carp edema virus surveillance in the koi trade: early detection through shipping environment sampling and longitudinal monitoring of CEV outbreaks in a wholesaler facility

Carp edema virus (CEV), a member of the Poxviridae family, has been a significant pathogen in koi and common carp since its initial identification in Japan during the 1970s. CEV, the causative agent of Koi Sleepy Disease (KSD), can cause high mortality rates and has been reported in many countries and is often linked to the fish trade. The virus is typically detected through DNA analysis of gill tissues, where the highest viral loads are found. However, traditional sampling methods, such as gill sampling, are lethal, complicating routine surveillance, particularly in asymptomatic or high-value koi. This study aimed to evaluate nonlethal sampling methods for CEV surveillance in the koi trade. We analysed various shipping environment samples, such as shipping water and fish bag swabs, alongside gill swabs from anaesthetised fish and gills from naturally deceased fish. Using qPCR, we found that the sensitivity of environmental samples, particularly shipping water, was greater than that of direct fish samples. Latent class modelling estimated that the sensitivity associated with 1.5 mL shipping water samples was greater than 89%, making them a reliable alternative for early detection. All detected variants belonged to genogroup II. Some post-import outbreaks shared variants with earlier outbreaks or shipping environment samples, suggesting that the detected DNA generally reflected infectious particles rather than just free environmental DNA and indicating that CEV can go unnoticed for several months after importation. These findings highlight the utility of environmental samples for effective, non-invasive surveillance and improved biosecurity management in the koi trade.

cds46, a highly variable carp edema virus gene

Carp edema virus disease (CEVD) is a severe viral illness that causes substantial economic losses in wild and farmed common carp and koi. It is caused by carp edema virus (CEV), a member of the Poxviridae family, whose genetic diversity and genome evolution are poorly understood. Based on a genomic fragment of the 4a gene, two genogroups, genogroup I (gI) and genogroup II (gII), have been identified in samples of different origins. By analysing a series of recent samples, we highlight here a new genomic region of interest that varies by substitutions, indels and putative recombinations. In the Japanese reference sequence, this region encodes an ORF, cds46, whose function is unknown despite weak homologies with genes of some members of the Iridoviridae. Surprisingly, AlphaFold protein structure prediction analyses link cds46-encoded ORF with cellular endonucleases, providing insights into its possible origin. The ORF is absent in all gI haplotypes and in some gII haplotypes. Apart from the absence of cds46, gI haplotypes show an insertion of 121 bp with no homology to any viral sequence. When present, cds46 showed two groups of alleles differentiated by substitutions. The analysis of the cds46 locus showed that some samples from fish batches contained mixes of different haplotypes, irrespective of their origin (i.e. France, Japan or Israel). In a 2023 sample, we also found a virus carrying a gII-like atypical 4a allele first identified in France in 2015, indicating the limited but persistent spread of this virus in the country. The cds46 locus is a new target that may be useful for identifying and tracking CEV haplotypes.

Characteristics of pathology and transcriptome profiling reveal features of immune response of acutely infected and asymptomatic infected of carp edema virus in Koi

Koi sleepy disease (KSD) is a high mortality and infection viral disease caused by carp edema virus (CEV), which was a serious threat to aquaculture of common carp and export trade of Koi worldwide. Asymptomatic infection is an important cause of the difficulty in preventing KSD and its worldwide spread, because asymptomatic infection can be activated under appropriate condition. However, the understanding of the molecular correlates of these infections is still unknown. The purpose of this study was to compare the pathology change, enzyme activity, immunoglobulin activity, host and viral gene expression differences in acutely infected and cohabiting asymptomatic Koi infected with CEV. Healthy Koi were used as a control. The gross pathology, histopathology and ultrastructural pathology showed the difference and characteristics damage to the tissues of Koi under different infection conditions. Periodic Acid-Schiff stain (PAS), enzyme activity and immunoglobulin activity revealed changes in the immune response of gill tissue between acutely infected, asymptomatic infected and healthy Koi. A total of 111 and 2484 upregulated genes and 257 and 4940 downregulated genes were founded in healthy Koi vs asymptomatic infected Koi and healthy Koi vs acutely infected Koi, respectively. Additionally, 878 upregulated genes and 1089 downregulated genes were identified in asymptomatic vs. acutely infected Koi. Immune gene categories and their corresponding genes in different comparison groups were revealed. A total of 3, 59 and 28 immune-related genes were identified in the group of healthy Koi vs asymptomatic infected Koi, healthy Koi vs acutely infected Koi and asymptomatic infected Koi vs acutely infected Koi, respectively. Nineteen immune-related genes have the same expression manner both in healthy Koi vs acutely infected Koi and asymptomatic Koi vs acutely infected Koi, while 9 immune-related genes were differentially expressed only in asymptomatic Koi vs acutely infected Koi, which may play a role in viral reactivation. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative reverse transcription PCR (RT-qPCR), and the results were consistent with the RNA-Seq results. In conclusion, the data obtained in this study provide new evidence for further elucidating CEV-host interactions and the CEV infection mechanism and will facilitate the implementation of integrated strategies for controlling CEV infection and spread.