1887

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Volume 105, Issue 11

cds46, a highly variable carp edema virus gene Open Access

Abstract

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 family whose genetic diversity and genome evolution are poorly understood. Based on a genomic fragment of the 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 . 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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carp , epidemiology , Poxviridae and sleepy disease
Funding
This study was supported by the:
  • European Maritime and Fisheries Fund
    • Principle Award Recipient: LaurentBigarré
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-11-20
2024-12-02
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cds46, a highly variable carp edema virus gene
J. Gen. Virol. 105, 002048 (2024); https://doi.org/10.1099/jgv.0.002048
/content/journal/jgv/10.1099/jgv.0.002048
/content/journal/jgv/10.1099/jgv.0.002048
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