Base composition and adaptation of duck and goose circovirus for original and cross-host strains via codon-based investigation

With the emergence of cross-species transmission, Duck circovirus (DuCV) and Goose circovirus (GoCV) exhibit high prevalence in ducklings and goslings, posing a significant threat to poultry health. To further investigate the host adaptation of DuCV and GoCV, we conducted codon usage bias and host adaptation analysis across five different poultry hosts. It was revealed that the Capsid protein (CAP) of both DuCV and GoCV preferentially utilizes codons ending in A, with this codon preference primarily influenced by selective pressure. Principal Co-ordinates Analysis (PCoA) showed that the synonymous codon usage pattern (CUP) among the GoCV strains exhibited smaller differences both on Replication protein (REP) and CAP, larger divergences in synonymous CUPs were observed among the three DuCV genotypes (DuCV-1∼3). Moreover, the codon preference of DuCV-3-REP was more similar to GoCV compare to DuCV-1 and DuCV-2. GoCVs identified in duck had the highest Codon Adaptation Index (CAI) among the five different hosts compared to goose originated GoCVs. These findings provide valuable insights into the understanding of avian circovirus and have potential implications for developing effective control measures and vaccines.