Complete Genome Characterization of Canine Adenovirus From Türkiye With Next-Generation Sequencing

Abstract

Background: Determining the complete genome sequence data of adenoviruses has recently become greatly important due to their use by scientists as vectors in cancer studies and other fields, including vaccine development. However, the GenBank database currently has few complete genome sequences of adenoviruses, which are known for their large genomes. To address this gap, we analysed next-generation sequencing data obtained from our previous study to provide the complete genome sequence of the canine adenovirus-2 strain.

Methods: For the obtained canine adenovirus-2 strain (OQ596341), comparative genomics, recombination and phylogenetic analysis were conducted. This sequence was compared and phylogenetically analysed with the 20 complete genome sequences of canine adenovirus previously reported in GenBank worldwide, as well as partial E3 ORFA sequences obtained from Türkiye.

Results: The nucleotide similarity rates of the sequence obtained from this study with other CAdV-2 whole genomes are over 99.04%. The gene alignment results reveal that the OQ596341 was found to be closely related to the AC000020 reference genome and LC557011. There are two recombination events related to the genome in this study. Comparisons with other complete genome sequences revealed several previously unseen mutations. These mutations include H34Y in the E1A gene; P55A in the E1B 55K gene; D13N and D202N in the IVa2 gene; K679R, V934I and K989N in the Pol gene; E205K in the pTP gene; T455A in the pIIIa gene; A310V in the V gene; G151R in the protease gene; E268K in the 100K gene; G66S and G141S in the 33K gene; T14A, E250K, D287N and I293T in the E3 ORFA gene; and L193F in the E434K gene. Moreover, a comparison with partial sequences obtained from Türkiye revealed the E250K mutation in the E3 ORFA gene, which we report for the first time in Türkiye.

Conclusions: The complete CAdV-2 genome sequence obtained in the present study is the first sequence from Europe. Comparative analysis with other genomes revealed some unique mutations. This study is the first to report the E250K amino acid change in the E3 ORFA gene in Türkiye. We anticipate that this data can be used in future CAdV-2 vaccine development studies. Further studies are recommended to evaluate the impact of these mutations on viral tropism and other host interactions.

Keywords: Türkiye; canine adenovirus; dog; genome; next‐generation sequencing.

FIGURE 1

The genome alignment of eight CADV genomes obtained from dogs worldwide by Clinker (CAGECAT). Coding sequences are indicated by arrows. Genes are colour coordinated, with the same colours representing homologous genes. The colour variation from black to white between homologous genes indicates amino acid identity.

FIGURE 2

This phylogenetic tree was constructed using all the complete genome sequences of canine adenoviruses uploaded to GenBank to date. The tree was created using the neighbour‐joining method, with 1000 bootstrap replicates and the p‐distance parameter model in MEGA X. The reference strain is indicated by a red‐filled triangle, and the complete genome obtained from this study is indicated by a green‐filled square.

FIGURE 3

This phylogenetic tree was constructed using all the canine adenovirus sequences uploaded to GenBank from Türkiye to date. All the sequences uploaded from Türkiye are partial sequences of the E3 ORFA gene region. Only the E3 ORFA gene region of the complete genome sequence obtained from this study was used in the tree construction. The tree was created using the neighbour‐joining method, with 1000 bootstrap replicates and the p‐distance parameter model in MEGA X. The reference strain is indicated by a red‐filled triangle, and the complete genome obtained from this study is indicated by a green‐filled square.