Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

Abstract

Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host’s ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.

Evolutionary Analysis of a Parrot Bornavirus 2 Detected in a Sulphur-Crested Cockatoo (Cacatua galerita) Suggests a South American Ancestor

“…One strategy for viral phylogenetic analysis involves concatenating sequences from two or more genes, which enhances the phylogenetic signal compared to studies based on individual genes or entire genomes. This approach increases the statistical power of molecular evolution analysis and improves the accuracy of phylogenetic trees by providing a larger number of substitutions [ 35 , 36 , 37 , 38 ]. Several phylogenetic studies on avian bornaviruses have included partial N and M genes separately, as these are the most abundant available sequences for PaBVs [ 15 , 16 , 39 , 40 , 41 ].…”

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family

“…Despite the ICTV approach being traditional and widely used, we applied an additional method to obtain a more accurate phylogenetic tree with a higher resolution. For this, we applied the approach described in [52] with the only difference being that we used whole genome sequences to construct an alignment. Since the genome of the TsCV is extremely divergent from all other known representatives of the family, we used sequences belonging only to the closest relatives of the TsCV virus.…”

“…We used three approaches that propose de novo species partitions to confirm the species status of the TsCV virus as described previously in [52]: the GMYC [53], bPTP [54] and ASAP [55] methods. Calculations have been carried out for the ICTV set of representative genomes of the Caliciviridae family (Table A2), supplemented with genome sequences of unclassified caliciviruses that are most closely related to TsCV (Table A3).…”