Genomic Characterisation of a Highly Divergent Siadenovirus (Psittacine Siadenovirus F) from the Critically Endangered Orange-Bellied Parrot (Neophema chrysogaster)

Abstract

Siadenoviruses have been detected in wild and captive birds worldwide. Only nine siadenoviruses have been fully sequenced; however, partial sequences for 30 others, many of these from wild Australian birds, are also described. Some siadenoviruses, e.g., the turkey siadenovirus A, can cause disease; however, most cause subclinical infections. An example of a siadenovirus causing predominately subclinical infections is psittacine siadenovirus 2, proposed name psittacine siadenovirus F (PsSiAdV-F), which is enzootic in the captive breeding population of the critically endangered orange-bellied parrot (OBP, Neophema chrysogaster). Here, we have fully characterised PsSiAdV-F from an OBP. The PsSiAdV-F genome is 25,392 bp in length and contained 25 putative genes. The genome architecture of PsSiAdV-F exhibited characteristics similar to members within the genus Siadenovirus; however, the novel PsSiAdV-F genome was highly divergent, showing highest and lowest sequence similarity to skua siadenovirus A (57.1%) and psittacine siadenovirus D (31.1%), respectively. Subsequent phylogenetic analyses of the novel PsSiAdV-F genome positioned the virus into a phylogenetically distinct sub-clade with all other siadenoviruses and did not show any obvious close evolutionary relationship. Importantly, the resulted tress continually demonstrated that novel PsSiAdV-F evolved prior to all known members except the frog siadenovirus A in the evolution and possibly the ancestor of the avian siadenoviruses. To date, PsSiAdV-F has not been detected in wild parrots, so further studies screening PsSiAdV-F in wild Australian parrots and generating whole genome sequences of siadenoviruses of Australian native passerine species is recommended to fill the siadenovirus evolutionary gaps.

Keywords: Adenoviridae; evolution; next-generation sequencing; orange-bellied parrot; psittacine siadenovirus F; siadenovirus.

Figure 1

Schematic illustration of the selected siadenoviruses. Schematic map of the psittacine siadenovirus F (PsSiAdV-F, GenBank accession no. MW365934), in comparison with psittacine siadenovirus D (PsAdV-D; GenBank accession no. MN687905) and Skua siadenovirus A (SuAdV-A; GenBank accession no. HM585353) using CLC Genomic Workbench (version 9.5.4, CLC bio, a QIAGEN Company, Prismet, Aarhus C, Denmark). The arrows symbolise adenovirus genes and open reading frames (ORFs) predicted to code for proteins, indicating their direction of transcription. Each gene or ORF is colour coded, as indicated by the colour key in the legend.

Figure 2

Phylogenetic tree shows the possible evolutionary relationship of novel psittacine siadenovirus F with other selected AdVs. A maximum likelihood (ML) tree was constructed using concatenated amino acid sequences of the complete DNA-dependent DNA polymerase, pTP, penton, and hexon genes. Concatenated protein sequences were aligned with MAFTT (version 7.450) [33] in Geneious (version 20.0.3, Biomatters, Ltd., Auckland, New Zealand) under the BLOSUM62 scoring matrix and gap open penalty = 1.53. The gap > 20 residues were deleted from the alignments. The unrooted ML tree was constructed under the WAG substitution model, and 1000 bootstrap replicates were constructed using tools available in CLC Genomics Workbench (version 9.5.4, CLC bio, a QIAGEN Company, Prismet, Aarhus C, Denmark). The numbers on the left show bootstrap values as percentages, and the labels at branch tips refer to original host species followed by AdVs name and GenBank accession number in parentheses. The novel psittacine siadenovirus F is shown in the purple-coloured box.