Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)

Abstract

Marine bird populations have been declining globally with the factors driving this decline not fully understood. Viral diseases, including those caused by poxviruses, are a concern for endangered seabird species. In this study we have characterised a novel avipoxvirus, tentatively designated albatrosspox virus (ALPV), isolated from a skin lesion of an endangered New Zealand northern royal albatross (Diomedea sanfordi). The ALPV genome was 351.9 kbp in length and contained 336 predicted genes, seven of which were determined to be unique. The highest number of genes (313) in the ALPV genome were homologs of those in shearwaterpox virus 2 (SWPV2), while a further 10 were homologs to canarypox virus (CNPV) and an additional six to shearwaterpox virus 1 (SWPV1). Phylogenetic analyses positioned the ALPV genome within a distinct subclade comprising recently isolated avipoxvirus genome sequences from shearwater, penguin and passerine bird species. This is the first reported genome sequence of ALPV from a northern royal albatross and will help to track the evolution of avipoxvirus infections in this endangered species.

Keywords: avipoxvirus; complete genome; endangered; evolution; northern royal albatross.

Figure 1

Comparative genomic illustration of the novel ALPV. A sequence alignment using MAFFT in Geneious (version 10.2.2) was performed to compare ORFs between albatrosspox virus (ALPV, GenBank accession no. MW365933) and shearwaterpox virus 2 (SWPV2, GenBank accession no. KX857215). The arrows symbolise genes and open reading frames (ORFs), with orientation indicating their direction of transcription. Each gene or ORF is colour coded, as indicated by the key in the legend. The top graph represents the mean pairwise sequence identity over all pairs in the column between ALPV and SWPV2 (green: 100% identity; mustard: ≥30% and <100% identity; red: <30% identity).

Figure 2

Dot plots of the ALPV genome (x-axis) vs. other poxvirus genomes (y-axis). (A) ALPV vs SWPV2, (B) ALPV vs PEPV2, (C) ALPV vs CNPV, (D) ALPV vs MLPV, (E) ALPV vs SWPV1, (F) ALPV vs PEPV, (G) ALPV vs FGPV and (H) ALPV vs TKPV (refer to Table 2 for virus details and GenBank accession numbers). The Classic colour scheme was chosen in Geneious (version 10.2.2) for the dot plot lines according to the length of the match, from blue for short matches to red for matches over 100 bp long. Window size = 12.

Figure 3

Phylogenetic relationships between ALPV and other chordopoxviruses. A maximum likelihood (ML) tree was constructed from multiple alignments of the concatenated amino acid sequences of the selected nine poxvirus core proteins using CLC Genomic Workbench (version 9.5.4, CLC bio, a QIAGEN Company, Prismet, Aarhus C, Denmark). The numbers on the left show bootstrap values as percentages. The ML tree is displayed as a phylogram. The labels at branch tips refer to original ChPV GenBank accession numbers followed by abbreviated species names. Saltwater crocodilepox virus (SwCRV1) [36] was used as an outgroup. The position of the novel ALPV is highlighted using a purple box and the subclade relevant to ALPV is shown with pink shading.