Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Yellow-Eyed Penguin (Megadyptes antipodes)

Abstract

Emerging viral diseases have become a significant concern due to their potential consequences for animal and environmental health. Over the past few decades, it has become clear that viruses emerging in wildlife may pose a major threat to vulnerable or endangered species. Diphtheritic stomatitis, likely to be caused by an avipoxvirus, has been recognised as a significant cause of mortality for the endangered yellow-eyed penguin (Megadyptes antipodes) in New Zealand. However, the avipoxvirus that infects yellow-eyed penguins has remained uncharacterised. Here, we report the complete genome of a novel avipoxvirus, penguinpox virus 2 (PEPV2), which was derived from a virus isolate obtained from a skin lesion of a yellow-eyed penguin. The PEPV2 genome is 349.8 kbp in length and contains 327 predicted genes; five of these genes were found to be unique, while a further two genes were absent compared to shearwaterpox virus 2 (SWPV2). In comparison with penguinpox virus (PEPV) isolated from an African penguin, there was a lack of conservation within the central region of the genome. Subsequent phylogenetic analyses of the PEPV2 genome positioned it within a distinct subclade comprising the recently isolated avipoxvirus genome sequences from shearwater, canary, and magpie bird species, and demonstrated a high degree of sequence similarity with SWPV2 (96.27%). This is the first reported genome sequence of PEPV2 from a yellow-eyed penguin and will help to track the evolution of avipoxvirus infections in this rare and endangered species.

Keywords: avipoxvirus; complete genome; endangered yellow-eyed penguin; evolution; penguinpox virus 2.

Figure 1

Genomic illustration of the novel PEPV2. The arrows depict the direction of transcription of genes and open reading frames (ORFs). 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 PEPV2 and SWPV2 (green: 100% identity; mustard: ≥30% and <100% identity; red: <30% identity).

Figure 2

Dot plots of the PEPV2 genome (x-axis) vs. other sequenced avipoxvirus genomes (y-axis). (A) PEPV2 vs. SWPV2, (B) PEPV2 vs. CNPV, (C) PEPV2 vs. PEPV, and (D) PEPV2 vs. SWPV1. 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. Black arrows indicate the first region of major difference (PEPV2-158 to -170) and orange arrows indicate the second region of major difference (PEPV2-214 to -236). Window size = 12.

Figure 3

Phylogenetic relationship between PEPV2 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 Geneious (version 10.2.2). The numbers on the left show bootstrap values as percentages. The labels were aligned in the ML tree. The labels at branch tips refer to original ChPV GenBank accession numbers followed by abbreviated species names. The following abbreviations and GenBank accession details for the selected ChPVs used are: penguinpox virus 2 (PEPV2; MW296038), fowlpox virus standard vaccine strain (FWPV-S; MW142017), canarypox virus (CNPV; AY318871), pigeonpox virus (FeP2; KJ801920), penguinpox virus (PEPV; KJ859677), fowlpox virus (FWPV; AF198100, MF766430-32, MH709124-25, MH719203, MH734528, and AJ581527), fowlpox virus Australian vaccine strain (FWPV-S; MW142017) [48], shearwaterpox virus 1 (SWPV1; KX857216), shearwaterpox virus 2 (SWPV2; KX857215), turkeypox virus (TKPV; NC_028238); flamingopox virus (FGPV; MF678796), magpiepox virus (MPPV; MK903864), and mudlarkpox virus (MLPV; MT978051). Saltwater crocodile poxvirus (SwCRV1; MG450915) [38] was used as an outgroup. The novel PEPV2 is shown in bold font and pink text.