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.

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

“…Like many other avipoxviruses [ 25 , 28 , 29 ], the ALPV genome contained a well-conserved central coding region surrounded by two identical inverted terminal repeat (ITR) regions, comprising 4069 bp each (coordinates 1–4069 sense and 347,841–351,909 antisense orientation). The nucleotide composition of the ALPV genome was A + T rich (69.9%), which was in agreement with other avipoxviruses isolated from yellow-eyed penguin [ 19 ], shearwater [ 25 ] and passerine bird species [ 30 , 31 ] ( Table 1 ). The ALPV genome showed the highest nucleotide identities with penguinpox virus 2 (PEPV2, GenBank accession no.…”

“…The remaining ten gene products (ALPV-079, -155, -163, -165, -166, -167, -168, -175, -233 and -236) were homologous to ORFs of CNPV, and a further six gene products (ALPV-003, -009, -090, -127, -229 and -334) were homologs to SWPV1 ( Table 2 ). All conserved genes of ALPV showed the highest sequence similarity to homologs of avipoxviruses isolated from Pacific shearwater, canary and yellow-eyed penguin bird species, implying a common evolutionary history [ 19 , 25 , 32 ]. In comparison to SWPV2, two gene products (SWPV2-121 and -213) were absent from the ALPV genome, and a further nineteen genes were predicted to be truncated/fragmented ( Figure 1 and Table 2 ).…”

“…Clean raw reads (1.15 million) were mapped back to the assembled ALPV genome and resulted in an average coverage of 136.33x. The genome was annotated according to the previously published protocol [ 19 ] using Geneious software (version 10.2.2, Biomatters, Auckland, New Zealand). Open reading frames (ORFs) longer than 50 amino acids, with a methionine start codon (ATG) and minimal overlap with other ORFs (not exceeding 50% of one of the genes), were selected and annotated.…”

“…Invasive alien species, degradation or loss of nesting habitats, storms and flooding, and marine pollution or plastic ingestion are also significant factors in population declines [ 6 , 7 ]. Infectious diseases, including those caused by avipoxviruses, have been identified as an important risk factor in the conservation of small and endangered bird populations, including albatrosses [ 14 , 15 , 16 , 17 , 18 , 19 ]. The impact of the introduction of avipoxviruses has been severe for the avifauna of various archipelagos [ 20 ].…”

“…The behaviour of wild birds allows avian poxviruses to reach new hosts through bird migration, species introductions, and habitat change. Avipoxviruses have been identified as an important risk factor in the conservation of endangered bird populations [ 19 , 25 ]. In affected birds, avipoxvirus infection can cause two different forms of disease, defined as cutaneous or diphtheritic.…”