Genome sequence of an Australian strain of canid alphaherpesvirus 1

Whole-Genome Sequencing of Two Canine Herpesvirus 1 (CaHV-1) Isolates and Clinicopathological Outcomes of Infection in French Bulldog Puppies

Canine herpesvirus 1 (CaHV-1) infects dogs, causing neonatal death and ocular, neurological, respiratory, and reproductive problems in adults. Although CaHV-1 is widespread in canine populations, only four studies have focused on the CaHV-1 whole genome. In such context, two CaHV-1 strains from both the kidney and spleen of 20-day-old deceased French Bulldog puppies were recently isolated in Sardinia, Italy. The extracted viral DNA underwent whole-genome sequencing using the Illumina MiSeq platform. The Italian CaHV-1 genomes were nearly identical (>99%), shared the same tree branch, and clustered near the ELAL-1 (MW353125) and BTU-1 (KX828242) strains, enlarging the completely separated clade discussed by Lewin et al., in 2020. This study aims to provide new insights on the evolution of the CaHV-1, based on high-resolution whole-genome phylogenetic analysis, and on its clinicopathological characterization during a fatal outbreak in puppies.

Australasian Pigeon Circoviruses Demonstrate Natural Spillover Infection

Pigeon circovirus (PiCV) is considered to be genetically diverse, with a relatively small circular single-stranded DNA genome of 2 kb that encodes for a capsid protein (Cap) and a replication initiator protein (Rep). Australasia is known to be the origin of diverse species of the Order Columbiformes, but limited data on the PiCV genome sequence has hindered phylogeographic studies in this species. To fill this gap, this study was conducted to investigate PiCV in 118 characteristic samples from different birds across Australia using PCR and sequencing. Eighteen partial PiCV Rep sequences and one complete PiCV genome sequence were recovered from reservoir and aberrant hosts. Phylogenetic analyses revealed that PiCV circulating in Australia was scattered across three different subclades. Importantly, one subclade dominated within the PiCV sequenced from Australia and Poland, whereas other PiCV sequenced in this study were more closely related to the PiCV sequenced from China, USA and Japan. In addition, PiCV Rep sequences obtained from clinically affected plumed whistling duck, blue billed duck and Australian magpie demonstrated natural spillover of PiCV unveiled host generalist characteristics of the pigeon circovirus. These findings indicate that PiCV genomes circulating in Australia lack host adapted population structure but demonstrate natural spillover infection.

A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris)

Pantoea stewartii, a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle (Chaetocnema pulicaria) being the primary carrier. P. stewartii is a bacterium belonging to the order Enterobacterales and can lead to crop diseases that have a significant economic impact worldwide. Due to its high potential for spread, P. stewartii is classified as a quarantine organism in numerous countries. Despite its impact on agriculture, the limited genome sequences of P. stewartii hamper understanding of its pathogenicity and host specificity, and the development of effective control strategies. In this study, a P. stewartii strain (C10109_Jinnung) was discovered in the faecal matter of the Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris) in Australia, which to our knowledge is the first reported P. stewartii genome from a bird source. Whole-genome sequencing and phylogenomic analysis of strain C10109_Jinnung, obtained from a captive psittacine, provides new insights into the genetic diversity and potential transmission route for the spread of P. stewartii beyond insects and plants, where P. stewartii is typically studied. Our findings provide new insights into the potential transmission route for spread of P. stewartii and expand the known transmission agents beyond insects and plants. Expanding the catalogue of P. stewartii genomes is fundamental to improving understanding of the pathogenicity, evolution and dissemination, and to develop effective control strategies to reduce the substantial economic losses associated with P. stewartii in various crops and the potential impact of endangered animal species.

A Novel Pathogenic Avipoxvirus Infecting Vulnerable Cook's Petrel (Pterodroma cookii) in Australia Demonstrates a High Genomic and Evolutionary Proximity with South African Avipoxviruses

Avipoxviruses are assumed to be restricted to avian hosts and are considered to be important viral pathogens that may impact the conservation of many vulnerable or endangered birds. Recent reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission may be possible within birds and other species. Most of the avipoxviruses in wild and sea birds remain uncharacterized, and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel, full-length Cook's petrelpox virus (CPPV) genome from a vulnerable Cook's petrel (Pterodroma cookii), and this was followed by the detection of immature virions using transmission electron microscopy (TEM). The CPPV genome was 314,065 bp in length and contained 357 predicted open-reading frames (ORFs). While 323 of the ORFs of the CPPV genome had the greatest similarity with the gene products of other avipoxviruses, a further 34 ORFs were novel. Subsequent phylogenetic analyses showed that the CPPV was most closely related to other avipoxviruses that were isolated mostly from South African bird species and demonstrated the highest sequence similarity with a recently isolated flamingopox virus (88.9%) in South Africa. Considering the sequence similarity observed between CPPV and other avipoxviruses, TEM evidence of poxvirus particles, and phylogenetic position, this study concluded that CPPV is a distinct candidate of avipoxviruses. IMPORTANCE Emerging viral disease is a significant concern with potential consequences for human, animal, and environmental health. Over the past several decades, multiple novel viruses have been found in wildlife species, including birds, and they can pose a threat to vulnerable and endangered species. Cook's petrel is currently listed as vulnerable. The threats to the species vary, but are, to a large degree, due to anthropogenic impacts, such as climate change, habitat loss, pollution, and other disturbances by humans. Knowledge of viral pathogens, including poxvirus of Cook's petrel is currently virtually nonexistent.

Molecular characterisation of a novel pathogenic avipoxvirus from an Australian little crow (Corvus bennetti) directly from the clinical sample

Avipoxviruses are thought to be restricted to avian hosts and considered significant pathogens that may impact the conservation of many birds. However, reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission, within birds and other species, may be possible. The vast majority of avipoxviruses in wild birds remain uncharacterised and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel full-length crowpox virus genome from an Australian little crow (Corvus bennetti), followed by the detection of immature and intracellular mature virions using electron microscopy. The CRPV genome was 328,768 bp in length and contained 403 predicted open-reading frames. While 356 of the ORFs of CRPV genome had the greatest similarity with other avipoxviruses gene products, a further 47 ORFs were novel. Subsequent phylogenetic analyses showed that the CRPV was most closely related to other avipoxviruses isolated from passerine and marine bird species and demonstrated the highest sequence similarity with an albatrosspox virus (84.4%). Considering the sequence similarity observed between CRPV and other avipoxviruses and phylogenetic position, this study concluded that the CRPV to be a distinct available candidate of avipoxviruses.

Complete Mitochondrial Genome Sequence of a Seabird, Wedge-Tailed Shearwater (Ardenna pacifica)

Here, we report the complete mitochondrial genome sequence of a seabird, wedge-tailed shearwater (Ardenna pacifica). The circular genome has a size of 16,434 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The study provides a reference mitochondrial genome of wedge-tailed shearwater for further molecular studies.

Molecular and Phylogenetic Characterisation of a Highly Divergent Novel Parvovirus (Psittaciform Chaphamaparvovirus 2) in Australian Neophema Parrots

Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent and have recently been identified in many animals. However, the detection and characterisation of parvoviruses in psittacine birds are limited. Therefore, this study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 2 (PsChPV-2) under the genus Chaphamaparvovirus, which was identified in Australian Neophema birds. The PsChPV-2 genome is 4371 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 56.2% and 47.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 1 from a rainbow lorikeet (Trichoglossus moluccanus). Subsequent phylogenetic analyses exhibited that the novel PsChPV-2 is most closely related to other chaphamaparvoviruses of avian origin and has the greatest sequence identity with PsChPV-1 (60.6%). Further systematic investigation is warranted to explore the diversity with many avian-associated parvoviruses likely to be discovered.

Genomic characterisation of a novel avipoxvirus, magpiepox virus 2, from an Australian magpie (Gymnorhina tibicen terraereginae)

Avipoxviruses are large, double-stranded DNA viruses and are considered significant pathogens that may impact on the conservation of numerous bird species. The vast majority of avipoxviruses in wild birds remain uncharacterised and their genetic variability is unclear. Here, we fully sequenced a novel avipoxvirus, magpiepox virus 2 (MPPV2), which was isolated 62 years ago (in 1956) from an Australian black-backed magpie. The MPPV2 genome was 298,392 bp in length and contained 419 predicted open-reading frames (ORFs). While 43 ORFs were novel, a further 24 ORFs were absent compared with another magpiepox virus (MPPV) characterised in 2018. The MPPV2 genome contained an additional ten genes that were homologs to shearwaterpox virus 2 (SWPV2). Subsequent phylogenetic analyses showed that the novel MPPV2 was most closely related to other avipoxviruses isolated from passerine and shearwater bird species, and demonstrated a high degree of sequence similarity (95.0%) with MPPV.

Complete Mitochondrial Genome Sequence of the Magpie-Lark (Grallina cyanoleuca)

Here, we report the complete mitochondrial genome sequence of an Australian passerine bird, magpie-lark (Grallina cyanoleuca). The circular genome has a size of 16,933 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. This study provides a reference mitochondrial genome of magpie-lark for further molecular studies.

Emergence of a Novel Pathogenic Poxvirus Infection in the Endangered Green Sea Turtle (Chelonia mydas) Highlights a Key Threatening Process

Emerging viral disease is a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, multiple novel viruses have been found in wildlife species, including reptiles, and often pose a major threat to vulnerable species. However, whilst a large number of viruses have been described in turtles, information on poxvirus in cheloniids remains scarce, with no molecular sequence data available to date. This study characterizes, for the first time, a novel poxvirus, here tentatively designated cheloniid poxvirus 1 (ChePV-1). The affected cutaneous tissue, recovered from a green sea turtle (Chelonia mydas) captured off the Central Queensland coast of Australia, underwent histological examination, transmission electron microscopy (TEM), DNA extraction and genomic sequencing. The novel ChePV-1 was shown to be significantly divergent from other known poxviruses and showed the highest sequence similarity (89.3%) to avipoxviruses (shearwater poxvirus 2 (SWPV2)). This suggests the novel ChePV-1 may have originated from a common ancestor that diverged from an avipoxvirus-like progenitor. The genome contained three predicted unique genes and a further 15 genes being truncated/fragmented compared to SWPV2. This is the first comprehensive study that demonstrates evidence of poxvirus infection in a marine turtle species, as well as a rare example of an avipoxvirus crossing the avian-host barrier. This finding warrants further investigations into poxvirus infections between species in close physical proximity, as well as in vitro and in vivo studies of pathogenesis and disease.

Intensive ocular sampling for the detection of subclinical canine herpesvirus-1 shedding in dogs with experimentally-induced latent infection

Latent canine herpesvirus-1 (CaHV-1) infections are common in domestic dogs, but viral shedding patterns in dogs are poorly understood. Previous research failed to detect spontaneous subclinical ocular CaHV-1 shedding in dogs following ocular infection, a situation that is fundamentally distinct from many of the alphaherpesviruses closely related to CaHV-1. One possible explanation for this finding is that the sampling interval in the prior studies evaluating ocular shedding patterns was too infrequent to detect rapidly cleared, brief ocular viral shedding episodes. To evaluate for this potential viral shedding scenario, 10 laboratory beagles recovered from experimental primary ocular CaHV-1 infection and with latent CaHV-1infection were intensively monitored for viral reactivation and shedding for 28 days. Clinical ophthalmic examinations were performed daily. Ocular swab samples were collected for CaHV-1 polymerase chain reaction 3 times daily and CaHV-1 virus neutralizing antibody assays were evaluated at 2-week intervals. No abnormalities suggestive of recurrent CaHV-1 ocular disease were observed during clinical ophthalmic examination in the dogs during the study. Ocular CaHV-1 shedding was not detected by polymerase chain reaction and CaHV-1 virus neutralizing antibody titers remained stable in all dogs for the study duration. In the present study utilizing frequent multiple daily sample collections, no evidence of subclinical ocular CaHV-1 shedding was detected in mature dogs with experimentally-induced latent CaHV-1 infection.

Molecular characterisation of a novel pathogenic avipoxvirus from an Australian passerine bird, mudlark (Grallina cyanoleuca)

Avipoxviruses have been recognised as significant pathogens in the conservation of numerous bird species. However, the vast majority of the avipoxviruses that infect wild birds remain uncharacterised. Here, we characterise a novel avipoxvirus, mudlarkpox virus (MLPV) isolated from an Australian passerine bird, mudlark (Grallina cyanoleuca). In this study, tissues with histopathologically confirmed lesions consistent with avian pox were used for transmission electron microscopy, and showed characteristic ovoid to brick-shaped virions, indicative of infectious particles. The MLPV genome was >342.7 Kbp in length and contained six predicted novel genes and a further six genes were missing compared to shearwaterpox virus-2 (SWPV-2). Subsequent phylogenetic analyses of the MLPV genome positioned the virus within a distinct subclade also containing recently characterised avipoxvirus genomes from shearwater, canary and magpie bird species, and demonstrated a high degree of sequence similarity with SWPV-2 (94.92%).

Phylogenomic Analysis of Global Isolates of Canid Alphaherpesvirus 1

Canid alphaherpesvirus 1 (CHV-1) is a widespread pathogen of dogs with multiple associated clinical signs. There has been limited prior investigation into the genomics and phylogeny of this virus using whole viral genome analysis. Fifteen CHV-1 isolates were collected from animals with ocular disease based in the USA. Viral DNA was extracted for Illumina MiSeq full genome sequencing from each isolate. These data were combined with genomes of previously sequenced CHV-1 isolates obtained from hosts in the UK, Australia and Brazil. Genomic, recombinational and phylogenetic analysis were performed using multiple programs. Two isolates were separated into a clade apart from the remaining isolates and accounted for the majority of genomic distance (0.09%): one was obtained in 2019 from a USA-based host (ELAL-1) and the other in 2012 from a host in Brazil (BTU-1). ELAL-1 was found to contain variants previously reported in BTU-1 but also novel variants in the V57 gene region. Multiple non-synonymous variants were found in USA-based isolates in regions associated with antiviral resistance. Evidence of recombination was detected between ELAL-1 and BTU-1. Collectively, this represents evidence of trans-boundary transmission of a novel form of CHV-1, which highlights the importance of surveillance for this pathogen in domestic dog populations.

Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile (Crocodylus porosus)

Saltwater crocodilepox virus (SwCRV), belonging to the genus Crocodylidpoxvirus, are large DNA viruses posing an economic risk to Australian saltwater crocodile (Crocodylus porosus) farms by extending production times. Although poxvirus-like particles and sequences have been confirmed, their infection dynamics, inter-farm genetic variability and evolutionary relationships remain largely unknown. In this study, a poxvirus infection dynamics study was conducted on two C. porosus farms. One farm (Farm 2) showed twice the infection rate, and more concerningly, an increase in the number of early- to late-stage poxvirus lesions as crocodiles approached harvest size, reflecting the extended production periods observed on this farm. To determine if there was a genetic basis for this difference, 14 complete SwCRV genomes were isolated from lesions sourced from five Australian farms. They encompassed all the conserved genes when compared to the two previously reported SwCRV genomes and fell within three major clades. Farm 2′s SwCRV sequences were distributed across all three clades, highlighting the likely mode of inter-farm transmission. Twenty-four recombination events were detected, with one recombination event resulting in consistent fragmentation of the P4c gene in the majority of the Farm 2 SwCRV isolates. Further investigation into the evolution of poxvirus infection in farmed crocodiles may offer valuable insights in evolution of this viral family and afford the opportunity to obtain crucial information into natural viral selection processes in an in vivo setting.

Molecular characterisation of a novel pathogenic avipoxvirus from the Australian magpie (Gymnorhina tibicen)

Avipoxviruses are significant pathogens infecting a wide range of wild and domestic bird species globally. Here, we describe a novel genome sequence of magpiepox virus (MPPV) isolated from an Australian magpie. In the present study, histopathologically confirmed cutaneous pox lesions were used for transmission electron microscopic analysis, which demonstrated brick-shaped virions with regular spaced thread-like ridges, indicative of likely infectious particles. Subsequent analysis of the recovered MPPV genome positioned phylogenetically to a distinct sub-clade with the recently isolated avipoxvirus genome sequences from shearwater and canary bird species, and demonstrates a high degree of sequence similarity with CNPV (96.14%) and SWPV-2 (95.87%). The novel MPPV complete genome is missing 19 genes with a further 41 genes being truncated/fragmented compared to SWPV-2 and contains nine predicted unique genes. This is the first avipoxvirus complete genome sequence that infects Australian magpie.

Characterization of the first mitochondrial genome of a little Corella (Cacatua sanguinea) and its phylogenetic implications

This study was designed to sequence the first complete mitochondrial genome from a little corella (Cacatua sanguinea). The mitogenome sequence was circular and 16,695 bp in length. In comparison to other available mitogenome sequences belongs to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of C. sanguinea was dominated by higher AT (53.0%) than GC (47.0%) content. The complete mitogenome sequence determined in this study is useful for understanding the more profound evolutionary history and the conservation of C. sanguinea.

The first complete mitogenome of Indian ringneck (Psittacula krameri) demonstrates close phylogenetic relationship with Eclectus parrot

This study was aimed to sequence the first complete mitochondrial genome from an Indian ringneck parrot (Psittacula krameri). The mitogenome sequence was circular and 16,413 bp in length. In comparison to other available mitogenome sequences belonging to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes and a control region; however, this mitogenome missing a tRNA-Glu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of P. krameri was dominated by higher AT (53.5%) than GC (46.5%) content. The complete mitogenome sequence determined in this study would be useful to track the more profound evolutionary history and the conservation of P. krameri.

Molecular characterization of the first saltwater crocodilepox virus genome sequences from the world's largest living member of the Crocodylia

Crocodilepox virus is a large dsDNA virus belonging to the genus Crocodylidpoxvirus, which infects a wide range of host species in the order Crocodylia worldwide. Here, we present genome sequences for a novel saltwater crocodilepox virus, with two subtypes (SwCRV-1 and -2), isolated from the Australian saltwater crocodile. Affected belly skins of juvenile saltwater crocodiles were used to sequence complete viral genomes, and perform electron microscopic analysis that visualized immature and mature virions. Analysis of the SwCRV genomes showed a high degree of sequence similarity to CRV (84.53% and 83.70%, respectively), with the novel SwCRV-1 and -2 complete genome sequences missing 5 and 6 genes respectively when compared to CRV, but containing 45 and 44 predicted unique genes. Similar to CRV, SwCRV also lacks the genes involved in virulence and host range, however, considering the presence of numerous hypothetical and or unique genes in the SwCRV genomes, it is completely reasonable that the genes encoding these functions are present but not recognized. Phylogenetic analysis suggested a monophyletic relationship between SwCRV and CRV, however, SwCRV is quite distinct from other chordopoxvirus genomes. These are the first SwCRV complete genome sequences isolated from saltwater crocodile skin lesions.

The first complete mitogenome of red-bellied parrot (Poicephalus rufiventris) resolves phylogenetic status within Psittacidae

This paper describes the genomic architecture of a complete mitogenome from a red-bellied parrot (Poicephalus rufiventris). The mitogenome sequence was circular and 15,524 bp in length. Compared to other Psittacidae species, the genome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes, and two control regions, however, the mitogenome was missing a part of control region and a tRNA-Leu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1569 bp, respectively. The overall base composition of the mitogenome of P. rufiventris was dominated by higher AT (51.6%) than GC (48.4%) content. The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and the conservation of P. rufiventris.

Molecular and microscopic characterization of a novel Eastern grey kangaroopox virus genome directly from a clinical sample

Poxviruses are large DNA viruses with varying zoonotic potential, and are recognised in a broad range of wildlife. Although poxviruses have been detected in kangaroos, their genetic relationships to poxviruses in other animals and humans is not well understood. Here, we present a novel genome sequence of a marsupial poxvirus, the Eastern grey kangaroopox virus (EKPV-NSW), isolated from a wild eastern grey kangaroo. In the present study, histopathologically confirmed epidermal pox lesions were used to recover the full-length viral genome and perform electron microscopic analysis, with both immature virions and intracellular mature virions detected. Subsequent analysis of the EKPV-NSW genome demonstrated the highest degree of sequence similarity with EKPV-SC strain (91.51%), followed by WKPV-WA (87.93%), and MOCV1 (44.05%). The novel EKPV-NSW complete genome encompasses most of the chordopoxviruses protein coding genes (138) that are required for genome replication and expression, with only three essential protein coding genes being absent. The novel EKPV-NSW is missing 28 predicted genes compared to the recently isolated EKPV-SC, and carries 21 additional unique genes, encoding unknown proteins. Phylogenetic and recombination analyses showed EKPV-NSW to be the distinct available candidate genome of chordopoxviruses.