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

Abstract

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.

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

“…Interestingly, ChePV-1 was shown to be highly genetically divergent from poxviruses that infect other reptilian species, such as CRV in Nile crocodiles and SwCRV-1 and −2 in saltwater crocodiles, with a GC content of 62% in all three reptilian viruses further supporting this divergence [ 19 , 20 , 21 ]. These phylogenetic relationships of ChePV-1 are unexpected findings considering that avipoxviruses tend to show a high degree of host–virus codivergence, typically with host specificity expressed at the level of phylogenetic order [ 55 ].…”

“…Currently, the only accepted genus known to infect reptiles is the Crocodylidpoxvirus genus, known to infect many crocodilian reptile species. It is represented by the Nile crocodile poxvirus (CRV) first isolated from Nile crocodiles ( Crocodylus niloticus ) [ 19 ], and the still-unassigned saltwater crocodilepox viruses, first isolated from Australian saltwater crocodiles ( Crocodylus porosus ) [ 20 , 21 ]. Poxviruses have also been suspected of infecting other reptile species, in most cases based on gross lesions or intracytoplasmic inclusions seen on electron microscopy; these include Hermann’s tortoise ( Testudo hermanni ) [ 22 ], the flap-necked chameleon [ 23 ], the tegu lizard ( Slavator merianae ) and the desert tortoise ( Gopherus agassizi ) [ 24 ].…”

Characterization of a Near-Complete Genome Sequence of a Chaphamaparvovirus from an Australian Boobook Owl (Ninox boobook)

“…The sequencing data were analyzed as per an established pipeline ( 11 – 14 ) using Geneious version 10.2.2 (Biomatters, New Zealand) and CLC Genomics Workbench version 9.5.4. Briefly, 37,770,262 raw reads were preprocessed to remove Illumina adapters, ambiguous base calls, and poor-quality reads (reads trimmed using a quality score limit of 0.05; ambiguous nucleotides up to 15 bp trimmed using CLC Genomics Workbench), followed by mapping against barn owl ( Tyto alba ) ( 15 ) and Escherichia coli (GenBank accession no.…”

Genome Sequence of a Beak and Feather Disease Virus from an Unusual Novel Host, Australian Boobook Owl (Ninox boobook)

“…Sequencing data were analyzed as per established pipeline ( 12 – 15 ) using Geneious (version 10.2.2; Biomatters, New Zealand) and CLC Genomics Workbench (version 9.5.4). Briefly, a total of 37,770,262 raw reads were preprocessed to remove the Illumina adapter, ambiguous base calls, and poor-quality reads (trim using quality score, limit 0.05; trim ambiguous nucleotides up to 15 using CLC Genomics Workbench), followed by mapping against barn owl ( Tyto alba ) ( 16 ) and Escherichia coli (GenBank accession no.…”