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

Abstract

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.

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

“…However, relatively little is known about the origins, infection dynamics, genetic diversity and inter-farm genetic variability among the circulated SwCRV in saltwater crocodiles. In agreement with other crocodilian poxviruses [6,7], saltwater crocodilepox viruses are morphologically similar to orthopoxvirus virions, demonstrating a brick-like shape with rounded corners and a dumbbell-shaped central core and lateral bodies [3,4]. Furthermore, intracellular mature virions of SwCRV display the regular crisscross surface structure pattern, which is characteristic of parapoxvirus virions [3,4,7,8].…”

“…The evolutionary origin of poxviruses is still ill-defined, however, it is believed that their genomes have evolved over thousands of years through both gene gain and loss, mainly through horizontal gene transfer and gene duplication events [1,2]. The saltwater crocodilepox virus (SwCRV) belongs to the genus Crocodylidpoxvirus, a member of the subfamily Chordopoxvirinae in the family Poxviridae and is a known causative agent of poxviral lesions on Australian saltwater crocodile skin (Crocodylus porosus) [3,4]. Although the International Committee on Taxonomy of Viruses formally recognised crocodile poxviruses under the genus Crocodylidpoxvirus [5], at this stage, no taxonomic classification has been granted for SwCRV.…”

“…Although the International Committee on Taxonomy of Viruses formally recognised crocodile poxviruses under the genus Crocodylidpoxvirus [5], at this stage, no taxonomic classification has been granted for SwCRV. A recent study suggested that there were likely two major SwCRV subtypes naturally circulating in the saltwater crocodile population [3] on one farm. However, relatively little is known about the origins, infection dynamics, genetic diversity and inter-farm genetic variability among the circulated SwCRV in saltwater crocodiles.…”

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

“…Animal sampling was obtained in accordance with approved guidelines set by the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (1997) and approved by the Charles Sturt University Animal Ethics Committee (Research Authority permit 09/046), and the total genomic DNA was extracted using an established protocol (Sarker, Das, et al 2017;Sarker, Das, et al 2018). The genomic library preparation and sequencing was performed according to the published protocol (Sarker, Roberts, et al 2017;Sarker, Isberg, et al 2018;Sutherland et al 2019). Briefly, the paired-end library with an insert size of 301 bp was prepared using the Illumina Nextera XT DNA Library Prep V3 Kit (Illumina V R Inc., San Diego, CA) according to the manufacturer's instructions.…”

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

“…The total genomic DNA was extracted using previously established protocol (Sarker, Das et al 2018. The genomic library preparation and sequencing were performed according to the published protocol (Sarker, Roberts et al 2017;Sarker, Isberg et al 2018). Briefly, the paired-end library with an insert size of 301 bp was prepared using the Illumina Nextera XT DNA Library Perp V3 Kit (IlluminaV R Inc., San Diego, CA, USA) according to the manufacturer's instructions.…”