Genomic characterization of a novel poxvirus from a flying fox: evidence for a new genus?

Abstract

The carcass of an Australian little red flying fox (Pteropus scapulatus) which died following entrapment on a fence was submitted to the laboratory for Australian bat lyssavirus exclusion testing, which was negative. During post-mortem, multiple nodules were noted on the wing membranes, and therefore degenerate PCR primers targeting the poxvirus DNA polymerase gene were used to screen for poxviruses. The poxvirus PCR screen was positive and sequencing of the PCR product demonstrated very low, but significant, similarity with the DNA polymerase gene from members of the Poxviridae family. Next-generation sequencing of DNA extracted from the lesions returned a contig of 132 353 nucleotides (nt), which was further extended to produce a near full-length viral genome of 133 492 nt. Analysis of the genome revealed it to be AT-rich with inverted terminal repeats of at least 1314 nt and to contain 143 predicted genes. The genome contains a surprisingly large number (29) of genes not found in other poxviruses, one of which appears to be a homologue of the mammalian TNF-related apoptosis-inducing ligand (TRAIL) gene. Phylogenetic analysis indicates that the poxvirus described here is not closely related to any other poxvirus isolated from bats or other species, and that it likely should be placed in a new genus.

Characterization of Eptesipoxvirus, a novel poxvirus from a microchiropteran bat

“…Additional EPTV genes that are otherwise orthopoxvirus specific are scattered throughout the genome: EPTV-045, -141, -146, and -167 are orthologs of VACV-O2L, -A42R, -A47L, and -B16R, and encode a glutare-doxin-like protein, a profilin-like protein, the immunoprevalent protein, and an IL-1 beta-receptor-like protein, respectively. EPTV also encodes a chemokine-binding protein (EPTV-140) as well as a partial schlafen-like protein (EPTV-160) that have only been found in orthopoxviruses, yokapoxvirus (YKV), and the recently sequenced pteropoxvirus [13, 39].…”

“…Seven conserved poxviral proteins (previously used in [10] and [13]): RPO147, RAP94, mRNA capping enzyme large subunit, P4a precursor, RPO132, VETF-L, and DNA primase were extracted from VOCs and aligned using MUSCLE [28] in Base-By-Base. MEGA6.06 was used to create a Maximum-likelihood tree using the LG model with the G + I rate parameter [29].…”

“…Eptesipoxvirus (EPTV) was isolated in North America [10], Eidolon helvum poxvirus 1 in West Africa [11], and a third virus was identified only by electron microscopy in South Australia [12]. Since only small amounts of sequence data were obtained from the first 2 viruses, the first complete genome of a bat-associated poxvirus was not published until 2016, from a Pteropox virus isolated in North Western Australia [13].…”

Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea)

“…Previous metagenomic studies on bats have revealed several novel viruses from a diverse group of viral families [13,16,18,48,49]. The virus families discovered in this study have been detected in several species of bats by conventional PCR and next generation sequencing, including adenoviruses [16,50,51], bunyaviruses [52,53,54], flaviviruses [55,56,57], herpesviruses [16,49,58,59], paramyxoviruses [60,61,62], papillomaviruses [14,16,63,64], parvoviruses [12,59,65,66], picornaviruses [15,59,67], polyomaviruses [14,68,69,70], poxviruses [16,71,72] and reoviruses [73,74,75,76].…”

Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review

“…The p28-like protein homologs of Cotia virus and BeAn58058 form a high bootstrap clade ( Figure 4 ). Despite Eptesipox virus forming a well-supported clade with Pteropox virus, both viruses were isolated from bats, which could suggest an adaptation of p28 to the host [ 98 , 99 ]. However, p28-like protein homologs of entomopoxvirus and mimivirus formed an external clade ( Figure 4 ).…”