Abstract
The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as “Bopivirus C”. Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8–15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.
Highlights
All sample containers were immediately refrigerated after collection, transported to the Laboratory of Virology within the Department of Physiology, Anatomy, and Microbiology at La Trobe University. 0.1 g of each specimen was placed in RNase-free tubes with 1 mL of phosphate-buffered saline (PBS; 10% w/v) and kept frozen at −80 ◦ C
Illumina sequencing of twelve deer faecal samples generated a total of 269,043,972 paired-end (PE) reads, representing a total of
Similar tree topology was found based on P1, 2C, 3CD, and VP1 aa sequences supported by high bootstrap values in all three phylogenetic trees (Figure S1). These findings suggest deer/bopivirus could belong to a novel species in this genus Bopivirus
Summary
During the last two decades, the use of high-throughput DNA sequencing technologies has allowed the identification of novel, highly divergent viral species and those that cannot be detected by conventional culture and sequence-dependent methods [2]. It has dramatically increased viral discovery from various environmental and animal 4.0/). Samples, including novel picornaviruses [3]. Picornaviruses are ubiquitous, small, nonenveloped positive-sense RNA viruses infecting mainly mammals and birds [3,4]. Novel picornaviruses have been reported in Magellanic penguins [5], Cherry
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