Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract

Abstract

Picobirnaviruses (PBVs) have been detected in several species of animals worldwide; however, data pertaining to their presence in Australian wild and domestic animals are limited. Although PBVs are mostly found in faecal samples, their detection in blood and respiratory tract samples raises questions concerning their tropism and pathogenicity. We report here PBV detection in wild deer and cattle from southeastern Australia. Through metagenomics, the presence of PBV genogroups I (GI) and II (GII) were detected in deer serum and plasma. Molecular epidemiology studies targeting the partial RNA-dependent RNA polymerase gene were performed in a wide range of specimens (serum, faeces, spleen, lung, nasal swabs, and trachea) collected from wild deer and cattle, with PCR amplification obtained in all specimen types except lung and spleen. Our results reveal the predominance of GI and concomitant detection of both genogroups in wild deer and cattle. In concordance with other studies, the detected GI sequences displayed high genetic diversity, however in contrast, GII sequences clustered into three distinct clades. Detection of both genogroups in the upper respiratory tract (trachea and nasal swab) of deer in the present study gives more evidence about the respiratory tract tropism of PBV. Although much remains unknown about the epidemiology and tropism of PBVs, our study suggests a wide distribution of these viruses in southeastern Australia.

Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

“…Viruses of the family Picobirnaviridae are non-enveloped, bi-segmented, double-stranded RNA (dsRNA) viruses of approximately 2.4 to 2.7 kb in length, which contain two functional genes, a structural capsid gene and an RNA-dependent RNA polymerase (RdRp) gene 42 . Evidence of picobirnavirus (PBV) sequences have been reported in humans, invertebrates, environmental water samples and a wide range of animals, including birds worldwide 12 , 42 – 47 . In this study, two contigs of 444 nt and 345 nt in length (coverage 4.86× and 11.15×, respectively), were detected and were found to be psittacine picobirnaviruses.…”

Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

“…This study utilised previously collected samples to investigate Australian wild deer infection status [11][12][13]. Briefly, opportunistic sampling during field necropsies was carried out on deer culled for other reasons in New South Wales and Victoria (Figure 1) from August 2019 to June 2021 with the assistance of recreational and professional hunters.…”

“…Bioinformatics analysis was conducted as described previously [13]. Briefly, Illumina reads were demultiplexed and trimmed using Trim_Galore v0.4.5 with the minimum sequence length set to 50 bp and Phred Quality of 25.…”

“…Each supernatant was filtered through 0.8 µm polyethersulfone (PES) (Sartorius cat#: VK01P042) spin filters at 17,000× g for 1 min. Filtrates were nuclease treated using benzonase and micrococcal nuclease (37 • C for 2 h), followed by nucleic acid extraction using the QIAamp ® Viral RNA mini kit (Qiagen, Valencia, CA, USA) as previously described [13]. cDNA synthesis and amplification were performed using the Whole Transcriptome Amplification Kit (WTA2, Sigma-Aldrich, Darmstadt, Germany).…”

“…Addressing this knowledge gap is essential for anticipating how viruses might be transmitted to other animals and controlling diseases. Therefore, our team has been investigating the infection status of wild deer in Australia [11][12][13].…”