Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

Rowena Chong; Mang Shi; Catherine E Grueber; Edward C Holmes; Carolyn Hogg; Katherine Belov; Vanessa R Barrs

Listed as endangered, the Tasmanian devil is facing the threat of extinction due to a contagious 52 cancer, devil facial tumour disease (DFTD), that has caused drastic declines in wild devil 53 populations by 77% since its discovery in 1996 [3] . There are currently two forms of DFTD 54 affecting devils; DFT1 and DFT2 [4] . In an attempt to save the species from extinction, an C a p t i v e Z o o A 1 3 9 , 8 2 7 , 8 6 6 2 1 9 , 4 9 6 Z o o A 2 6 , 7 0 4 , 8 4 2 2 8 1 , 8 5 7 Z o o B C a p t i v e Z o o B 1 2 8 , 1 4 9 , 4 0 8 1 9 6 , 9 1 9 Z o o B 3 3 , 0 0 2 , 7 9 0 2 6 7 , 5 3 6 M a r i a I s l a n d W i l d M I 1 2 9 , 7 8 3 , 3 9 0 2 6 1 , 4 8 3 M I 4 2 , 8 5 6 , 8 5 0 1 5 3 , 8 0 4 B u c k b y s R o a d W i l d B R 1 2 8 , 5 8 9 , 5 5 6 3 5 8 , 3 2 7 B R 4 2 , 6 0 2 , 7 5 2 8 4 , 6 4 6 W u k a l i n a / M t W i l l i a m N a t i o n a l P a r k W i l d w M W 1 2 9 , 9 8 1 , 8 5 6 2 6 4 , 2 0 5 w M W 4 8 , 9 1 1 , 7 2 8 3 1 3 , 1 5 4 S t o n y H e a d W i l d S H 1 3 6 , 7 0 6 , 3 6 0 3 2 5 , 7 6 9 S H 4 3 , 0 9 5 , 2 7 4 4 9 , 8 1 2 T o t a l 7 9 3 , 0 3 8 , 4 3 6 1 , 6 2 6 , 1 9 9 2 3 7 , 1 7 4 , 2 3 6 1 , 1 5 0 , 8 0 9 13 The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/443457 doi: bioRxiv preprint and 6 (DePBV1 -6) with two separate strains occurring in DePBV1 and DePBV5. Phylogenetic The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/443457 doi: bioRxiv preprint 18 respectively, both of which encode partial E1 protein, an ATP-dependent DNA helicase required 397 for viral replication [51] . Since the two fragments shared approximately 64% similarity to each 398 other, it suggests the presence of two distinct papillomavirus species, which we have tentatively 399 designated as Devil papillomavirus 1 and 2 (DePV1 and -2). Phylogenetic analysis based on the 400 E1 protein showed that DePV1 and 2 form a distinct cluster with Bettongia penicillata The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/443457 doi: bioRxiv preprint 21 Within-library viral diversity (alpha diversity) as characterised by our meta-transcriptomics 474 approach was significantly different between captive and wild populations (p < 0.05). In general, 475 captive populations had lower diversity in their faecal viromes compared to wild populations, as 476 measured using the chao1 metric. However, when considering bacteriophage alone, we did not 477 find any significant associations between devil populations (captive or wild) in either diversity or 478 abundance. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/443457 doi: bioRxiv preprint 23 Compared to VLP metagenomics, meta-transcriptomics is non-viral specific, requires less 524 sample processing, and reveals the entire transcriptome within a sample [20, 64] . Omitting