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Darwin Deltavirus Detective Detour
In the pilot search of vertebrate SRA libraries for CoV and deltavirus (DV) there was a cluster of libraries matching the previously identifed lassie virus (Lesser Dog-like Bat deltavirus).
These libraries were identified via protein-level search and assembled with coronaSPAdes
Cluster 1 - Zebra Finch
From: Smithsonian Tropical Research Institute, Panama
Part of a study on the effects of androgens on avian musclur transcriptomes. These are three Zebra Finch, common to central Australia.
Animal Source: "Male zebra finches were collected from a laboratory colony at University of California, Los Angeles (Los Angeles, California), at which they were housed in open-flight aviaries (1.8 × 1.8 × 1.2 m)"
Cluster 2 - Zebra Finch
From: East Carolina University
Part of a study on the response to West Nile Virus.
Animal Source: Unknown
Cluster 3 - Yellow Bellied Tit
From: Institute of Zoology, Chinese Academy of Sciences.
Biostudy link and references in this paper.
Supplementary Table 1 contains information about the source of these birds. Appear to be wild-caught in China and from a single animal (different organs). HufuM1_F captured in Huairou District, Beijing, China - lat: 40.39° long: 116.66°.
- SRR7244693, HufuM1_F, lung ** Representative Genome sample
- SRR7244695, HufuM1_K, kidney
- SRR7244696, HufuM1_H, heart
- SRR7244698, HufuM1_L, liver
Cluster 4 - Gouldian Finch
From: University of Porto, Portugal
Part of a study on genome and transcriptome of Gouldian Finch. Samples were "regenerative skin". This animal is identified as Gould03_RNA or Black_03.
- SRR7504989, Black_03
Animal Source: "Black (n=21) and red-headed (n=21) captive birds 109were obtained from 13 private aviaries in Portugal (Table S1)" Table S1 doesn't have additional relevant information.
Cluster 5 - Black Headed Bunting
From: University of Dehli
Part of this study on RNA-Seq study of blood collected from photosensitive and photorefractory blackheaded buntings exposed to first long day. Released 2020-04-17.
Animal Source: Unknown
Sequence analysis
Darwin DV sequence assemblies from each of the above libraries are available as well as complete genome. Unclear if a whole genome has been acquired as the assembly from SRR7244693 did not over overlapping ends and the graph was isolated.
The available sequence shows characteristic folding for a deltavirus. (see above)
Each contig has a complete or near-complete dAg and these are invariable among samples (confirm this?).
What is perhaps the most surprsing is that sequence alignment of the available fragments shows that the sequenes are barely diverged with a few SNPs seperating each respective cluster. This suggests a very recent outbreak of this deltavirus but how it is linking these clusters is unclear.
This is also a clear example of zoonotic spillover between related species, Zebra Finch, Yellow-belly Tits, Gouldian Finch and Black Headed Bunting.
