Panoramic Parvovirus Strain Discovery Data Chain
| ParvoDB ID | PV008634 | GenBank Accession | OP019746 |
| Subfamily | Parvovirinae | Genus | Dependoparvovirus |
| Species | Dependoparvovirus primate1 | Sequence Length | 4668 |
| Definition | UNVERIFIED: Adeno-associated virus 2 isolate CVR_6 sequence. | Submission Date | 2022-07-18 |
| Strain Name | CVR_6 | Sampling Date | 2022-04 |
| Sampling Country | United Kingdom | Location | Scotland, United Kingdom |
| Submitted By | Ho,A., Orton,R., Tayler,R., Asamaphan,P., Tong,L., Smollett,K., Davis,C., Manali,M., McDonald,S.E., Pollock,L., Evans,C., McMenamin,J., Roy,K., Marsh,K., Divala,T., Holden,M., Lockhart,M., Yirrell,D., Currie,S., Shepherd,S.J., Jackson,C., Gunson,R., MacLean,A., McInnes,N., Battle,R., Hollenbach,J., Henderson,P., Chand,M., Hamilton,M.S., Estrada-Rivadeneyra,D., Levin,M., Robertson,D.L., Filipe,A., Willett,B., Breuer,J., Semple,M.G. VI, Turner,D., Baillie,J.K. and Thomson,E.C. | Submitting Institution | MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Sir Michael Stoker Building, Glasgow, Scotland G61 1QH, UK |
| Original Host | Homo sapiens; age = <22 | Sample Type | clinical samples |
| Standardized Host Name | Homo sapiens | Host Tax Rank | species |
| Standardized Host Class | Mammalia | Standardized Host Order | Primates |
| Environmental Origin | - N/A - | Reagent Origin | - N/A - |
| Number | Reagent/Consumables | Purpose | PMID/Url | Reference |
|---|---|---|---|---|
| 1 | AAV2 pAAV-CAG-tdTomato viral preparation | Used to coat plates for Anti-AAV2 ELISA Assay. | 36996873 | View Related Publication |
| 2 | Forward ITR primer | Used for AAV2 qRT-PCR to detect a 62bp amplicon of the AAV2 inverted terminal repeat region. | ||
| 3 | Reverse ITR primer | Used for AAV2 qRT-PCR to detect a 62bp amplicon of the AAV2 inverted terminal repeat region. | ||
| 4 | AAV2 ITR hydrolysis probe | Used for AAV2 qRT-PCR to detect a 62bp amplicon of the AAV2 inverted terminal repeat region. | ||
| 5 | DNaseI (Ambion) | Used to treat nucleic acid samples for improved detection of RNA viruses in metagenomic sequencing. | ||
| 6 | Ribo-Zero Plus rRNA Depletion Kit (Illumina) | Used for ribosomal depletion in RNA virus detection for metagenomic sequencing. | ||
| 7 | SuperScript III (Invitrogen) | Used for reverse transcription in RNA virus detection for metagenomic sequencing. | ||
| 8 | NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB) | Used for double-strand DNA synthesis in RNA virus detection for metagenomic sequencing. | ||
| 9 | NEBNext Microbiome DNA Enrichment Kit (NEB) | Used to partially remove host DNA for improved detection of DNA viruses in metagenomic sequencing. | ||
| 10 | KAPA LTP kit (Roche) | Used for library preparation in metagenomic sequencing. | ||
| 11 | NEBNext Multiplex oligos for Illumina (NEB) | Used for indexing in the library preparation for metagenomic sequencing. | ||
| 12 | VirCapSeq-VERT Capture Panel probes (Roche) | Used for target enrichment sequencing, covering genomes of 207 viral taxa known to infect vertebrates. | ||
| 13 | Alkaline Phosphatase yellow (Merck) | Used in Anti-AAV2 ELISA Assay for measuring absorbance. | ||
| 14 | Fixative solution (PFA:storage buffer) | Used for post-staining fixation in spatial analysis (Codex Phenocycler). | ||
| 15 | PBS-T containing 5% BSA | Used to block plates before sample addition in Anti-AAV2 ELISA Assay. | ||
| 16 | Anti-Human IgM (Merck) | Used as secondary antibody in Anti-AAV2 ELISA Assay to detect human IgM. | ||
| 17 | Anti-Human IgG (Merck) | Used as secondary antibody in Anti-AAV2 ELISA Assay to detect human IgG. | ||
| 18 | Goat Anti-Mouse IgG (Merck) | Used as secondary antibody for the positive control in Anti-AAV2 ELISA Assay. | ||
| 19 | Custom conjugated antibodies (Akoya Biosciences) | Used for staining in CO-Detection by indEXing (CODEX) analysis. | ||
| 20 | Target Specific RNA probes (Advanced Cell Diagnostics) | Used for in situ hybridisation to detect AAV2, HHV6, and Adenovirus 41 RNA. | ||
| 21 | Vectamount mounting media (Vector Laboratories) | Used for mounting stained slides for in situ hybridisation. |