Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV001769 GenBank Accession MG973212
Subfamily Parvovirinae Genus Erythroparvovirus
Species Erythroparvovirus primate1 Sequence Length 285
Definition Human parvovirus B19 isolate TF230 capsid protein 1 (VP1), protein X, and capsid protein 2 (VP2) genes, partial cds. Submission Date 2018-02-17
Strain Name TF230 Sampling Date 2013-06-10
Sampling Country Brazil Location Regional Hospital of Tefé, Brazil
Submitted By Figueiredo,R.M.P., Souza,M.I.R., Silva,A.J.C., Amorim,V.S., Souza,V.C., Nascimento,V.A. and Naveca,F.G. Submitting Institution Laboratory of Infectious Disease Ecology in the Amazon - IDEA, Leonidas & Maria Deane Institute - ILMD Fiocruz Amazonia, 476 Terezina Street Adrianopolis, Manaus, Amazonas 69.057-070, Brazil
Original Host Homo sapiens Sample Type serum 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 Blood smear test Initial screening of patients for malaria. 31508787 View Related Publication
2 QIAamp viral RNA Mini-Kit (Qiagen, Hilden, Germany) RNA extraction from serum samples for dengue virus detection.
3 Semi-nested multiplex PCR protocol Detection of DENV RNA.
4 DNA PureLink viral RNA/DNA Mini-Kit (Invitrogen, Carlsbad, CA, USA) Isolation of total nucleic-acid from serum samples for B19V DNA detection.
5 Nested-PCR protocol Detection of B19V DNA.
6 PVP1 (5′- ACAAGCCTGGGCAAGTTAGC-3′) Forward primer for the first PCR reaction.
7 PVP2 (5′- CTGCACCAGTGCTGGCTTCT-3′) Reverse primer for the first PCR reaction and primer for the nested-PCR reaction.
8 PVP3 (5′- TGGGCCTGGCAATGAGCTAC-3′) Primer for the nested-PCR reaction.
9 Agarose gel Electrophoresis to visualize nested-PCR products.
10 Ethidium bromide Staining agent to visualize DNA in agarose gel under UV light.
11 Polyethylene glycol (PEG) 8000 (Promega, WI, USA) Solution for precipitating amplicons.
12 NaCl Component of the solution used for amplicon precipitation.
13 BigDye v3.1 (Applied Biosystems, USA) Nucleotide sequencing of PCR products.
14 Human parvovirus B19 RefSeq Genome (NC_000883.2) Reference for contig assembly.
15 GenBank + EMBL + DDBJ + PDB + RefSeq sequences Databases for BLAST analysis against the consensus nucleotide sequence.
16 Simian parvovirus sequence (U26342) Negative control in phylogenetic analysis.
17 MEGA7 Alignment of nucleotide sequences for phylogenetic analysis.
18 GIMP v2.8.10 Final edition of the phylogenetic tree.