Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV026512 GenBank Accession MN082387
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 249
Definition Human bocavirus strain Hu/HBOV3/Rikh-268-Venda-2018 NS1 gene, partial cds. Submission Date 2019-06-18
Strain Name Hu/HBOV3/Rikh-268-Venda-2018 Sampling Date 2018-03-28
Sampling Country South Africa Location Vhembe region, Limpopo province of South Africa, South Africa
Submitted By Rikhotso,M.C. Submitting Institution Microbiology, The University of Venda, University Road, Thohoyandou, Limpopo 0950, South Africa
Original Host Homo sapiens Sample Type fecal 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 Guanidinium thiocyanate It is used in the Boom method for DNA extraction due to its lysing and nuclease inactivating properties. 32218240 View Related Publication
2 Silica particles Used in the Boom method for binding nucleic acids during DNA extraction.
3 HBoV real-time PCR commercial kit (Liferiver, Shanghai, China) Used to detect HBoV1-4 genotypes via real-time PCR.
4 Corbett Research Rotor-Gene 6000 Used for performing real-time multiplex PCR for HBoV genotyping.
5 TopTaq Master Mix Kit (Qiagen) Used for PCR amplification of HBoV-positive samples.
6 Primers for HBoV genotyping Used for PCR targeting the NS1 gene to identify HBoV1, HBoV2/4, and HBoV3.
7 2% agarose gel Used for visualizing PCR products stained with ethidium bromide.
8 Ethidium bromide Used to stain DNA in agarose gels for visualization under UV light.
9 ABI 3500XL Genetic Analyzer POP7TM (Thermo-Scientific) Used for Sanger DNA sequencing of positive samples to confirm HBoV genotypes.
10 CFX96 (Bio-Rad) real-time PCR Used to determine co-infection with other enteric viruses via the Allplex gastrointestinal panel virus assays from Seegene Technologies Inc.
11 Allplex gastrointestinal panel virus assays (Seegene Technologies Inc., California, USA) Used to detect the prevalence of other enteric viruses in stool samples of HBoV-positive patients.