Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV004669 GenBank Accession ON855072
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 514
Definition Human bocavirus 1 isolate HBoV-1_LVCA_4340 VP1 and VP2 genes, partial cds. Submission Date 2022-06-22
Strain Name HBoV-1_LVCA_4340 Sampling Date 2019-02
Sampling Country Brazil Location RiodeJaneiro, Brazil
Submitted By do Nascimento,L.G., Sarmento,S.K., Leonardo,R., Gutierrez,M.B., Malta,F.C., de Oliveira,J.M., Guerra,C.R., Coutinho,R., Miagostovich,M.P. and Fumian,T.M. Submitting Institution Laboratorio de Virologia Comparada e Ambiental, Fundacao Oswaldo Cruz, Avenida Brasil, 4365, Rio de Janeiro, Rio de Janeiro 21040-360, Brasil
Original Host Homo sapiens Sample Type bivalve mollusks samples(mussels and oysters)
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 Proteinase K solution (100 μg/mL, Invitrogen, Carlsbad, CA, USA) Added and mixed with digestive tissues of samples for processing. 36366459 View Related Publication
2 PP7 bacteriophage Used as an internal process control for spiking samples.
3 NucleoMag RNA Virus Extraction Kit (Macherey-Nagel, Dueren, Germany) Used for extraction of viral nucleic acids from homogenate.
4 SuperScript III Platinum One-Step qRT-PCR Kit (ThermoFisher Scientific, Invitrogen Division, Carlsbad, CA, USA) Used for TaqMan-based RT-qPCR reactions for norovirus, RVA, and HAV detection.
5 TaqMan Universal Master Mix kit (Applied Biosystems, Foster City, CA, USA) Used for TaqMan-based qPCR reactions for HAdV and HBoV detection.
6 Primers and Probes for norovirus detection (COG1F, COG1R, RING1, COG2F, COG2R, RING2). Used for amplification of target regions in norovirus during RT-qPCR assays.
7 Primers and Probes for RVA detection (NSP3-F, NSP3-R1, NSP3). Used for amplification of target regions in RVA during RT-qPCR assays.
8 Primers and Probes for HAV detection (HAV68, HAV240, HAV150p) Used for amplification of target regions in HAV during RT-qPCR assays.
9 Primers and Probes for HAdV detection (AdF, AdR, AdP1) Used for amplification of target regions in HAdV during qPCR assays.
10 Primers and Probes for HBoV detection (HBoV1, HBoV1, HBoV234, HBoV3, HBoV24) Used for amplification of target regions in HBoV during qPCR assays.
11 Multiplex primers for norovirus sequencing (MON431, G2SKR) Used for RT-PCR to further characterize norovirus strains.
12 Multiplex primers for RVA sequencing (VP6-F, VP6-R) Used for RT-PCR to further characterize RVA strains.
13 Multiplex primers for HAdV sequencing (Hex1deg, Hex2deg) Used for PCR to further characterize HAdV strains.
14 Multiplex primers for HBoV sequencing (AK-VP-F1, AK-VP-R1, AK-VP-F2, AK-VP-R2) Used for nested PCR to further characterize HBoV strains.
15 QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA, USA) Used for purification of PCR/RT-PCR amplicons.
16 BigDye Terminator v. 3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) Used for the sequencing of purified amplicons.