2021-05-01
ENA first public
2021-04-30
ENA last update
ERC000033
ENA-CHECKLIST
SAMEA8662995
External Id
EPI_ISL_632692
GISAID Accession ID
Dutch COVID-19 response team
INSDC center alias
Dutch COVID-19 response team
INSDC center name
2021-05-01T00:28:04Z
INSDC first public
2021-04-30T16:42:44Z
INSDC last update
public
INSDC status
ERS6347530
SRA accession
Run346_BC92
Submitter Id
Submission account for department of Viroscience’s Research Teams, ErasmusMC
broker name
not provided
collecting institution
2020-10-15
collection date
Dutch COVID-19 response team
collector name
Human coronavirus 2019
common name
A SARS-CoV-2 specific multiplex PCR for Nanopore sequencing was performed, similar to amplicon-based approaches as previously described. In short, primers for 86 overlapping amplicons spanning the entire genome were designed using primal. The amplicon length was set to 500bp with 75bp overlap between the different amplicons. The libraries were generated using the native barcode kits from Nanopore (EXP-NBD104 and EXP-NBD114 and SQK-LSK109) and sequenced on a R9.4 flow cell multiplexing up to 24 samples per sequence run. Raw data was demultiplexed, amplicon primers were trimmed and human data was removed by mapping against the human reference genome.
description
Netherlands
geographic location (country and/or sea)
Zuid-Holland
geographic location (region and locality)
Human
http://purl.obolibrary.org/obo/NCBITaxon_9606
host common name
not collected
host health state
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
host scientific name
not provided
host sex
restricted access
host subject id
hCoV-19/Netherlands/ZH-EMC-815/2020
isolate
not collected
isolation source host associated
Severe acute respiratory syndrome coronavirus 2
http://purl.obolibrary.org/obo/NCBITaxon_2697049
organism
active surveillance in response to outbreak
sample capture status
Dutch COVID-19 response sample sequencing
title