Severe acute respiratory syndrome coronavirus 2
A SARS-CoV-2 specfic 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.
ENA-FIRST-PUBLIC
2023-05-19
ENA-LAST-UPDATE
2023-05-19
External Id
SAMEA113534215
GISAID Accession ID
EPI_ISL_17686371
INSDC center alias
Dutch COVID-19 response team
INSDC center name
Dutch COVID-19 response team
INSDC first public
2023-05-19T20:16:52Z
INSDC last update
2023-05-19T20:16:52Z
INSDC status
public
Submitter Id
Run848_BC72
broker name
Submission account for department of Viroscience's Research Teams, ErasmusMC
collecting institution
not provided
collection date
2023
collector name
Dutch COVID-19 response team
common name
Human coronavirus 2019
geographic location (country and/or sea)
Netherlands
geographic location (region and locality)
Noord-Brabant
host common name
Human
host health state
not collected
host scientific name
Homo sapiens
host sex
not provided
host subject id
restricted access
isolate
hCoV-19/Netherlands/NB-EMC-5357/2023
isolation source host-associated
Throat/Nasal
sample capture status
active surveillance in response to outbreak
sample name
Run848_BC72
scientific_name
Severe acute respiratory syndrome coronavirus 2