Dutch COVID-19 response sample sequencing
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.
organism
Severe acute respiratory syndrome coronavirus 2
host health state
not collected
host scientific name
Homo sapiens
collection date
2023
sample capture status
active surveillance in response to outbreak
scientific_name
Severe acute respiratory syndrome coronavirus 2
common name
Human coronavirus 2019
host subject id
restricted access
geographic location (region and locality)
Zuid-Holland
host common name
Human
host sex
not provided
isolate
hCoV-19/Netherlands/ZH-EMC-8781/2024
collector name
Dutch COVID-19 response team
ENA-FIRST-PUBLIC
2024-07-23T20:44:53Z
ENA-LAST-UPDATE
2024-07-23T20:44:53Z
GISAID Accession ID
EPI_ISL_19281404
collecting institution
not provided
isolation source host-associated
Throat/Nasal
geographic location (country and/or sea)
Netherlands
ENA-FIRST-PUBLIC
2024-07-23
ENA-LAST-UPDATE
2024-07-23