organism: Severe acute respiratory syndrome coronavirus 2
description: 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.
identifiers.namespace: BioSample
identifiers.id: SAMEA111330171
identifiers.namespace: Dutch COVID-19 response team
identifiers.id: Run719_BC40
attributes.tag: collecting institution
attributes.value: not provided
attributes.tag: collection date
attributes.value: 2022-08-10
attributes.tag: collector name
attributes.value: Dutch COVID-19 response team
attributes.tag: geographic location (country and/or sea)
attributes.value: Netherlands
attributes.tag: geographic location (region and locality)
attributes.value: Zuid-Holland
attributes.tag: GISAID Accession ID
attributes.value: EPI_ISL_14798595
attributes.tag: host common name
attributes.value: Human
attributes.tag: host health state
attributes.value: not collected
attributes.tag: host scientific name
attributes.value: Homo sapiens
attributes.tag: host sex
attributes.value: not provided
attributes.tag: host subject id
attributes.value: restricted access
attributes.tag: isolate
attributes.value: hCoV-19/Netherlands/ZH-EMC-6648/2022
attributes.tag: isolation source host-associated
attributes.value: not collected
attributes.tag: sample capture status
attributes.value: active surveillance in response to outbreak
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-09-10
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-09-10