characteristics.text: ERC000033
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-05-27T12:14:01Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-08-23T18:21:01Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110037338
characteristics.characteristic: External Id
characteristics.text: EPI_ISL_12822455
characteristics.characteristic: GISAID Accession ID
characteristics.text: Dutch COVID-19 response team
characteristics.characteristic: INSDC center name
characteristics.text: 2022-05-27T12:14:01Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-08-23T18:21:01Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12081062
characteristics.characteristic: SRA accession
characteristics.text: Run653_BC34
characteristics.characteristic: Submitter Id
characteristics.text: ERASMUS MC, UNIVERISTY MEDICAL CENTER
characteristics.characteristic: broker name
characteristics.text: not provided
characteristics.characteristic: collecting institution
characteristics.text: 2022-01-28
characteristics.characteristic: collection date
characteristics.text: Dutch COVID-19 response team
characteristics.characteristic: collector name
characteristics.text: Human coronavirus 2019
characteristics.characteristic: common name
characteristics.text: 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.
characteristics.characteristic: description
characteristics.text: Netherlands
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: Zuid-Holland
characteristics.characteristic: geographic location (region and locality)
characteristics.text: Human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: host common name
characteristics.text: not collected
characteristics.characteristic: host health state
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: host scientific name
characteristics.text: not provided
characteristics.characteristic: host sex
characteristics.text: restricted access
characteristics.characteristic: host subject id
characteristics.text: hCoV-19/Netherlands/ZH-EMC-5944/2022
characteristics.characteristic: isolate
characteristics.text: not collected
characteristics.characteristic: isolation source host associated
characteristics.text: Severe acute respiratory syndrome coronavirus 2
characteristics.characteristic: organism
characteristics.text: active surveillance in response to outbreak
characteristics.characteristic: sample capture status
characteristics.text: Severe acute respiratory syndrome coronavirus 2
characteristics.characteristic: scientific_name
characteristics.text: Dutch COVID-19 response sample sequencing
characteristics.characteristic: title