title: Dutch COVID-19 response sample sequencing
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.
attributes.tag: ENA first public
attributes.value: 2022-05-30
attributes.tag: ENA last update
attributes.value: 2022-05-30
attributes.tag: External Id
attributes.value: SAMEA14491464
attributes.tag: GISAID Accession ID
attributes.value: EPI_ISL_12956856
attributes.tag: INSDC center alias
attributes.value: Dutch COVID-19 response team
attributes.tag: INSDC center name
attributes.value: Dutch COVID-19 response team
attributes.tag: INSDC first public
attributes.value: 2022-05-30T20:16:23Z
attributes.tag: INSDC last update
attributes.value: 2022-05-30T20:16:23Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: Run659_BC04
attributes.tag: broker name
attributes.value: Submission account for department of Viroscience's Research Teams, ErasmusMC
attributes.tag: collecting institution
attributes.value: not provided
attributes.tag: collection date
attributes.value: 2022-05-12
attributes.tag: collector name
attributes.value: Dutch COVID-19 response team
attributes.tag: common name
attributes.value: Human coronavirus 2019
attributes.tag: geographic location (country and/or sea)
attributes.value: Netherlands
attributes.tag: geographic location (region and locality)
attributes.value: Zuid-Holland
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-6030/2022
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: sample name
attributes.value: Run659_BC04