demo_dataset_golden_Jan_2022.xlsx

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U	V	W	X	Y	Z	AA	AB	AC	AD	AE	AF	AG	AH	AI	AJ	AK	AL	AM	AN	AO	AP	AQ	AR	AS	AT	AU	AV	AW	AX	AY	AZ	BA	BB	BC	BD	BE	BF	BG	BH	BI	BJ	BK	BL	BM	BN	BO	BP	BQ	BR	BS	BT	BU	BV	BW	BX	BY	BZ	CA	CB	CC	CD	CE	CF	CG	CH	CI	CJ	CK	CL	CM	CN	CO	CP	CQ	CR	CS	CT	CU	CV
1	Database Identifiers												Sample collection and processing																															Host Information																	Host vaccination information					Host exposure information												Host reinfection information						Sequencing												Bioinformatics and QC metrics
2	specimen collector sample ID	third party lab service provider name	third party lab sample ID	case ID	Related specimen primary ID	IRIDA sample name	umbrella bioproject accession	bioproject accession	biosample accession	SRA accession	GenBank accession	GISAID accession	sample collected by	sample collector contact email	sample collector contact address	sequence submitted by	sequence submitter contact email	sequence submitter contact address	sample collection date	sample collection date precision	sample received date	geo_loc_name (country)	geo_loc_name (state/province/territory)	geo_loc_name (city)	organism	isolate	purpose of sampling	purpose of sampling details	NML submitted specimen type	Related specimen relationship type	anatomical material	anatomical part	body product	environmental material	environmental site	collection device	collection method	collection protocol	specimen processing	lab host	passage number	passage method	biomaterial extracted	host (common name)	host (scientific name)	host health state	host health status details	host health outcome	host disease	host age	host age unit	host age bin	host gender	host residence geo_loc name (country)	host residence geo_loc name (state/province/territory)	host subject ID	symptom onset date	signs and symptoms	pre-existing conditions and risk factors	complications	host vaccination status	vaccine name	number of vaccine doses received	first dose vaccination date	last dose vaccination date	location of exposure geo_loc name (country)	destination of most recent travel (city)	destination of most recent travel (state/province/territory)	destination of most recent travel (country)	most recent travel departure date	most recent travel return date	travel history	exposure event	exposure contact level	host role	exposure setting	exposure details	prior SARS-CoV-2 infection	prior SARS-CoV-2 infection isolate	prior SARS-CoV-2 infection date	prior SARS-CoV-2 antiviral treatment	prior SARS-CoV-2 antiviral treatment agent	prior SARS-CoV-2 antiviral treatment date	purpose of sequencing	purpose of sequencing details	sequencing date	library ID	amplicon size	library preparation kit	flow cell barcode	sequencing instrument	sequencing protocol name	sequencing protocol	sequencing kit number	amplicon pcr primer scheme	raw sequence data processing method	dehosting method	consensus sequence name	consensus sequence filename	consensus sequence filepath
3	abcd1234											EPI_ISL_436489	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-12-15	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-abcd1234/2021	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Nasopharynx (NP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	33	year	30 - 39	Female																															Baseline surveillance (random sampling)	Not Provided	2022-01-02		1200	Illumina Library Prep Kit		Illumina NovaSeq 6000		Viral sequencing was preformed using a tiled amplicon strategy using the Freed (2020) amplicon primer scheme and an Illumina Library Prep Kit. Sequencing was performed on an Illumina NovaSeq 6000 sequencing instrument.		Freed	BCCDC_filter_process_method 1.5.1	https://github.com/phac-nml/ncov-dehoster
4	abcd1235											EPI_ISL_436491	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-12-17	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-abcd1235/2021	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Oropharynx (OP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	67	year	60 - 69	Male																															Targeted surveillance (non-random sampling)	Testing asymptomatic patients	2022-01-02		1200	Illumina Library Prep Kit		Illumina NextSeq 550		Viral sequencing was preformed using a tiled amplicon strategy using the Freed (2020) amplicon primer scheme and an Illumina Library Prep Kit. Sequencing was performed on an Illumina NextSeq 550 sequencing instrument.		Freed	BCCDC_filter_process_method 1.5.1	https://github.com/phac-nml/ncov-dehoster
5	abcd1236											EPI_ISL_555555	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-12-15	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-abcd1236/2021	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Nasopharynx (NP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	89	year	80 - 89	Female																															Screening for Variants of Concern (VoC)	Not Provided	2022-01-02		1200	Illumina Library Prep Kit		Illumina MiSeq		Viral sequencing was preformed using a tiled amplicon strategy using the Freed (2020) amplicon primer scheme and an Illumina Library Prep Kit. Sequencing was performed on an Illumina MiSeq sequencing instrument.		Freed	BCCDC_filter_process_method 1.5.2	https://github.com/phac-nml/ncov-dehoster
6	abcd1237											EPI_ISL_888887	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-12-21	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-abcd1237/2021	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Nasopharynx (NP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	11	year	10 - 19	Female																															Sample has epidemiological link to Omicron Variant	Not Provided	2022-01-02		2000	Illumina Library Prep Kit		Illumina MiSeq		Viral sequencing was preformed using a tiled amplicon strategy using the Resende (2020) amplicon primer scheme and an Illumina Library Prep Kit. Sequencing was performed on an Illumina MiSeq sequencing instrument.		Resende	Trimmomatic 0.38	https://github.com/phac-nml/ncov-dehoster
7	abcd1238											EPI_ISL_999991	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-12-30	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-abcd1238/2021	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Not Applicable	Not Applicable	Not Applicable	Not Applicable	Not Applicable	Saline gargle (mouth rinse and gargle)								Homo sapiens				COVID-19	2	year	0 - 9	Male																															Surveillance of international border crossing by air travel or ground transport	Airport testing	2022-01-02		400	Native Barcoding Kit		Oxford Nanopore MinION		Viral sequencing was preformed using a tiled amplicon strategy using the ARTIC V4 amplicon primer scheme and a Native Barcoding Kit. Sequencing was performed on an Oxford Nanopore MinION sequencing instrument.		ARTIC V4	https://github.com/phac-nml/ncov2019-artic-nf	Nanostripper 1.0
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