demo_scenarios_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	RR-SAMP33456												Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)			Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)			2021-12-30	day		Canada	Saskatchewan		Severe acute respiratory syndrome coronavirus 2	Not Provided	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Oropharynx (OP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	23	year	20 - 29	Male																															Baseline surveillance (random sampling)	Not Provided	2022-01-03		1200bp	Illumina prep kit		Illumina NextSeq 2000		Viral sequencing was performed using on a tiling amplicon approach based on the Midnight primer amplicon scheme. Sequencing was performed using an Illumina NextSeq 2000 sequencing instrument.		Midnight	https://github.com/RR-SC2/supersweetpipeline	https://github.com/RR-SC2/dehosting
4	abcd1234			PH-2468ANT								EPI_ISL_436489	National Microbiology Laboratory (NML)			National Microbiology Laboratory (NML)			2021-03-16	day		Canada	Newfoundland and Labrador		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/NML-abcd1234/2021	Diagnostic testing	Not Provided	Swab		Not Applicable	Nasopharynx (NP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	36	year	30 - 39	Female	Canada	Newfoundland and Labrador											Antarctica			Antarctica			travelled to outpost where there was an exposure				Contact with Known COVID-19 Case								Surveillance of international border crossing by air travel	Not Provided	2021-03-24			NEBNext ARTIC SARS-CoV-2 FS Library Prep Kit		Illumina MiSeq	ARTIC V3	Viral sequencing was performed using on a tiling amplicon approach based on the NEB VarSkip primer amplicon scheme. Sequencing was performed using an Illumina MiSeq sequencing instrument.		NEB VarSkip primers	https://github.com/phac-nml/ncov2019-artic-nf	https://github.com/phac-nml/ncov-dehoster
5	BC-8585858585											EPI_ISL_436499	BCCDC Public Health Laboratory			BCCDC Public Health Laboratory			2021-10-04	day		Canada	British Columbia		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/BC-BC-8585858585/2021	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	46	year	40 - 49	Male									Astrazeneca (Vaxzevria)	1	2021-07-01																				Intra-jurisdictional outbreak investigation	Not Provided	2021-10-07		1200bp	Illumina prep kit and Nextera XT indices		Illumina NovaSeq 6000		Viral sequencing was performed using on a tiling amplicon approach based on the Freed primer amplicon scheme with added spike-in primers, using an Illumina prep kit and Nextera XT indices. Sequencing was performed using an Illumina NextSeq 2000 sequencing instrument.		Freed + spike-in primers	https://github.com/jaleezyy/covid-19-signal	https://github.com/jaleezyy/covid-19-signal
6	MB-xyz456	Switch Health	SW12345678									EPI_ISL_555555	Manitoba Cadham Provincial Laboratory			National Microbiology Laboratory (NML)			2021-12-23	day		Canada	Manitoba		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/MB-MB-xyz456/2021	Diagnostic testing	Not Provided	Swab		Not Applicable	Nasopharynx (NP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	Missing	Missing	30 - 39	Missing																															Baseline surveillance (random sampling)	Not Provided	2021-12-27		400bp			Illumina MiSeq	ARTIC V4	Viral sequencing was performed using on a tiling amplicon approach based on the ARTIC 4.1 primer amplicon scheme. Sequencing was performed using an Illumina MiSeq sequencing instrument.		ARTIC V4.1	https://github.com/phac-nml/ncov2019-artic-nf	https://github.com/phac-nml/ncov-dehoster
7	AB-VOC-555											EPI_ISL_999991	Alberta ProvLab North (APLN)			Alberta ProvLab North (APLN)			2022-01-05	day		Canada	Alberta		Severe acute respiratory syndrome coronavirus 2	hCov-19/Canada/AB-AB-VOC-555/2022	Diagnostic testing	Not Provided	Not Applicable		Not Applicable	Oropharynx (OP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable								Homo sapiens				COVID-19	Missing	Missing	30 - 39	Missing																															Screening for Variants of Concern (VoC)	Screened for S gene target failure (S dropout)	2022-01-12		400bp			Oxford Nanopore MinION	ARTIC V4	Viral sequencing was performed using on a tiling amplicon approach based on the Midnight primer amplicon scheme. Sequencing was performed using an Oxford Nanopore sequencing instrument.		Midnight	https://github.com/ABPHL/ncov2019-process	Not Applicable
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