sars-cov-2-data-spec-json/PHA4GE SARS-CoV-2 Standardised Terms.csv at master · pha4ge/sars-cov-2-data-spec-json · GitHub

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Interface Label;Required/Optional;Definition;Ontology;Value Type;Example;Guidance;Values
specimen collector sample ID;Required;The user-defined name for the sample. ;GENEPIO:0001123;String;prov_rona_99;Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible.;
umbrella bioproject accession;Optional;The INSDC umbrella accession number of the BioProject to which the BioSample belongs. ;GENEPIO:0001133;Bioproject_ID;PRJNA623807;Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects.;
bioproject accession;Optional;The INSDC accession number of the BioProject(s) to which the BioSample belongs. ;GENEPIO:0001136;Bioproject_ID;PRJNA12345;Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects.;
biosample accession;Recommended;The identifier assigned to a BioSample in INSDC archives.;GENEPIO:0001139;Biosample_ID;SAMN14180202;Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA.;
SRA accession;Optional;The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.;GENEPIO:0001142;SRA_ID;SRR11177792;Store the accession assigned to the submitted 'run'. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR.;
GenBank/ENA/DDBJ accession;Optional;The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.;GENEPIO:0001145;Genbank_ID;MN908947.3;Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly).;
GISAID accession;Optional;The GISAID accession number assigned to the sequence.;GENEPIO:0001147;GISAID_ID;EPI_ISL_123456;Store the accession returned from the GISAID submission.;
GISAID virus name;Optional;The user-defined GISAID virus name assigned to the sequence.;GENEPIO:0100282;String;hCoV-19/Canada/prov_rona_99/2020;GISAID virus names should be in the format 'hCoV-19/Country/Identifier/year'.;
host specimen voucher;Optional;Identifier for the physical specimen.;GENEPIO:0100283;String;URI: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542 INSDC triplet: UAM:Mamm:52179;Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=[<institution-code>:[<collection-code>:]]<specimen_id>): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier;
sample collected by;Required;The name of the agency that collected the original sample.;GENEPIO:0001153;String;Public Health Agency of Canada;The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions.;
sample collector contact email;Optional;The email address of the contact responsible for follow-up regarding the sample.;GENEPIO:0001156;Email;johnnyblogs@lab.ca;The email address can represent a specific individual or laboratory.;
sample collector contact address;Optional;The mailing address of the agency submitting the sample.;GENEPIO:0001158;String;655 Lab St,Vancouver, British Columbia, V5N 2A2, Canada;The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code;
sequence submitted by;Required;The name of the agency that generated the sequence.;GENEPIO:0001159;String;Centers for Disease Control and Prevention;The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions.;
sequence submitter contact email;Optional;The email address of the contact responsible for follow-up regarding the sequence.;GENEPIO:0001165;Email;RespLab@lab.ca;The email address can represent a specific individual or laboratory.;
sequence submitter contact address;Optional;The mailing address of the agency submitting the sequence.;GENEPIO:0001167;String;123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada;The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code;
sample collection date;Required;The date on which the sample was collected. ;GENEPIO:0001174;Date;19/03/2020;Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add 'jitter' to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ðreceived dateð may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format 'YYYY-MM-DD'.;
sample received date;Optional;The date on which the sample was received.;GENEPIO:0001179;Date;20/03/2020;The date the sample was received by a lab that was not the point of collection. ISO 8601 standard 'YYYY-MM-DD'.;
geo_loc name (country);Required;The country of origin of the sample.;GENEPIO:0001181;Enums;South Africa [GAZ:00001094];Provide the country name from the pick list in the template;"['Afghanistan [GAZ:00006882]', 'Albania [GAZ:00002953]', 'Algeria [GAZ:00000563]', 'American Samoa [GAZ:00003957]', 'Andorra [GAZ:00002948]', 'Angola [GAZ:00001095]', 'Anguilla [GAZ:00009159]', 'Antarctica [GAZ:00000462]', 'Antigua and Barbuda [GAZ:00006883]', 'Argentina [GAZ:00002928]', 'Armenia [GAZ:00004094]', 'Aruba [GAZ:00004025]', 'Ashmore and Cartier Islands [GAZ:00005901]', 'Australia [GAZ:00000463]', 'Austria [GAZ:00002942]', 'Azerbaijan [GAZ:00004941]', 'Bahamas [GAZ:00002733]', 'Bahrain [GAZ:00005281]', 'Baker Island [GAZ:00007117]', 'Bangladesh [GAZ:00003750]', 'Barbados [GAZ:00001251]', 'Bassas da India [GAZ:00005810]', 'Belarus [GAZ:00006886]', 'Belgium [GAZ:00002938]', 'Belize [GAZ:00002934]', 'Benin [GAZ:00000904]', 'Bermuda [GAZ:00001264]', 'Bhutan [GAZ:00003920]', 'Bolivia [GAZ:00002511]', 'Borneo [GAZ:00025355]', 'Bosnia and Herzegovina [GAZ:00006887]', 'Botswana [GAZ:00001097]', 'Bouvet Island [GAZ:00001453]', 'Brazil [GAZ:00002828]', 'British Virgin Islands [GAZ:00003961]', 'Brunei [GAZ:00003901]', 'Bulgaria [GAZ:00002950]', 'Burkina Faso [GAZ:00000905]', 'Burundi [GAZ:00001090]', 'Cambodia [GAZ:00006888]', 'Cameroon [GAZ:00001093]', 'Canada [GAZ:00002560]', 'Cape Verde [GAZ:00001227]', 'Cayman Islands [GAZ:00003986]', 'Central African Republic [GAZ:00001089]', 'Chad [GAZ:00000586]', 'Chile [GAZ:00002825]', 'China [GAZ:00002845]', 'Christmas Island [GAZ:00005915]', 'Clipperton Island [GAZ:00005838]', 'Cocos Islands [GAZ:00009721]', 'Colombia [GAZ:00002929]', 'Comoros [GAZ:00005820]', 'Cook Islands [GAZ:00053798]', 'Coral Sea Islands [GAZ:00005917]', 'Costa Rica [GAZ:00002901]', ""Cote d'Ivoire [GAZ:00000906]"", 'Croatia [GAZ:00002719]', 'Cuba [GAZ:00003762]', 'Curacao [GAZ:00012582]', 'Cyprus [GAZ:00004006]', 'Czech Republic [GAZ:00002954]', 'Democratic Republic of the Congo [GAZ:00001086]', 'Denmark [GAZ:00005852]', 'Djibouti [GAZ:00000582]', 'Dominica [GAZ:00006890]', 'Dominican Republic [GAZ:00003952]', 'Ecuador [GAZ:00002912]', 'Egypt [GAZ:00003934]', 'El Salvador [GAZ:00002935]', 'Equatorial Guinea [GAZ:00001091]', 'Eritrea [GAZ:00000581]', 'Estonia [GAZ:00002959]', 'Eswatini [GAZ:00001099]', 'Ethiopia [GAZ:00000567]', 'Europa Island [GAZ:00005811]', 'Falkland Islands (Islas Malvinas) [GAZ:00001412]', 'Faroe Islands [GAZ:00059206]', 'Fiji [GAZ:00006891]', 'Finland [GAZ:00002937]', 'France [GAZ:00003940]', 'French Guiana [GAZ:00002516]', 'French Polynesia [GAZ:00002918]', 'French Southern and Antarctic Lands [GAZ:00003753]', 'Gabon [GAZ:00001092]', 'Gambia [GAZ:00000907]', 'Gaza Strip [GAZ:00009571]', 'Georgia [GAZ:00004942]', 'Germany [GAZ:00002646]', 'Ghana [GAZ:00000908]', 'Gibraltar [GAZ:00003987]', 'Glorioso Islands [GAZ:00005808]', 'Greece [GAZ:00002945]', 'Greenland [GAZ:00001507]', 'Grenada [GAZ:02000573]', 'Guadeloupe [GAZ:00067142]', 'Guam [GAZ:00003706]', 'Guatemala [GAZ:00002936]', 'Guernsey [GAZ:00001550]', 'Guinea [GAZ:00000909]', 'Guinea-Bissau [GAZ:00000910]', 'Guyana [GAZ:00002522]', 'Haiti [GAZ:00003953]', 'Heard Island and McDonald Islands [GAZ:00009718]', 'Honduras [GAZ:00002894]', 'Hong Kong [GAZ:00003203]', 'Howland Island [GAZ:00007120]', 'Hungary [GAZ:00002952]', 'Iceland [GAZ:00000843]', 'India [GAZ:00002839]', 'Indonesia [GAZ:00003727]', 'Iran [GAZ:00004474]', 'Iraq [GAZ:00004483]', 'Ireland [GAZ:00002943]', 'Isle of Man [GAZ:00052477]', 'Israel [GAZ:00002476]', 'Italy [GAZ:00002650]', 'Jamaica [GAZ:00003781]', 'Jan Mayen [GAZ:00005853]', 'Japan [GAZ:00002747]', 'Jarvis Island [GAZ:00007118]', 'Jersey [GAZ:00001551]', 'Johnston Atoll [GAZ:00007114]', 'Jordan [GAZ:00002473]', 'Juan de Nova Island [GAZ:00005809]', 'Kazakhstan [GAZ:00004999]', 'Kenya [GAZ:00001101]', 'Kerguelen Archipelago [GAZ:00005682]', 'Kingman Reef [GAZ:00007116]', 'Kiribati [GAZ:00006894]', 'Kosovo [GAZ:00011337]', 'Kuwait [GAZ:00005285]', 'Kyrgyzstan [GAZ:00006893]', 'Laos [GAZ:00006889]', 'Latvia [GAZ:00002958]', 'Lebanon [GAZ:00002478]', 'Lesotho [GAZ:00001098]', 'Liberia [GAZ:00000911]', 'Libya [GAZ:00000566]', 'Liechtenstein [GAZ:00003858]', 'Line Islands [GAZ:00007144]', 'Lithuania [GAZ:00002960]', 'Luxembourg [GAZ:00002947]', 'Macau [GAZ:00003202]', 'Madagascar [GAZ:00001108]', 'Malawi [GAZ:00001105]', 'Malaysia [GAZ:00003902]', 'Maldives [GAZ:00006924]', 'Mali [GAZ:00000584]', 'Malta [GAZ:00004017]', 'Marshall Islands [GAZ:00007161]', 'Martinique [GAZ:00067143]', 'Mauritania [GAZ:00000583]', 'Mauritius [GAZ:00003745]', 'Mayotte [GAZ:00003943]', 'Mexico [GAZ:00002852]', 'Micronesia [GAZ:00005862]', 'Midway Islands [GAZ:00007112]', 'Moldova [GAZ:00003897]', 'Monaco [GAZ:00003857]', 'Mongolia [GAZ:00008744]', 'Montenegro [GAZ:00006898]', 'Montserrat [GAZ:00003988]', 'Morocco [GAZ:00000565]', 'Mozambique [GAZ:00001100]', 'Myanmar [GAZ:00006899]', 'Namibia [GAZ:00001096]', 'Nauru [GAZ:00006900]', 'Navassa Island [GAZ:00007119]', 'Nepal [GAZ:00004399]', 'Netherlands [GAZ:00002946]', 'New Caledonia [GAZ:00005206]', 'New Zealand [GAZ:00000469]', 'Nicaragua [GAZ:00002978]', 'Niger [GAZ:00000585]', 'Nigeria [GAZ:00000912]', 'Niue [GAZ:00006902]', 'Norfolk Island [GAZ:00005908]', 'North Korea [GAZ:00002801]', 'North Macedonia [GAZ:00006895]', 'North Sea [GAZ:00002284]', 'Northern Mariana Islands [GAZ:00003958]', 'Norway [GAZ:00002699]', 'Oman [GAZ:00005283]', 'Pakistan [GAZ:00005246]', 'Palau [GAZ:00006905]', 'Panama [GAZ:00002892]', 'Papua New Guinea [GAZ:00003922]', 'Paracel Islands [GAZ:00010832]', 'Paraguay [GAZ:00002933]', 'Peru [GAZ:00002932]', 'Philippines [GAZ:00004525]', 'Pitcairn Islands [GAZ:00005867]', 'Poland [GAZ:00002939]', 'Portugal [GAZ:00004126]', 'Puerto Rico [GAZ:00006935]', 'Qatar [GAZ:00005286]', 'Republic of the Congo [GAZ:00001088]', 'Reunion [GAZ:00003945]', 'Romania [GAZ:00002951]', 'Ross Sea [GAZ:00023304]', 'Russia [GAZ:00002721]', 'Rwanda [GAZ:00001087]', 'Saint Helena [GAZ:00000849]', 'Saint Kitts and Nevis [GAZ:00006906]', 'Saint Lucia [GAZ:00006909]', 'Saint Pierre and Miquelon [GAZ:00003942]', 'Saint Martin [GAZ:00005841]', 'Saint Vincent and the Grenadines [GAZ:02000565]', 'Samoa [GAZ:00006910]', 'San Marino [GAZ:00003102]', 'Sao Tome and Principe [GAZ:00006927]', 'Saudi Arabia [GAZ:00005279]', 'Senegal [GAZ:00000913]', 'Serbia [GAZ:00002957]', 'Seychelles [GAZ:00006922]', 'Sierra Leone [GAZ:00000914]', 'Singapore [GAZ:00003923]', 'Sint Maarten [GAZ:00012579]', 'Slovakia [GAZ:00002956]', 'Slovenia [GAZ:00002955]', 'Solomon Islands [GAZ:00005275]', 'Somalia [GAZ:00001104]', 'South Africa [GAZ:00001094]', 'South Georgia and the South Sandwich Islands [GAZ:00003990]', 'South Korea [GAZ:00002802]', 'South Sudan [GAZ:00233439]', 'Spain [GAZ:00003936]', 'Spratly Islands [GAZ:00010831]', 'Sri Lanka [GAZ:00003924]', 'State of Palestine [GAZ:00002475]', 'Sudan [GAZ:00000560]', 'Suriname [GAZ:00002525]', 'Svalbard [GAZ:00005396]', 'Swaziland [GAZ:00001099]', 'Sweden [GAZ:00002729]', 'Switzerland [GAZ:00002941]', 'Syria [GAZ:00002474]', 'Taiwan [GAZ:00005341]', 'Tajikistan [GAZ:00006912]', 'Tanzania [GAZ:00001103]', 'Thailand [GAZ:00003744]', 'Timor-Leste [GAZ:00006913]', 'Togo [GAZ:00000915]', 'Tokelau [GAZ:00260188]', 'Tonga [GAZ:00006916]', 'Trinidad and Tobago [GAZ:00003767]', 'Tromelin Island [GAZ:00005812]', 'Tunisia [GAZ:00000562]', 'Turkey [GAZ:00000558]', 'Turkmenistan [GAZ:00005018]', 'Turks and Caicos Islands [GAZ:00003955]', 'Tuvalu [GAZ:00009715]', 'USA [GAZ:00002459]', 'Uganda [GAZ:00001102]', 'Ukraine [GAZ:00002724]', 'United Arab Emirates [GAZ:00005282]', 'United Kingdom [GAZ:00002637]', 'Uruguay [GAZ:00002930]', 'Uzbekistan [GAZ:00004979]', 'Vanuatu [GAZ:00006918]', 'Venezuela [GAZ:00002931]', 'Viet Nam [GAZ:00003756]', 'Virgin Islands [GAZ:00003959]', 'Wake Island [GAZ:00007111]', 'Wallis and Futuna [GAZ:00007191]', 'West Bank [GAZ:00009572]', 'Western Sahara [GAZ:00000564]', 'Yemen [GAZ:00005284]', 'Zambia [GAZ:00001107]', 'Zimbabwe [GAZ:00001106]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
geo_loc name (state/province/territory);Required;The state/province/territory of origin of the sample.;GENEPIO:0001185;String;Western Cape;Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz;
geo_loc name (county/region);Optional;The county/region of origin of the sample.;GENEPIO:0100280;String;Derbyshire;Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz;
geo_loc name (city);Optional;The city of origin of the sample.;GENEPIO:0001189;String;Vancouver;Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz;
geo_loc latitude;Optional;The latitude coordinates of the geographical location of sample collection.;OBI:0001620;String;38.98 N;Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format 'd[d.dddd] N|S'.;
geo_loc longitude;Optional;The longitude coordinates of the geographical location of sample collection.;OBI:0001621;String;77.11 W;Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format 'd[dd.dddd] W|E'.;
organism;Required;Taxonomic name of the organism.;GENEPIO:0001191;Enums;Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049];Select 'Severe acute respiratory syndrome coronavirus 2' if sequencing SARS-CoV-2. If another Coronaviridae is being sequenced, provide the taxonomic name from NCBITaxon. Search for taxonomy terms at https://www.ebi.ac.uk/ols/ontologies/ncbitaxon.;['Coronaviridae [NCBITaxon:11118]', ' Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
isolate;Required;Identifier of the specific isolate.;GENEPIO:0001644;String;SARS-CoV-2/human/USA/CA-CDPH-001/2020;This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the 'isolate' name is propagated throughtout different databases. As such, structure the 'isolate' name to be ICTV/INSDC compliant in the following format: 'SARS-CoV-2/host/country/sampleID/date'.;
culture collection;Optional;The name of the source collection and unique culture identifier. ;GENEPIO:0100284;String;"/culture_collection=""ATCC:26370""";Format: '<institution-code>:[<collection-code>:]<culture_id>'. For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.;
purpose of sampling;Recommended;The reason that the sample was collected.;GENEPIO:0001198;Enums;Diagnostic Testing [GENEPIO:0100002];Select a value from the pick list in the template.;['Cluster/Outbreak Investigation [GENEPIO:0100001]', 'Diagnostic Testing [GENEPIO:0100002]', 'Research [GENEPIO:0100003]', ' Protocol Testing [GENEPIO:0100024]', 'Surveillance [GENEPIO:0100004]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
purpose of sampling details;Optional;Further details pertaining to the reason the sample was collected.;GENEPIO:0001200;String;Screening of bat specimens in museum collections.;Provide a free text description of the sampling strategy or samples collected.;
sample plan name;Optional;The name of the sample plan implemented for sample collection.;GENEPIO:0100285;String;CanCOGeN Sampling Strategy 1.0;Provide the name and version of the sample plan outlining the sample strategy.;
sample collected in quarantine;Optional;Whether the sample was collected from an individual in quarantine.;GENEPIO:0100277;Enums;Yes [NCIT:C49488];Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template.;['Yes [NCIT:C49488]', 'No [NCIT:C49487]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
anatomical material;Optional;A substance obtained from an anatomical part of an organism e.g. tissue, blood.;GENEPIO:0001211;Enums;Blood [UBERON:0000178];Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.;['Blood [UBERON:0000178]', 'Fluid [UBERON:0006314]', ' Fluid (Cerebrospinal (CSF)) [UBERON:0001359]', ' Fluid (Pericardial) [UBERON:0002409]', ' Fluid (Pleural) [UBERON:0001087]', ' Fluid (Vaginal) [UBERON:0036243]', ' Fluid (Amniotic) [UBERON:0000173]', 'Saliva [UBERON:0001836]', 'Tissue [UBERON:0000479]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
anatomical part;Optional;An anatomical part of an organism e.g. oropharynx. ;GENEPIO:0001214;Enums;Nasopharynx (NP) [UBERON:0001728];Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.;['Anus [UBERON:0001245]', 'Duodenum [UBERON:0002114]', 'Eye [UBERON:0000970]', 'Intestine [UBERON:0000160]', 'Lower respiratory tract [UBERON:0001558]', ' Bronchus [UBERON:0002185]', ' Lung [UBERON:0002048]', ' Bronchiole [UBERON:0002186]', ' Alveolar sac [UBERON:0002169]', ' Pleural sac [UBERON:0009778]', ' Pleural cavity [UBERON:0002402]', ' Trachea [UBERON:0003126]', 'Rectum [UBERON:0001052]', 'Skin [UBERON:0001003]', 'Stomach [UBERON:0000945]', 'Upper respiratory tract [UBERON:0001557]', ' Anterior Nares [UBERON:2001427]', ' Esophagus [UBERON:0001043]', ' Ethmoid sinus [UBERON:0002453]', ' Nasal Cavity [UBERON:0001707]', ' Middle Nasal Turbinate [UBERON:0005921]', ' Inferior Nasal Turbinate [UBERON:0005922]', ' Nasopharynx (NP) [UBERON:0001728]', ' Oropharynx (OP) [UBERON:0001729]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
body product;Optional;A substance excreted/secreted from an organism e.g. feces, urine, sweat.;GENEPIO:0001216;Enums;Feces [UBERON:0001988];Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.;['Breast Milk [UBERON:0001913]', 'Feces [UBERON:0001988]', 'Mucus [UBERON:0000912]', 'Semen [UBERON:0006530]', 'Sputum [UBERON:0007311]', 'Sweat [UBERON:0001089]', 'Tear [UBERON:0001827]', 'Urine [UBERON:0001088]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
environmental material;Optional;A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.;GENEPIO:0001223;Enums;Face Mask [OBI:0002787];Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.;['Air vent [ENVO:03501208]', 'Banknote [ENVO:00003896]', 'Bed rail [ENVO:03501209]', 'Building Floor [ENVO:01000486]', 'Cloth [ENVO:02000058]', 'Control Panel [ENVO:03501210]', 'Door [ENVO:03501220]', 'Door Handle [ENVO:03501211]', 'Face Mask [OBI:0002787]', 'Face Shield [OBI:0002791]', 'Food [FOODON:00002403]', 'Food Packaging [FOODON:03490100]', 'Glass [ENVO:01000481]', 'Handrail [ENVO:03501212]', 'Hospital Gown [OBI:0002796]', 'Light Switch [ENVO:03501213]', 'Locker [ENVO:03501214]', 'N95 Mask [OBI:0002790]', 'Nurse Call Button [ENVO:03501215]', 'Paper [ENVO:03501256]', 'Particulate Matter [ENVO:01000060]', 'Plastic [ENVO:01000404]', 'PPE Gown [GENEPIO:0100025]', 'Sewage [ENVO:00002018]', 'Sink [ENVO:01000990]', 'Soil [ENVO:00001998]', 'Stainless Steel [ENVO:03501216]', 'Tissue Paper [ENVO:03501217]', 'Toilet Bowl [ENVO:03501218]', 'Water [ENVO:00002006]', ' Wastewater [ENVO:00002001]', 'Window [ENVO:03501219]', 'Wood [ENVO:00002040]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
environmental site;Optional;An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.;GENEPIO:0001232;Enums;Hospital [ENVO:00002173];Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.;['Acute care facility [ENVO:03501135]', 'Animal house [ENVO:00003040]', 'Bathroom [ENVO:01000422]', 'Clinical assessment centre [ENVO:03501136]', 'Conference venue [ENVO:03501127]', 'Corridor [ENVO:03501121]', 'Daycare [ENVO:01000927]', 'Emergency room (ER) [ENVO:03501145]', 'Family practice clinic [ENVO:03501186]', 'Group home [ENVO:03501196]', 'Homeless shelter [ENVO:03501133]', 'Hospital [ENVO:00002173]', 'Intensive Care Unit (ICU) [ENVO:03501152]', 'Long Term Care Facility [ENVO:03501194]', 'Patient room [ENVO:03501180]', 'Prison [ENVO:03501204]', 'Production Facility [ENVO:01000536]', 'School [ENVO:03501130]', 'Sewage Plant [ENVO:00003043]', 'Subway train [ENVO:03501109]', 'Wet market [ENVO:03501198]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
collection device;Optional;The instrument or container used to collect the sample e.g. swab.;GENEPIO:0001234;Enums;Swab [GENEPIO:0100027];Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.;['Air filter [ENVO:00003968]', 'Blood Collection Tube [OBI:0002859]', 'Bronchoscope [OBI:0002826]', 'Collection Container [OBI:0002088]', 'Collection Cup [GENEPIO:0100026]', 'Fibrobronchoscope Brush [OBI:0002825]', 'Filter [GENEPIO:0100103]', 'Fine Needle [OBI:0002827]', 'Microcapillary tube [OBI:0002858]', 'Micropipette [OBI:0001128]', 'Needle [OBI:0000436]', 'Serum Collection Tube [OBI:0002860]', 'Sputum Collection Tube [OBI:0002861]', 'Suction Catheter [OBI:0002831]', 'Swab [GENEPIO:0100027]', 'Urine Collection Tube [OBI:0002862]', 'Virus Transport Medium [OBI:0002866]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
collection method;Optional;The process used to collect the sample e.g. phlebotomy, necropsy.;GENEPIO:0001241;Enums;Bronchoalveolar Lavage (BAL) [GENEPIO:0100032];Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.;['Amniocentesis [NCIT:C52009]', 'Aspiration [NCIT:C15631]', ' Suprapubic Aspiration [GENEPIO:0100028]', ' Tracheal Aspiration [GENEPIO:0100029]', ' Vacuum Aspiration [GENEPIO:0100030]', 'Biopsy [OBI:0002650]', ' Needle Biopsy [OBI:0002651]', 'Filtration [OBI:0302885]', 'Air Filtration [GENEPIO:0100031] ', 'Lavage [OBI:0600044]', ' Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]', ' Gastric Lavage [GENEPIO:0100033]', 'Lumbar Puncture [NCIT:C15327]', 'Necropsy [MMO:0000344]', 'Phlebotomy [NCIT:C28221]', 'Rinsing [GENEPIO:0002116]', ' Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]', 'Scraping [GENEPIO:0100035]', 'Swabbing [GENEPIO:0002117]', 'Finger Prick [GENEPIO:0100036]', 'Washout Tear Collection [GENEPIO:0100038]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
collection protocol;Optional;The name and version of a particular protocol used for sampling.;GENEPIO:0001243;String;SC2SamplingProtocol 1.2;Provide the name and version of the protocol used to collect the samples.;
specimen processing;Recommended;Any processing applied to the sample during or after receiving the sample. ;GENEPIO:0001253;Enums;Virus Passage [GENEPIO:0100039];Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in 'lab host', 'passage number', and 'passage method' fields. If none of the processes in the pick list apply, put 'not applicable'.;['Virus Passage [GENEPIO:0100039]', 'RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]', 'Specimens Pooled [OBI:0600016]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
lab host;Optional;Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.;GENEPIO:0001255;Enums;Vero E6 Cell Line [BTO:0004755];Type of cell line used for propagation. Select a value form the pick list. If not passaged, put 'not applicable'.;['293/ACE2 Cell Line [GENEPIO:0100041]', 'Caco2 Cell Line [BTO:0000195]', 'Calu3 Cell Line [BTO:0002750]', 'EFK3B Cell Line [GENEPIO:0100042]', 'HEK293T Cell Line [BTO:0002181]', 'HRCE Cell Line [GENEPIO:0100043]', 'Huh7 Cell Line [BTO:0001950]', 'LLCMk2 Cell Line [CLO:0007330]', 'MDBK Cell Line [BTO:0000836]', 'NHBE Cell Line [BTO:0002924]', 'PK-15 Cell Line [BTO:0001865]', 'RK-13 Cell Line [BTO:0002909]', 'U251 Cell Line [BTO:0002035]', 'Vero Cell Line [BTO:0001444]', ' Vero E6 Cell Line [BTO:0004755]', ' Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
passage number;Optional;Number of passages.;GENEPIO:0001261;Int;3;Provide number of known passages. If not passaged, put 'not applicable';
passage method;Optional;Description of how organism was passaged.;GENEPIO:0001264;String;AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.;Free text. Provide a short description. If not passaged, put 'not applicable'.;
biomaterial extracted;Optional;The biomaterial extracted from samples for the purpose of sequencing.;GENEPIO:0001266;Enums;RNA (Total) [OBI:0000895];Provide the biomaterial extracted from the pick list in the template.;['mRNA (cDNA) [OBI:0002754]', 'RNA (Total) [OBI:0000895]', 'RNA (Poly-A) [OBI:0000869]', 'RNA (Ribo-Depleted) [OBI:0002627]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
data abstraction details;Optional;A description of how any data elements were altered to preserve patient privacy.;GENEPIO:0100278;String;Jitter added to publicly shared collection dates to prevent re-identifiability.;If applicable, provide a description of how each data element was abstracted.;
host (common name);Optional;The commonly used name of the host.;GENEPIO:0001386;Enums;Human [NCBITaxon:9606];"Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put ""not applicable"".";['Human [NCBITaxon:9606]', 'Bat [NCBITaxon:9397]', 'Cat [NCBITaxon:9685]', 'Chicken [NCBITaxon:9031]', 'Civet [NCBITaxon:9673]', 'Cow [NCBITaxon:9913]', 'Dog [NCBITaxon:9615]', 'Lion [NCBITaxon:9689]', 'Mink [NCBITaxon:452646]', 'Pangolin [NCBITaxon:9973]', 'Pig [NCBITaxon:9825]', 'Pigeon [NCBITaxon:8930]', 'Tiger [NCBITaxon:9694]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host (scientific name);Required;The taxonomic, or scientific name of the host.;GENEPIO:0001387;Enums;Homo sapiens [NCBITaxon:9606];"Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put ""not applicable"".";['Bos taurus [NCBITaxon:9913]', 'Canis lupus familiaris [NCBITaxon:9615]', 'Chiroptera [NCBITaxon:9397]', 'Columbidae [NCBITaxon:8930]', 'Felis catus [NCBITaxon:9685]', 'Gallus gallus [NCBITaxon:9031]', 'Homo sapiens [NCBITaxon:9606]', 'Manis [NCBITaxon:9973]', 'Manis javanica [NCBITaxon:9974]', 'Neovison vison [NCBITaxon:452646]', 'Panthera leo [NCBITaxon:9689]', 'Panthera tigris [NCBITaxon:9694]', 'Rhinolophidae [NCBITaxon:58055]', 'Rhinolophus affinis [NCBITaxon:59477]', 'Sus scrofa domesticus [NCBITaxon:9825]', 'Viverridae [NCBITaxon:9673]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host health state;Optional;Health status of the host at the time of sample collection.;GENEPIO:0001388;Enums;Asymptomatic [NCIT:C3833];If known, select a value from the pick list.;['Asymptomatic [NCIT:C3833]', 'Deceased [NCIT:C28554]', 'Healthy [NCIT:C115935]', 'Recovered [NCIT:C49498]', 'Symptomatic [NCIT:C25269]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host health status details;Optional;Further details pertaining to the health or disease status of the host at time of collection.;GENEPIO:0001389;Enums;Hospitalized (ICU) [GENEPIO:0100046];If known, select a value from the pick list.;['Hospitalized [NCIT:C25179]', ' Hospitalized (Non-ICU) [GENEPIO:0100045]', 'Hospitalized (ICU) [GENEPIO:0100046] ', 'Mechanical Ventilation [NCIT:C70909]', 'Medically Isolated [GENEPIO:0100047]', ' Medically Isolated (Negative Pressure) [GENEPIO:0100048]', 'Self-quarantining [NCIT:C173768]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host disease;Required;The name of the disease experienced by the host.;GENEPIO:0001391;Enums;COVID-19 [MONDO:0100096];"This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under Òhost health state detailsÓ. ""COVID-19"" should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put Ònot applicableÓ.";['COVID-19 [MONDO:0100096]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host health outcome;Optional;Disease outcome in the host.;GENEPIO:0001390;Enums;Recovered [NCIT:C49498];If known, select a value from the pick list.;['Deceased [NCIT:C28554]', 'Deteriorating [NCIT:C25254]', 'Recovered [NCIT:C49498]', 'Stable [NCIT:C30103]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host age;Recommended;Age of host at the time of sampling.;GENEPIO:0001392;Integer_or_Range;79;If known, provide age. Age-binning is also acceptable.;
host age unit;Recommended;The units used to measure the host's age.;GENEPIO:0001393;Enums;years [UO:0000036];If known, provide the age units used to measure the host's age from the pick list.;['months [UO:0000035]', 'years [UO:0000036]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host age bin;Recommended;The age category of the host at the time of sampling.;GENEPIO:0001394;Enums;50 - 59 [GENEPIO:0100054];Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative.;['0 - 9 [GENEPIO:0100049]', '10 - 19 [GENEPIO:0100050]', '20 - 29 [GENEPIO:0100051]', '30 - 39 [GENEPIO:0100052]', '40 - 49 [GENEPIO:0100053]', '50 - 59 [GENEPIO:0100054]', '60 - 69 [GENEPIO:0100055]', '70 - 79 [GENEPIO:0100056]', '80 - 89 [GENEPIO:0100057]', '90 - 99 [GENEPIO:0100058]', '100+ [GENEPIO:0100059]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host gender;Recommended;The gender of the host at the time of sample collection.;GENEPIO:0001395;Enums;Male [NCIT:C46109];If known, select a value from the pick list.;['Female [NCIT:C46110]', 'Male [NCIT:C46109]', 'Non-binary Gender [GSSO:000132]', 'Transgender (assigned male at birth) [GSSO:004004]', 'Transgender (assigned female at birth) [GSSO:004005]', 'Undeclared [NCIT:C110959]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host residence geo_loc name (country);Optional;The country where the host resides.;GENEPIO:0001396;Enums;South Africa [GAZ:00001094];If known, select a value from the pick list.;"['Afghanistan [GAZ:00006882]', 'Albania [GAZ:00002953]', 'Algeria [GAZ:00000563]', 'American Samoa [GAZ:00003957]', 'Andorra [GAZ:00002948]', 'Angola [GAZ:00001095]', 'Anguilla [GAZ:00009159]', 'Antarctica [GAZ:00000462]', 'Antigua and Barbuda [GAZ:00006883]', 'Argentina [GAZ:00002928]', 'Armenia [GAZ:00004094]', 'Aruba [GAZ:00004025]', 'Ashmore and Cartier Islands [GAZ:00005901]', 'Australia [GAZ:00000463]', 'Austria [GAZ:00002942]', 'Azerbaijan [GAZ:00004941]', 'Bahamas [GAZ:00002733]', 'Bahrain [GAZ:00005281]', 'Baker Island [GAZ:00007117]', 'Bangladesh [GAZ:00003750]', 'Barbados [GAZ:00001251]', 'Bassas da India [GAZ:00005810]', 'Belarus [GAZ:00006886]', 'Belgium [GAZ:00002938]', 'Belize [GAZ:00002934]', 'Benin [GAZ:00000904]', 'Bermuda [GAZ:00001264]', 'Bhutan [GAZ:00003920]', 'Bolivia [GAZ:00002511]', 'Borneo [GAZ:00025355]', 'Bosnia and Herzegovina [GAZ:00006887]', 'Botswana [GAZ:00001097]', 'Bouvet Island [GAZ:00001453]', 'Brazil [GAZ:00002828]', 'British Virgin Islands [GAZ:00003961]', 'Brunei [GAZ:00003901]', 'Bulgaria [GAZ:00002950]', 'Burkina Faso [GAZ:00000905]', 'Burundi [GAZ:00001090]', 'Cambodia [GAZ:00006888]', 'Cameroon [GAZ:00001093]', 'Canada [GAZ:00002560]', 'Cape Verde [GAZ:00001227]', 'Cayman Islands [GAZ:00003986]', 'Central African Republic [GAZ:00001089]', 'Chad [GAZ:00000586]', 'Chile [GAZ:00002825]', 'China [GAZ:00002845]', 'Christmas Island [GAZ:00005915]', 'Clipperton Island [GAZ:00005838]', 'Cocos Islands [GAZ:00009721]', 'Colombia [GAZ:00002929]', 'Comoros [GAZ:00005820]', 'Cook Islands [GAZ:00053798]', 'Coral Sea Islands [GAZ:00005917]', 'Costa Rica [GAZ:00002901]', ""Cote d'Ivoire [GAZ:00000906]"", 'Croatia [GAZ:00002719]', 'Cuba [GAZ:00003762]', 'Curacao [GAZ:00012582]', 'Cyprus [GAZ:00004006]', 'Czech Republic [GAZ:00002954]', 'Democratic Republic of the Congo [GAZ:00001086]', 'Denmark [GAZ:00005852]', 'Djibouti [GAZ:00000582]', 'Dominica [GAZ:00006890]', 'Dominican Republic [GAZ:00003952]', 'Ecuador [GAZ:00002912]', 'Egypt [GAZ:00003934]', 'El Salvador [GAZ:00002935]', 'Equatorial Guinea [GAZ:00001091]', 'Eritrea [GAZ:00000581]', 'Estonia [GAZ:00002959]', 'Eswatini [GAZ:00001099]', 'Ethiopia [GAZ:00000567]', 'Europa Island [GAZ:00005811]', 'Falkland Islands (Islas Malvinas) [GAZ:00001412]', 'Faroe Islands [GAZ:00059206]', 'Fiji [GAZ:00006891]', 'Finland [GAZ:00002937]', 'France [GAZ:00003940]', 'French Guiana [GAZ:00002516]', 'French Polynesia [GAZ:00002918]', 'French Southern and Antarctic Lands [GAZ:00003753]', 'Gabon [GAZ:00001092]', 'Gambia [GAZ:00000907]', 'Gaza Strip [GAZ:00009571]', 'Georgia [GAZ:00004942]', 'Germany [GAZ:00002646]', 'Ghana [GAZ:00000908]', 'Gibraltar [GAZ:00003987]', 'Glorioso Islands [GAZ:00005808]', 'Greece [GAZ:00002945]', 'Greenland [GAZ:00001507]', 'Grenada [GAZ:02000573]', 'Guadeloupe [GAZ:00067142]', 'Guam [GAZ:00003706]', 'Guatemala [GAZ:00002936]', 'Guernsey [GAZ:00001550]', 'Guinea [GAZ:00000909]', 'Guinea-Bissau [GAZ:00000910]', 'Guyana [GAZ:00002522]', 'Haiti [GAZ:00003953]', 'Heard Island and McDonald Islands [GAZ:00009718]', 'Honduras [GAZ:00002894]', 'Hong Kong [GAZ:00003203]', 'Howland Island [GAZ:00007120]', 'Hungary [GAZ:00002952]', 'Iceland [GAZ:00000843]', 'India [GAZ:00002839]', 'Indonesia [GAZ:00003727]', 'Iran [GAZ:00004474]', 'Iraq [GAZ:00004483]', 'Ireland [GAZ:00002943]', 'Isle of Man [GAZ:00052477]', 'Israel [GAZ:00002476]', 'Italy [GAZ:00002650]', 'Jamaica [GAZ:00003781]', 'Jan Mayen [GAZ:00005853]', 'Japan [GAZ:00002747]', 'Jarvis Island [GAZ:00007118]', 'Jersey [GAZ:00001551]', 'Johnston Atoll [GAZ:00007114]', 'Jordan [GAZ:00002473]', 'Juan de Nova Island [GAZ:00005809]', 'Kazakhstan [GAZ:00004999]', 'Kenya [GAZ:00001101]', 'Kerguelen Archipelago [GAZ:00005682]', 'Kingman Reef [GAZ:00007116]', 'Kiribati [GAZ:00006894]', 'Kosovo [GAZ:00011337]', 'Kuwait [GAZ:00005285]', 'Kyrgyzstan [GAZ:00006893]', 'Laos [GAZ:00006889]', 'Latvia [GAZ:00002958]', 'Lebanon [GAZ:00002478]', 'Lesotho [GAZ:00001098]', 'Liberia [GAZ:00000911]', 'Libya [GAZ:00000566]', 'Liechtenstein [GAZ:00003858]', 'Line Islands [GAZ:00007144]', 'Lithuania [GAZ:00002960]', 'Luxembourg [GAZ:00002947]', 'Macau [GAZ:00003202]', 'Madagascar [GAZ:00001108]', 'Malawi [GAZ:00001105]', 'Malaysia [GAZ:00003902]', 'Maldives [GAZ:00006924]', 'Mali [GAZ:00000584]', 'Malta [GAZ:00004017]', 'Marshall Islands [GAZ:00007161]', 'Martinique [GAZ:00067143]', 'Mauritania [GAZ:00000583]', 'Mauritius [GAZ:00003745]', 'Mayotte [GAZ:00003943]', 'Mexico [GAZ:00002852]', 'Micronesia [GAZ:00005862]', 'Midway Islands [GAZ:00007112]', 'Moldova [GAZ:00003897]', 'Monaco [GAZ:00003857]', 'Mongolia [GAZ:00008744]', 'Montenegro [GAZ:00006898]', 'Montserrat [GAZ:00003988]', 'Morocco [GAZ:00000565]', 'Mozambique [GAZ:00001100]', 'Myanmar [GAZ:00006899]', 'Namibia [GAZ:00001096]', 'Nauru [GAZ:00006900]', 'Navassa Island [GAZ:00007119]', 'Nepal [GAZ:00004399]', 'Netherlands [GAZ:00002946]', 'New Caledonia [GAZ:00005206]', 'New Zealand [GAZ:00000469]', 'Nicaragua [GAZ:00002978]', 'Niger [GAZ:00000585]', 'Nigeria [GAZ:00000912]', 'Niue [GAZ:00006902]', 'Norfolk Island [GAZ:00005908]', 'North Korea [GAZ:00002801]', 'North Macedonia [GAZ:00006895]', 'North Sea [GAZ:00002284]', 'Northern Mariana Islands [GAZ:00003958]', 'Norway [GAZ:00002699]', 'Oman [GAZ:00005283]', 'Pakistan [GAZ:00005246]', 'Palau [GAZ:00006905]', 'Panama [GAZ:00002892]', 'Papua New Guinea [GAZ:00003922]', 'Paracel Islands [GAZ:00010832]', 'Paraguay [GAZ:00002933]', 'Peru [GAZ:00002932]', 'Philippines [GAZ:00004525]', 'Pitcairn Islands [GAZ:00005867]', 'Poland [GAZ:00002939]', 'Portugal [GAZ:00004126]', 'Puerto Rico [GAZ:00006935]', 'Qatar [GAZ:00005286]', 'Republic of the Congo [GAZ:00001088]', 'Reunion [GAZ:00003945]', 'Romania [GAZ:00002951]', 'Ross Sea [GAZ:00023304]', 'Russia [GAZ:00002721]', 'Rwanda [GAZ:00001087]', 'Saint Helena [GAZ:00000849]', 'Saint Kitts and Nevis [GAZ:00006906]', 'Saint Lucia [GAZ:00006909]', 'Saint Pierre and Miquelon [GAZ:00003942]', 'Saint Martin [GAZ:00005841]', 'Saint Vincent and the Grenadines [GAZ:02000565]', 'Samoa [GAZ:00006910]', 'San Marino [GAZ:00003102]', 'Sao Tome and Principe [GAZ:00006927]', 'Saudi Arabia [GAZ:00005279]', 'Senegal [GAZ:00000913]', 'Serbia [GAZ:00002957]', 'Seychelles [GAZ:00006922]', 'Sierra Leone [GAZ:00000914]', 'Singapore [GAZ:00003923]', 'Sint Maarten [GAZ:00012579]', 'Slovakia [GAZ:00002956]', 'Slovenia [GAZ:00002955]', 'Solomon Islands [GAZ:00005275]', 'Somalia [GAZ:00001104]', 'South Africa [GAZ:00001094]', 'South Georgia and the South Sandwich Islands [GAZ:00003990]', 'South Korea [GAZ:00002802]', 'South Sudan [GAZ:00233439]', 'Spain [GAZ:00003936]', 'Spratly Islands [GAZ:00010831]', 'Sri Lanka [GAZ:00003924]', 'State of Palestine [GAZ:00002475]', 'Sudan [GAZ:00000560]', 'Suriname [GAZ:00002525]', 'Svalbard [GAZ:00005396]', 'Swaziland [GAZ:00001099]', 'Sweden [GAZ:00002729]', 'Switzerland [GAZ:00002941]', 'Syria [GAZ:00002474]', 'Taiwan [GAZ:00005341]', 'Tajikistan [GAZ:00006912]', 'Tanzania [GAZ:00001103]', 'Thailand [GAZ:00003744]', 'Timor-Leste [GAZ:00006913]', 'Togo [GAZ:00000915]', 'Tokelau [GAZ:00260188]', 'Tonga [GAZ:00006916]', 'Trinidad and Tobago [GAZ:00003767]', 'Tromelin Island [GAZ:00005812]', 'Tunisia [GAZ:00000562]', 'Turkey [GAZ:00000558]', 'Turkmenistan [GAZ:00005018]', 'Turks and Caicos Islands [GAZ:00003955]', 'Tuvalu [GAZ:00009715]', 'USA [GAZ:00002459]', 'Uganda [GAZ:00001102]', 'Ukraine [GAZ:00002724]', 'United Arab Emirates [GAZ:00005282]', 'United Kingdom [GAZ:00002637]', 'Uruguay [GAZ:00002930]', 'Uzbekistan [GAZ:00004979]', 'Vanuatu [GAZ:00006918]', 'Venezuela [GAZ:00002931]', 'Viet Nam [GAZ:00003756]', 'Virgin Islands [GAZ:00003959]', 'Wake Island [GAZ:00007111]', 'Wallis and Futuna [GAZ:00007191]', 'West Bank [GAZ:00009572]', 'Western Sahara [GAZ:00000564]', 'Yemen [GAZ:00005284]', 'Zambia [GAZ:00001107]', 'Zimbabwe [GAZ:00001106]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
host ethnicity;Optional;The self-identified ethnicity(ies) of the host.;GECKO:0000061;String;Indigenous, European;If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative.;
host subject ID;Optional;A unique identifier by which each host can be referred to e.g. #131;GENEPIO:0001398;String;BCxy123;Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward.;
case ID;Optional;The identifier used to specify an epidemiologically detected case of disease.;GENEPIO:0100281;String;ABCD1234;Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing.;
symptom onset date;Optional;The date on which the symptoms began or were first noted.;GENEPIO:0001399;Date;16/03/2020;"If known, provide the symptom onset date in ISO 8601 standard format ""YYYY-MM-DD"".";
signs and symptoms;Optional;A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.;GENEPIO:0001400;Enums;Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145];Select all of the symptoms experienced by the host from the pick list.;['Abnormal lung auscultation [HP:0030829]', ' Ageusia (complete loss of taste) [HP:0041051]', ' Parageusia (distorted sense of taste) [HP:0031249]', ' Hypogeusia (reduced sense of taste) [HP:0000224]', 'Abnormality of the sense of smell [HP:0004408]', ' Anosmia (lost sense of smell) [HP:0000458]', ' Hyposmia (reduced sense of smell) [HP:0004409]', 'Acute Respiratory Distress Syndrome [HP:0033677]', 'Altered mental status [HP:0011446]', 'Arrhythmia [HP:0011675]', ' Cognitive impairment [HP:0100543]', ' Coma [HP:0001259]', ' Confusion [HP:0001289]', ' Delirium (sudden severe confusion) [HP:0031258]', ' Inability to arouse (inability to stay awake) [GENEPIO:0100061]', ' Irritability [HP:0000737]', ' Loss of speech [HP:0002371]', 'Asthenia (generalized weakness) [HP:0025406]', 'Chest tightness or pressure [HP:0031352]', ' Rigors (fever shakes) [HP:0025145]', 'Chills (sudden cold sensation) [HP:0025143]', 'Conjunctival injection [HP:0030953]', 'Conjunctivitis (pink eye) [HP:0000509]', 'Coryza [MP:0001867]', 'Cough [HP:0012735]', ' Nonproductive cough (dry cough) [HP:0031246]', ' Productive cough (wet cough) [HP:0031245]', 'Cyanosis (blueish skin discolouration) [HP:0000961]', ' Acrocyanosis [HP:0001063]', ' Circumoral cyanosis (bluish around mouth) [HP:0032556]', ' Cyanotic face (bluish face) [GENEPIO:0100062]', ' Central Cyanosis [GENEPIO:0100063]', ' Cyanotic lips (bluish lips) [GENEPIO:0100064]', ' Peripheral Cyanosis [GENEPIO:0100065]', 'Dyspnea (breathing difficulty) [HP:0002094]', 'Diarrhea (watery stool) [HP:0002014]', 'Dry gangrene [MP:0031127]', 'Encephalitis (brain inflammation) [HP:0002383]', 'Encephalopathy [HP:0001298]', 'Fatigue (tiredness) [HP:0012378]', 'Fever [HP:0001945]', ' Fever (>=38\xc2\xbaC) [GENEPIO:0100066]', 'Glossitis (inflammation of the tongue) [HP:0000206]', 'Ground Glass Opacities (GGO) [GENEPIO:0100067]', 'Headache [HP:0002315]', 'Hemoptysis (coughing up blood) [HP:0002105]', 'Hypocapnia [HP:0012417]', 'Hypotension (low blood pressure) [HP:0002615]', 'Hypoxemia (low blood oxygen) [HP:0012418]', ' Silent hypoxemia [GENEPIO:0100068]', 'Internal hemorrhage (internal bleeding) [HP:0011029]', 'Loss of Fine Movements [NCIT:C121416]', 'Low appetite [HP:0004396]', 'Malaise (general discomfort/unease) [HP:0033834]', 'Meningismus/nuchal rigidity [HP:0031179]', 'Muscle weakness [HP:0001324]', 'Nasal obstruction (stuffy nose) [HP:0001742]', 'Nausea [HP:0002018]', 'Nose bleed [HP:0000421]', 'Otitis [GENEPIO:0100069]', 'Pain [HP:0012531]', ' Abdominal pain [HP:0002027]', ' Arthralgia (painful joints) [HP:0002829]', ' Chest pain [HP:0100749]', ' Pleuritic chest pain [HP:0033771]', ' Myalgia (muscle pain) [HP:0003326]', 'Pharyngitis (sore throat) [HP:0025439]', 'Pharyngeal exudate [GENEPIO:0100070]', 'Pleural effusion [HP:0002202]', 'Pneumonia [HP:0002090]', 'Prostration [GENEPIO:0100071]', 'Pseudo-chilblains [HP:0033696]', ' Pseudo-chilblains on fingers (covid fingers) [GENEPIO:0100072]', ' Pseudo-chilblains on toes (covid toes) [GENEPIO:0100073]', 'Rash [HP:0000988]', 'Rhinorrhea (runny nose) [HP:0031417]', 'Seizure [HP:0001250]', ' Motor seizure [HP:0020219]', 'Shivering (involuntary muscle twitching) [HP:0025144]', 'Slurred speech [HP:0001350]', 'Sneezing [HP:0025095]', 'Sputum Production [HP:0033709]', 'Stroke [HP:0001297]', 'Swollen Lymph Nodes [HP:0002716]', 'Tachypnea (accelerated respiratory rate) [HP:0002789]', 'Vertigo (dizziness) [HP:0002321]', 'Vomiting (throwing up) [HP:0002013]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
pre-existing conditions and risk factors;Optional;"Patient pre-existing conditions and risk factors.
Pre-existing condition: A medical condition that existed prior to the current infection.
Risk Factor: A variable associated with an increased risk of disease or infection.";GENEPIO:0001401;Enums;Asthma [HP:0002099];Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.;"['Age 60+ [VO:0004925]', 'Anemia [HP:0001903]', 'Anorexia [HP:0002039]', 'Birthing labor [NCIT:C92743]', 'Bone marrow failure [NCIT:C80693]', 'Cancer [MONDO:0004992]', ' Breast cancer [MONDO:0007254]', ' Colorectal cancer [MONDO:0005575]', ' Hematologic malignancy [DOID:2531]', ' Lung cancer [MONDO:0008903]', ' Metastatic disease [MONDO:0024880]', 'Cancer treatment [NCIT:C16212]', ' Cancer surgery [NCIT:C157740]', ' Chemotherapy [NCIT:C15632]', ' Adjuvant chemotherapy [NCIT:C15360]', 'Cardiac disorder [NCIT:C3079]', 'Arrhythmia [HP:0011675]', ' Cardiac disease [MONDO:0005267]', ' Cardiomyopathy [HP:0001638]', ' Cardiac injury [GENEPIO:0100074]', ' Hypertension (high blood pressure) [HP:0000822]', ' Hypotension (low blood pressure) [HP:0002615]', 'Cesarean section [HP:0011410]', 'Chronic cough [GENEPIO:0100075]', 'Chronic gastrointestinal disease [GENEPIO:0100076]', 'Chronic lung disease [HP:0006528]', 'Corticosteroids [NCIT:C211]', 'Diabetes mellitus (diabetes) [HP:0000819]', ' Type I diabetes mellitus (T1D) [HP:0100651]', ' Type II diabetes mellitus (T2D) [HP:0005978]', 'Eczema [HP:0000964]', 'Electrolyte disturbance [HP:0003111]', ' Hypocalcemia [HP:0002901]', ' Hypokalemia [HP:0002900]', ' Hypomagnesemia [HP:0002917]', 'Encephalitis (brain inflammation) [HP:0002383]', 'Epilepsy [MONDO:0005027]', 'Hemodialysis [NCIT:C15248]', 'Hemoglobinopathy [MONDO:0044348]', 'Human immunodeficiency virus (HIV) [MONDO:0005109]', ' Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]', ' HIV and antiretroviral therapy (ART) [NCIT:C16118]', 'Immunocompromised [NCIT:C14139]', ' Lupus [MONDO:0004670]', 'Inflammatory bowel disease (IBD) [MONDO:0005265]', ' Colitis [HP:0002583]', ' Ulcerative colitis [HP:0100279]', "" Crohn's disease [HP:0100280]"", 'Renal disorder [NCIT:C3149]', ' Renal disease [MONDO:0005240]', ' Chronic renal disease [HP:0012622]', ' Renal failure [HP:0000083]', 'Liver disease [MONDO:0005154]', ' Chronic liver disease [NCIT:C113609]', ' Fatty liver disease (FLD) [HP:0001397]', 'Myalgia (muscle pain) [HP:0003326]', 'Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]', 'Neurological disorder [MONDO:0005071]', ' Neuromuscular disorder [MONDO:0019056]', 'Obesity [HP:0001513]', ' Severe obesity [MONDO:0005139]', 'Respiratory disorder [MONDO:0005087]', ' Asthma [HP:0002099]', ' Chronic bronchitis [HP:0004469]', ' Chronic pulmonary disease [HP:0006528]', ' Chronic obstructive pulmonary disease [HP:0006510]', ' Emphysema [HP:0002097]', ' Lung disease [MONDO:0005275]', ' Chronic lung disease [HP:0006528]', ' Pulmonary fibrosis [HP:0002206]', 'Pneumonia [HP:0002090]', ' Respiratory failure [HP:0002878]', ' Adult respiratory distress syndrome [HP:0033677]', ' Newborn respiratory distress syndrome [MONDO:0009971]', ' Tuberculosis [MONDO:0018076]', 'Postpartum (\xe2\x89\xa46 weeks) [GENEPIO:0100077]', 'Pregnancy [NCIT:C25742]', 'Rheumatic disease [MONDO:0005554]', 'Sickle cell disease [MONDO:0011382]', 'Substance use [NBO:0001845]', ' Alcohol abuse [MONDO:0002046]', ' Drug abuse [GENEPIO:0100078]', ' Injection drug abuse [GENEPIO:0100079]', ' Smoking [NBO:0015005]', ' Vaping [NCIT:C173621]', 'Tachypnea (accelerated respiratory rate) [HP:0002789]', 'Transplant [NCIT:C159659]', ' Cardiac transplant [GENEPIO:0100080]', ' Hematopoietic stem cell transplant (bone marrow transplant) [NCIT:C131759]', ' Kidney transplant [NCIT:C157332]', ' Liver transplant [GENEPIO:0100081]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
complications;Optional;Patient medical complications that are believed to have occurred as a result of host disease.;GENEPIO:0001402;Enums;Acute respiratory failure [MONDO:0001208];Select all of the complications experienced by the host from the pick list.;"['Abnormal blood oxygen level [HP:0500165]', 'Acute kidney injury [HP:0001919]', 'Acute lung injury [MONDO:0015796]', ' Ventilation induced lung injury (VILI) [GENEPIO:0100092]', 'Acute respiratory failure [MONDO:0001208]', 'Arrhythmia (complication) [HP:0011675]', ' Tachycardia [HP:0001649]', ' Polymorphic ventricular tachycardia (VT) [HP:0031677]', ' Tachyarrhythmia [GENEPIO:0100084]', 'Noncardiogenic pulmonary edema [GENEPIO:0100085]', ' Acute respiratory distress syndrome (ARDS) [HP:0033677]', ' COVID-19 associated ARDS (CARDS) [NCIT:C171551]', ' Neurogenic pulmonary edema (NPE) [GENEPIO:0100086]', 'Cardiac injury [GENEPIO:0100087]', 'Cardiac arrest [HP:0001695]', 'Cardiogenic shock [HP:0030149]', 'Blood clot [HP:0001977]', ' Arterial clot [HP:0004420]', ' Deep vein thrombosis (DVT) [HP:0002625]', ' Pulmonary embolism (PE) [HP:0002204]', 'Cardiomyopathy [HP:0001638]', 'Central nervous system invasion [MONDO:0024619]', 'Stroke (complication) [HP:0001297]', ' Central Nervous System Vasculitis [MONDO:0003346]', ' Acute ischemic stroke [HP:0002140]', 'Coma [HP:0001259]', 'Convulsions [HP:0011097]', 'COVID-19 associated coagulopathy (CAC) [NCIT:C171562]', 'Cystic fibrosis [MONDO:0009061]', 'Cytokine release syndrome [MONDO:0600008]', 'Disseminated intravascular coagulation (DIC) [MPATH:108]', 'Encephalopathy [HP:0001298]', 'Fulminant myocarditis [GENEPIO:0100088]', 'Guillain-Barr\xc3\xa9 syndrome [MONDO:0016218]', 'Internal hemorrhage (complication; internal bleeding) [HP:0011029]', ' Intracerebral haemorrhage [MONDO:0013792]', 'Kawasaki disease [MONDO:0012727]', ' Complete Kawasaki disease [GENEPIO:0100089]', ' Incomplete Kawasaki disease [GENEPIO:0100090]', 'Liver dysfunction [HP:0001410]', ' Acute liver injury [GENEPIO:0100091]', 'Long COVID-19 [MONDO:0100233]', 'Meningitis [HP:0001287]', 'Migraine [HP:0002076]', 'Miscarriage [HP:0005268]', 'Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]', 'Muscle injury [GENEPIO:0100093]', 'Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]', 'Myocardial infarction (heart attack) [MONDO:0005068]', ' Acute myocardial infarction [MONDO:0004781]', ' ST-segment elevation myocardial infarction [MONDO:0041656]', 'Myocardial injury [HP:0001700]', 'Neonatal complications [NCIT:C168498]', 'Organ failure [GENEPIO:0100094]', ' Heart failure [HP:0001635]', ' Liver failure [MONDO:0100192]', 'Paralysis [HP:0003470]', 'Pneumothorax (collapsed lung) [HP:0002107]', ' Spontaneous pneumothorax [HP:0002108]', ' Spontaneous tension pneymothorax [MONDO:0002075]', 'Pneumonia (complication) [HP:0002090]', ' COVID-19 pneumonia [NCIT:C171550]', 'Pregancy complications [HP:0001197]', 'Rhabdomyolysis [HP:0003201]', 'Secondary infection [IDO:0000567]', ' Secondary staph infection [GENEPIO:0100095]', ' Secondary strep infection [GENEPIO:0100096]', 'Seizure (complication) [HP:0001250]', ' Motor seizure [HP:0020219]', 'Sepsis/Septicemia [HP:0100806]', ' Sepsis (systemic inflammatory response to infection) [IDO:0000636]', ' Septicemia (bloodstream infection) [NCIT:C3364]', 'Shock [HP:0031273]', ' Hyperinflammatory shock [GENEPIO:0100097]', ' Refractory cardiogenic shock [GENEPIO:0100098]', ' Refractory cardiogenic plus vasoplegic shock [GENEPIO:0100099]', ' Septic shock [NCIT:C35018]', 'Vasculitis [HP:0002633]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
host vaccination status;Optional;The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).;GENEPIO:0001404;Enums;Fully Vaccinated [GENEPIO:0100100];Select the vaccination status of the host from the pick list.;['Fully Vaccinated [GENEPIO:0100100]', 'Partially Vaccinated [GENEPIO:0100101]', 'Not Vaccinated [GENEPIO:0100102]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
vaccine name;Optional;The name of the vaccine(s) administered.;GENEPIO:0001405;String;BNT162b2, Pfizer-BioNTech;Free text. Provide the scientific/research name of the vaccine followed by the name of the manufacturer, separated by a comma.;
number of vaccine doses received;Optional;The number of doses of the vaccine recived by the host.;GENEPIO:0001406;Int;2;Record how many doses of the vaccine the host has received.;
first dose vaccination date;Optional;The date the host was first vaccinated.;GENEPIO:0001407;Date;26/02/2021;Provide the date that the first dose of the vaccine was administered. Provide the first dose vaccination date in ISO 8601 standard format 'YYYY-MM-DD'.;
last dose vacicnation date;Optional;The date the host received their last dose of vaccine.;GENEPIO:0001408;Date;09/04/2021;Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format 'YYYY-MM-DD'.;
location of exposure geo_loc name (country);Optional;The country where the host was likely exposed to the causative agent of the illness.;GENEPIO:0001410;Enums;South Africa [GAZ:00001094];This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list.;"['Afghanistan [GAZ:00006882]', 'Albania [GAZ:00002953]', 'Algeria [GAZ:00000563]', 'American Samoa [GAZ:00003957]', 'Andorra [GAZ:00002948]', 'Angola [GAZ:00001095]', 'Anguilla [GAZ:00009159]', 'Antarctica [GAZ:00000462]', 'Antigua and Barbuda [GAZ:00006883]', 'Argentina [GAZ:00002928]', 'Armenia [GAZ:00004094]', 'Aruba [GAZ:00004025]', 'Ashmore and Cartier Islands [GAZ:00005901]', 'Australia [GAZ:00000463]', 'Austria [GAZ:00002942]', 'Azerbaijan [GAZ:00004941]', 'Bahamas [GAZ:00002733]', 'Bahrain [GAZ:00005281]', 'Baker Island [GAZ:00007117]', 'Bangladesh [GAZ:00003750]', 'Barbados [GAZ:00001251]', 'Bassas da India [GAZ:00005810]', 'Belarus [GAZ:00006886]', 'Belgium [GAZ:00002938]', 'Belize [GAZ:00002934]', 'Benin [GAZ:00000904]', 'Bermuda [GAZ:00001264]', 'Bhutan [GAZ:00003920]', 'Bolivia [GAZ:00002511]', 'Borneo [GAZ:00025355]', 'Bosnia and Herzegovina [GAZ:00006887]', 'Botswana [GAZ:00001097]', 'Bouvet Island [GAZ:00001453]', 'Brazil [GAZ:00002828]', 'British Virgin Islands [GAZ:00003961]', 'Brunei [GAZ:00003901]', 'Bulgaria [GAZ:00002950]', 'Burkina Faso [GAZ:00000905]', 'Burundi [GAZ:00001090]', 'Cambodia [GAZ:00006888]', 'Cameroon [GAZ:00001093]', 'Canada [GAZ:00002560]', 'Cape Verde [GAZ:00001227]', 'Cayman Islands [GAZ:00003986]', 'Central African Republic [GAZ:00001089]', 'Chad [GAZ:00000586]', 'Chile [GAZ:00002825]', 'China [GAZ:00002845]', 'Christmas Island [GAZ:00005915]', 'Clipperton Island [GAZ:00005838]', 'Cocos Islands [GAZ:00009721]', 'Colombia [GAZ:00002929]', 'Comoros [GAZ:00005820]', 'Cook Islands [GAZ:00053798]', 'Coral Sea Islands [GAZ:00005917]', 'Costa Rica [GAZ:00002901]', ""Cote d'Ivoire [GAZ:00000906]"", 'Croatia [GAZ:00002719]', 'Cuba [GAZ:00003762]', 'Curacao [GAZ:00012582]', 'Cyprus [GAZ:00004006]', 'Czech Republic [GAZ:00002954]', 'Democratic Republic of the Congo [GAZ:00001086]', 'Denmark [GAZ:00005852]', 'Djibouti [GAZ:00000582]', 'Dominica [GAZ:00006890]', 'Dominican Republic [GAZ:00003952]', 'Ecuador [GAZ:00002912]', 'Egypt [GAZ:00003934]', 'El Salvador [GAZ:00002935]', 'Equatorial Guinea [GAZ:00001091]', 'Eritrea [GAZ:00000581]', 'Estonia [GAZ:00002959]', 'Eswatini [GAZ:00001099]', 'Ethiopia [GAZ:00000567]', 'Europa Island [GAZ:00005811]', 'Falkland Islands (Islas Malvinas) [GAZ:00001412]', 'Faroe Islands [GAZ:00059206]', 'Fiji [GAZ:00006891]', 'Finland [GAZ:00002937]', 'France [GAZ:00003940]', 'French Guiana [GAZ:00002516]', 'French Polynesia [GAZ:00002918]', 'French Southern and Antarctic Lands [GAZ:00003753]', 'Gabon [GAZ:00001092]', 'Gambia [GAZ:00000907]', 'Gaza Strip [GAZ:00009571]', 'Georgia [GAZ:00004942]', 'Germany [GAZ:00002646]', 'Ghana [GAZ:00000908]', 'Gibraltar [GAZ:00003987]', 'Glorioso Islands [GAZ:00005808]', 'Greece [GAZ:00002945]', 'Greenland [GAZ:00001507]', 'Grenada [GAZ:02000573]', 'Guadeloupe [GAZ:00067142]', 'Guam [GAZ:00003706]', 'Guatemala [GAZ:00002936]', 'Guernsey [GAZ:00001550]', 'Guinea [GAZ:00000909]', 'Guinea-Bissau [GAZ:00000910]', 'Guyana [GAZ:00002522]', 'Haiti [GAZ:00003953]', 'Heard Island and McDonald Islands [GAZ:00009718]', 'Honduras [GAZ:00002894]', 'Hong Kong [GAZ:00003203]', 'Howland Island [GAZ:00007120]', 'Hungary [GAZ:00002952]', 'Iceland [GAZ:00000843]', 'India [GAZ:00002839]', 'Indonesia [GAZ:00003727]', 'Iran [GAZ:00004474]', 'Iraq [GAZ:00004483]', 'Ireland [GAZ:00002943]', 'Isle of Man [GAZ:00052477]', 'Israel [GAZ:00002476]', 'Italy [GAZ:00002650]', 'Jamaica [GAZ:00003781]', 'Jan Mayen [GAZ:00005853]', 'Japan [GAZ:00002747]', 'Jarvis Island [GAZ:00007118]', 'Jersey [GAZ:00001551]', 'Johnston Atoll [GAZ:00007114]', 'Jordan [GAZ:00002473]', 'Juan de Nova Island [GAZ:00005809]', 'Kazakhstan [GAZ:00004999]', 'Kenya [GAZ:00001101]', 'Kerguelen Archipelago [GAZ:00005682]', 'Kingman Reef [GAZ:00007116]', 'Kiribati [GAZ:00006894]', 'Kosovo [GAZ:00011337]', 'Kuwait [GAZ:00005285]', 'Kyrgyzstan [GAZ:00006893]', 'Laos [GAZ:00006889]', 'Latvia [GAZ:00002958]', 'Lebanon [GAZ:00002478]', 'Lesotho [GAZ:00001098]', 'Liberia [GAZ:00000911]', 'Libya [GAZ:00000566]', 'Liechtenstein [GAZ:00003858]', 'Line Islands [GAZ:00007144]', 'Lithuania [GAZ:00002960]', 'Luxembourg [GAZ:00002947]', 'Macau [GAZ:00003202]', 'Madagascar [GAZ:00001108]', 'Malawi [GAZ:00001105]', 'Malaysia [GAZ:00003902]', 'Maldives [GAZ:00006924]', 'Mali [GAZ:00000584]', 'Malta [GAZ:00004017]', 'Marshall Islands [GAZ:00007161]', 'Martinique [GAZ:00067143]', 'Mauritania [GAZ:00000583]', 'Mauritius [GAZ:00003745]', 'Mayotte [GAZ:00003943]', 'Mexico [GAZ:00002852]', 'Micronesia [GAZ:00005862]', 'Midway Islands [GAZ:00007112]', 'Moldova [GAZ:00003897]', 'Monaco [GAZ:00003857]', 'Mongolia [GAZ:00008744]', 'Montenegro [GAZ:00006898]', 'Montserrat [GAZ:00003988]', 'Morocco [GAZ:00000565]', 'Mozambique [GAZ:00001100]', 'Myanmar [GAZ:00006899]', 'Namibia [GAZ:00001096]', 'Nauru [GAZ:00006900]', 'Navassa Island [GAZ:00007119]', 'Nepal [GAZ:00004399]', 'Netherlands [GAZ:00002946]', 'New Caledonia [GAZ:00005206]', 'New Zealand [GAZ:00000469]', 'Nicaragua [GAZ:00002978]', 'Niger [GAZ:00000585]', 'Nigeria [GAZ:00000912]', 'Niue [GAZ:00006902]', 'Norfolk Island [GAZ:00005908]', 'North Korea [GAZ:00002801]', 'North Macedonia [GAZ:00006895]', 'North Sea [GAZ:00002284]', 'Northern Mariana Islands [GAZ:00003958]', 'Norway [GAZ:00002699]', 'Oman [GAZ:00005283]', 'Pakistan [GAZ:00005246]', 'Palau [GAZ:00006905]', 'Panama [GAZ:00002892]', 'Papua New Guinea [GAZ:00003922]', 'Paracel Islands [GAZ:00010832]', 'Paraguay [GAZ:00002933]', 'Peru [GAZ:00002932]', 'Philippines [GAZ:00004525]', 'Pitcairn Islands [GAZ:00005867]', 'Poland [GAZ:00002939]', 'Portugal [GAZ:00004126]', 'Puerto Rico [GAZ:00006935]', 'Qatar [GAZ:00005286]', 'Republic of the Congo [GAZ:00001088]', 'Reunion [GAZ:00003945]', 'Romania [GAZ:00002951]', 'Ross Sea [GAZ:00023304]', 'Russia [GAZ:00002721]', 'Rwanda [GAZ:00001087]', 'Saint Helena [GAZ:00000849]', 'Saint Kitts and Nevis [GAZ:00006906]', 'Saint Lucia [GAZ:00006909]', 'Saint Pierre and Miquelon [GAZ:00003942]', 'Saint Martin [GAZ:00005841]', 'Saint Vincent and the Grenadines [GAZ:02000565]', 'Samoa [GAZ:00006910]', 'San Marino [GAZ:00003102]', 'Sao Tome and Principe [GAZ:00006927]', 'Saudi Arabia [GAZ:00005279]', 'Senegal [GAZ:00000913]', 'Serbia [GAZ:00002957]', 'Seychelles [GAZ:00006922]', 'Sierra Leone [GAZ:00000914]', 'Singapore [GAZ:00003923]', 'Sint Maarten [GAZ:00012579]', 'Slovakia [GAZ:00002956]', 'Slovenia [GAZ:00002955]', 'Solomon Islands [GAZ:00005275]', 'Somalia [GAZ:00001104]', 'South Africa [GAZ:00001094]', 'South Georgia and the South Sandwich Islands [GAZ:00003990]', 'South Korea [GAZ:00002802]', 'South Sudan [GAZ:00233439]', 'Spain [GAZ:00003936]', 'Spratly Islands [GAZ:00010831]', 'Sri Lanka [GAZ:00003924]', 'State of Palestine [GAZ:00002475]', 'Sudan [GAZ:00000560]', 'Suriname [GAZ:00002525]', 'Svalbard [GAZ:00005396]', 'Swaziland [GAZ:00001099]', 'Sweden [GAZ:00002729]', 'Switzerland [GAZ:00002941]', 'Syria [GAZ:00002474]', 'Taiwan [GAZ:00005341]', 'Tajikistan [GAZ:00006912]', 'Tanzania [GAZ:00001103]', 'Thailand [GAZ:00003744]', 'Timor-Leste [GAZ:00006913]', 'Togo [GAZ:00000915]', 'Tokelau [GAZ:00260188]', 'Tonga [GAZ:00006916]', 'Trinidad and Tobago [GAZ:00003767]', 'Tromelin Island [GAZ:00005812]', 'Tunisia [GAZ:00000562]', 'Turkey [GAZ:00000558]', 'Turkmenistan [GAZ:00005018]', 'Turks and Caicos Islands [GAZ:00003955]', 'Tuvalu [GAZ:00009715]', 'USA [GAZ:00002459]', 'Uganda [GAZ:00001102]', 'Ukraine [GAZ:00002724]', 'United Arab Emirates [GAZ:00005282]', 'United Kingdom [GAZ:00002637]', 'Uruguay [GAZ:00002930]', 'Uzbekistan [GAZ:00004979]', 'Vanuatu [GAZ:00006918]', 'Venezuela [GAZ:00002931]', 'Viet Nam [GAZ:00003756]', 'Virgin Islands [GAZ:00003959]', 'Wake Island [GAZ:00007111]', 'Wallis and Futuna [GAZ:00007191]', 'West Bank [GAZ:00009572]', 'Western Sahara [GAZ:00000564]', 'Yemen [GAZ:00005284]', 'Zambia [GAZ:00001107]', 'Zimbabwe [GAZ:00001106]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
destination of most recent travel (city);Optional;The name of the city that was the destination of most recent travel.;GENEPIO:0001411;String;New York City;Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz;
destination of most recent travel (state/province/territory);Optional;The name of the province that was the destination of most recent travel.;GENEPIO:0001412;String;California;Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz;
destination of most recent travel (country);Optional;The name of the country that was the destination of most recent travel.;GENEPIO:0001413;String;United Kingdom;Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz;
most recent travel departure date;Optional;The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.;GENEPIO:0001414;Date;16/03/2020;Provide the travel departure date in ISO 8601 standard format 'YYYY-MM-DD'.;
most recent travel return date;Optional;The date of a person's most recent return to some residence from a journey originating at that residence.;GENEPIO:0001415;Date;26/04/2020;Provide the travel return date in ISO 8601 standard format 'YYYY-MM-DD'.;
travel history;Optional;Travel history in last six months.;GENEPIO:0001416;String;Canada, Vancouver, USA, Seattle, Italy, Milan;Specify the countries (and more granular locations if known) travelled in the last six months, can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text.;
exposure event;Optional;Event leading to exposure.;GENEPIO:0001417;Enums;Mass Gathering [GENEPIO:0100237];If known, select the exposure event from the pick list.;['Mass Gathering [GENEPIO:0100237]', ' Convention [GENEPIO:0100238]', ' Convocation [GENEPIO:0100239]', ' Agricultural Event [GENEPIO:0100240]', 'Religious Gathering [GENEPIO:0100241]', ' Mass [GENEPIO:0100242]', 'Social Gathering [PCO:0000033]', ' Baby Shower [PCO:0000039]', ' Community Event [PCO:0000034]', ' Family Gathering [GENEPIO:0100243]', ' Family Reunion [GENEPIO:0100244]', ' Funeral [GENEPIO:0100245]', ' Party [PCO:0000035]', ' Potluck [PCO:0000037]', ' Wedding [PCO:0000038]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
exposure contact level;Optional;The exposure transmission contact type.;GENEPIO:0001418;Enums;Direct (human-to-human contact) [TRANS:0000001];Select direct or indirect exposure from the pick list.;['Direct (human-to-human contact) [TRANS:0000001]', 'Indirect contact [GENEPIO:0100246]', ' Close contact (face-to-face contact) [GENEPIO:0100247]', ' Casual contact [GENEPIO:0100248]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
host role;Optional;The role of the host in relation to the exposure setting.;GENEPIO:0001419;Enums;Patient [OMRSE:00000030];Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team.;['Attendee [GENEPIO:0100249]', ' Student [OMRSE:00000058]', 'Patient [OMRSE:00000030]', ' Inpatient [NCIT:C25182]', ' Outpatient [NCIT:C28293]', 'Passenger [GENEPIO:0100250]', 'Resident [GENEPIO:0100251]', 'Visitor [GENEPIO:0100252]', 'Volunteer [GENEPIO:0100253]', 'Work [GENEPIO:0100254]', ' Administrator [GENEPIO:0100255]', ' First Responder [GENEPIO:0100256]', ' Firefighter [GENEPIO:0100257]', ' Paramedic [GENEPIO:0100258]', ' Police Officer [GENEPIO:0100259]', ' Housekeeper [GENEPIO:0100260]', ' Kitchen Worker [GENEPIO:0100261]', ' Laboratory Worker [GENEPIO:0100262]', ' Nurse [OMRSE:00000014]', ' Personal Care Aid [GENEPIO:0100263]', ' Pharmacist [GENEPIO:0100264]', ' Physician [OMRSE:00000013]', ' Vet [GENEPIO:0100265]', 'Social role [OMRSE:00000001]', ' Acquaintance of case [GENEPIO:0100266]', ' Relative of case [GENEPIO:0100267]', ' Child of case [GENEPIO:0100268]', ' Parent of case [GENEPIO:0100269]', ' Father of case [GENEPIO:0100270]', ' Mother of case [GENEPIO:0100271]', ' Spouse of case [GENEPIO:0100272]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
exposure setting;Optional;The setting leading to exposure.;GENEPIO:0001428;Enums;Healthcare Setting [GENEPIO:0100201];Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.;"['Human Exposure [ECTO:3000005]', ' Contact with Known COVID-19 Case [GENEPIO:0100184]', ' Contact with Patient [GENEPIO:0100185]', ' Contact with Probable COVID-19 Case [GENEPIO:0100186]', ' Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]', ' Contact with Person with Fever and/or Cough [GENEPIO:0100188]', ' Contact with Person who Recently Travelled [GENEPIO:0100189]', 'Occupational, Residency or Patronage Exposure [GENEPIO:0100190]', ' Abbatoir [ECTO:1000033]', ' Animal Rescue [GENEPIO:0100191]', ' Childcare [GENEPIO:0100192]', ' Daycare [GENEPIO:0100193]', ' Nursery [GENEPIO:0100194]', ' Community Service Centre [GENEPIO:0100195]', ' Correctional Facility [GENEPIO:0100196]', ' Dormitory [GENEPIO:0100197]', ' Farm [ECTO:1000034]', ' First Nations Reserve [GENEPIO:0100198]', ' Funeral Home [GENEPIO:0100199]', ' Group Home [GENEPIO:0100200]', ' Healthcare Setting [GENEPIO:0100201]', ' Ambulance [GENEPIO:0100202]', ' Acute Care Facility [GENEPIO:0100203]', ' Clinic [GENEPIO:0100204]', ' Community Health Centre [GENEPIO:0100205]', ' Hospital [ECTO:1000035]', ' Emergency Department [GENEPIO:0100206]', ' ICU [GENEPIO:0100207]', ' Ward [GENEPIO:0100208]', ' Laboratory [ECTO:1000036]', ' Long-Term Care Facility [GENEPIO:0100209]', ' Pharmacy [GENEPIO:0100210]', "" Physician's Office [GENEPIO:0100211]"", ' Household [GENEPIO:0100212]', ' Insecure Housing (Homeless) [GENEPIO:0100213]', ' Occupational Exposure [GENEPIO:0100214]', ' Worksite [GENEPIO:0100215]', ' Office [ECTO:1000037]', ' Outdoors [GENEPIO:0100216]', ' Camp/camping [ECTO:5000009]', ' Hiking Trail [GENEPIO:0100217]', ' Hunting Ground [ECTO:6000030]', ' Ski Resort [GENEPIO:0100218]', ' Petting zoo [ECTO:5000008]', ' Place of Worship [GENEPIO:0100220]', ' Church [GENEPIO:0100221]', ' Mosque [GENEPIO:0100222]', ' Temple [GENEPIO:0100223]', ' Restaurant [ECTO:1000040]', ' Retail Store [ECTO:1000041]', ' School [GENEPIO:0100224]', ' Temporary Residence [GENEPIO:0100225]', ' Homeless Shelter [GENEPIO:0100226]', ' Hotel [GENEPIO:0100227]', ' Veterinary Care Clinic [GENEPIO:0100228]', 'Travel Exposure [GENEPIO:0100229]', ' Travelled on a Cruise Ship [GENEPIO:0100230]', ' Travelled on a Plane [GENEPIO:0100231]', ' Travelled on Ground Transport [GENEPIO:0100232]', ' Travelled outside Province/Territory [GENEPIO:0001118]', ' Travelled outside Canada [GENEPIO:0001119]', 'Other Exposure Setting [GENEPIO:0100235]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
exposure details;Optional;Additional host exposure information.;GENEPIO:0001431;String;Host role - Other: Bus Driver;Free text description of the exposure.;
prior SARS-CoV-2 infection;Optional;Whether there was prior SARS-CoV-2 infection.;GENEPIO:0001435;Enums;Prior infection [GENEPIO:0100234];If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list.;['Prior infection [GENEPIO:0100234]', 'No prior infection [GENEPIO:0100236]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
prior SARS-CoV-2 infection isolate;Optional;The identifier of the isolate found in the prior SARS-CoV-2 infection.;GENEPIO:0001436;String;SARS-CoV-2/human/USA/CA-CDPH-001/2020;Provide the isolate name of the most recent prior infection. Structure the 'isolate' name to be ICTV/INSDC compliant in the following format: 'SARS-CoV-2/host/country/sampleID/date'.;
prior SARS-CoV-2 infection date;Optional;The date of diagnosis of the prior SARS-CoV-2 infection.;GENEPIO:0001437;Date;23/01/2021;Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format 'YYYY-MM-DD'.;
prior SARS-CoV-2 antiviral treatment;Optional;Whether there was prior SARS-CoV-2 treatment with an antiviral agent.;GENEPIO:0001438;Enums;Prior antiviral treatment [GENEPIO:0100037];If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list.;['Prior antiviral treatment [GENEPIO:0100037]', 'No prior antiviral treatment [GENEPIO:0100233]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
prior SARS-CoV-2 antiviral treatment agent;Optional;The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.;GENEPIO:0001439;String;Remdesivir;Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put 'No treatment'. If multiple antiviral agents were administered, list them all separated by commas.;
prior SARS-CoV-2 antiviral treatment date;Optional;The date treatment was first administered during the prior SARS-CoV-2 infection.;GENEPIO:0001440;Date;28/01/2021;Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format 'YYYY-MM-DD'.;
purpose of sequencing;Recommended;The reason that the sample was sequenced.;GENEPIO:0001445;Enums;Baseline surveillance (random sampling) [GENEPIO:0100005];The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the 'purpose of sampling' field.;['Baseline surveillance (random sampling) [GENEPIO:0100005]', 'Targeted surveillance (non-random sampling) [GENEPIO:0100006]', ' Priority surveillance projects [GENEPIO:0100007]', ' Screening for Variants of Concern (VOC) [GENEPIO:0100008]', ' Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]', ' Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]', ' Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]', ' Re-infection surveillance [GENEPIO:0100010]', ' Vaccine escape surveillance [GENEPIO:0100011]', ' Travel-associated surveillance [GENEPIO:0100012]', ' Domestic travel surveillance [GENEPIO:0100013]', ' Interstate/ interprovincial travel surveillance [GENEPIO:0100275]', ' Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]', ' International travel surveillance [GENEPIO:0100014]', ' Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]', ' Surveillance of international border crossing by air travel [GENEPIO:0100016]', ' Surveillance of international border crossing by ground transport [GENEPIO:0100017]', ' Surveillance from international worker testing [GENEPIO:0100018]', 'Cluster/Outbreak investigation [GENEPIO:0100019]', ' Multi-jurisdictional outbreak investigation [GENEPIO:0100020]', ' Intra-jurisdictional outbreak investigation [GENEPIO:0100021]', 'Research [GENEPIO:0100022]', ' Viral passage experiment [GENEPIO:0100023]', ' Protocol testing [GENEPIO:0100024]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
purpose of sequencing details;Optional;The description of why the sample was sequenced providing specific details.;GENEPIO:0001446;Enums;Screened for S gene target failure (S dropout);Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection.;['Screened for S gene target failure (S dropout)', 'Screened for mink variants', 'Screened for B.1.1.7 variant', 'Screened for B.1.135 variant', 'Screened for P.1 variant', 'Screened due to travel history', 'Screened due to close contact with infected individual', 'Assessing public health control measures', 'Determining early introductions and spread', 'Investigating airline-related exposures', 'Investigating temporary foreign worker ', 'Investigating remote regions', 'Investigating health care workers', 'Investigating schools/universities', 'Investigating reinfection']
sequencing date;Optional;The date the sample was sequenced.;GENEPIO:0001447;Date;22/06/2020;Provide the sequencing date in ISO 8601 standard format 'YYYY-MM-DD'.;
library ID;Optional;The user-specified identifier for the library prepared for sequencing.;GENEPIO:0001448;String;XYZ_123345;The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID.;
amplicon size;Optional;The length of the amplicon generated by PCR amplification.;GENEPIO:0001449;String;300bp;Provide the amplicon size, including the units.;
library preparation kit;Optional;The name of the DNA library preparation kit used to generate the library being sequenced.;GENEPIO:0001450;String;Nextera XT;Provide the name of the library preparation kit used.;
flow cell barcode;Optional;The barcode of the flow cell used for sequencing.;GENEPIO:0001451;String;FAB06069;Provide the barcode of the flow cell used for sequencing the sample.;
sequencing instrument;Required;The model of the sequencing instrument used.;GENEPIO:0001452;Enums;Oxford Nanopore MinION [GENEPIO:0100142];Select the sequencing instrument from the pick list.;['Illumina sequencing instrument [GENEPIO:0100105]', ' Illumina Genome Analyzer [GENEPIO:0100106]', ' Illumina Genome Analyzer II [GENEPIO:0100107]', ' Illumina Genome Analyzer IIx [GENEPIO:0100108]', ' Illumina HiScanSQ [GENEPIO:0100109]', ' Illumina HiSeq [GENEPIO:0100110]', ' Illumina HiSeq X [GENEPIO:0100111]', ' Illumina HiSeq X Five [GENEPIO:0100112]', ' Illumina HiSeq X Ten [GENEPIO:0100113]', ' Illumina HiSeq 1000 [GENEPIO:0100114]', ' Illumina HiSeq 1500 [GENEPIO:0100115]', ' Illumina HiSeq 2000 [GENEPIO:0100116]', ' Illumina HiSeq 2500 [GENEPIO:0100117]', ' Illumina HiSeq 3000 [GENEPIO:0100118]', ' Illumina HiSeq 4000 [GENEPIO:0100119]', ' Illumina iSeq [GENEPIO:0100120]', ' Illumina iSeq 100 [GENEPIO:0100121]', ' Illumina NovaSeq [GENEPIO:0100122]', ' Illumina NovaSeq 6000 [GENEPIO:0100123]', ' Illumina MiniSeq [GENEPIO:0100124]', ' Illumina MiSeq [GENEPIO:0100125]', ' Illumina NextSeq [GENEPIO:0100126]', ' Illumina NextSeq 500 [GENEPIO:0100127]', ' Illumina NextSeq 550 [GENEPIO:0100128]', ' Illumina NextSeq 2000 [GENEPIO:0100129]', 'Pacific Biosciences sequencing instrument [GENEPIO:0100130]', ' PacBio RS [GENEPIO:0100131]', ' PacBio RS II [GENEPIO:0100132]', ' PacBio Sequel [GENEPIO:0100133]', ' PacBio Sequel II [GENEPIO:0100134]', 'Ion Torrent sequencing instrument [GENEPIO:0100135]', ' Ion Torrent PGM [GENEPIO:0100136]', ' Ion Torrent Proton [GENEPIO:0100137]', ' Ion Torrent S5 XL [GENEPIO:0100138]', ' Ion Torrent S5 [GENEPIO:0100139]', 'Oxford Nanopore sequencing instrument [GENEPIO:0100140]', ' Oxford Nanopore GridION [GENEPIO:0100141]', ' Oxford Nanopore MinION [GENEPIO:0100142]', ' Oxford Nanopore PromethION [GENEPIO:0100143]', 'BGI Genomics sequencing instrument [GENEPIO:0100144]', ' BGI SEQ-500 [GENEPIO:0100145]', 'MGI sequencing instrument [GENEPIO:0100146]', ' MGI DNBSEQ-T7 [GENEPIO:0100147]', ' MGI DNBSEQ-G400 [GENEPIO:0100148]', ' MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]', ' MGI DNBSEQ-G50 [GENEPIO:0100150]', 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']
sequencing protocol name;Recommended;The name and version number of the sequencing protocol used.;GENEPIO:0001453;String;1D_DNA_MinION, ARTIC Network Protocol V3;Provide the name and version of the sequencing protocol.;
sequencing protocol;Optional;The protocol used to generate the sequence.;GENEPIO:0001454;String;Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.;Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: 'Viral sequencing was performed following a tiling amplicon strategy using the <fill in> primer scheme. Sequencing was performed using a <fill in> sequencing instrument. Libraries were prepared using <fill in> library kit. ';
sequencing kit number;Optional;The manufacturer's kit number.;GENEPIO:0001455;String;AB456XYZ789;Alphanumeric value.;
amplicon pcr primer scheme;Optional;The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.;GENEPIO:0001456;String;https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv;Provide the name and version of the primer scheme used to generate the amplicons for sequencing.;
raw sequence data processing method;Recommended;The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.;GENEPIO:0001458;String;Porechop 0.2.3,Porechop 0.2.3;;
dehosting method;Recommended;The method used to remove host reads from the pathogen sequence.;GENEPIO:0001459;String;Nanostripper;Nanostripper;
consensus sequence name;Optional;The name of the consensus sequence.;GENEPIO:0001460;String;ncov123assembly3;ncov123assembly3;
consensus sequence filename;Optional;The name of the consensus sequence file.;GENEPIO:0001461;String;ncov123assembly.fasta;ncov123assembly.fasta;
consensus sequence filepath;Optional;The filepath of the consesnsus sequence file.;GENEPIO:0001462;String;/User/Documents/RespLab/Data/ncov123assembly.fasta;/User/Documents/RespLab/Data/ncov123assembly.fasta;
consensus sequence software name;Required;The name of software used to generate the consensus sequence.;GENEPIO:0001463;String;Ivar;Ivar;
consensus sequence software version;Required;The version of the software used to generate the consensus sequence.;GENEPIO:0001469;String;1.3;1.3;
breadth of coverage value;Optional;The percentage of the reference genome covered by the sequenced data, to a prescribed depth.;GENEPIO:0001472;Float;0.95;95%;
depth of coverage value;Optional;The average number of reads representing a given nucleotide in the reconstructed sequence.;GENEPIO:0001474;Float;400;400x;
depth of coverage threshold;Optional;The threshold used as a cut-off for the depth of coverage.;GENEPIO:0001475;Float;100;100x;
r1 fastq filename;Optional;The user-specified filename of the r1 FASTQ file.;GENEPIO:0001476;String;ABC123_S1_L001_R1_001.fastq.gz;ABC123_S1_L001_R1_001.fastq.gz;
r2 fastq filename;Optional;The user-specified filename of the r2 FASTQ file.;GENEPIO:0001477;String;ABC123_S1_L001_R2_001.fastq.gz;ABC123_S1_L001_R2_001.fastq.gz;
r1 fastq filepath;Optional;The filepath of the r1 FASTQ file.;GENEPIO:0001478;String;/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz;/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz;
r2 fastq filepath;Optional;The filepath of the r2 FASTQ file.;GENEPIO:0001479;String;/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz;/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz;
fast5 filename;Optional;The user-specified filename of the FAST5 file.;GENEPIO:0001480;String;batch1a_sequences.fast5;batch1a_sequences.fast5;
fast5 filepath;Optional;The filepath of the FAST5 file.;GENEPIO:0001481;String;/User/Documents/RespLab/Data/rona123assembly.fast5;/User/Documents/RespLab/Data/rona123assembly.fast5;
number of base pairs sequenced;Optional;The number of total base pairs generated by the sequencing process.;GENEPIO:0001482;Int;387566;387566;
consensus genome length;Optional;Size of the assembled genome described as the number of base pairs.;GENEPIO:0001483;Int;38677;38677;
Ns per 100 kbp;Optional;The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.;GENEPIO:0001484;Int;300;300;
reference genome accession;Optional;A persistent, unique identifier of a genome database entry.;GENEPIO:0001485;String;NC_045512.2;NC_045512.2;
bioinformatics protocol;Optional;The name and version number of the bioinformatics protocol used.;GENEPIO:0001489;String;https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members;https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members;
lineage/clade name;Optional;The name of the lineage or clade.;GENEPIO:0001500;String;B.1.1.7;Provide the Pangolin or Nextstrain lineage/clade name.;
lineage/clade analysis software name;Optional;The name of the software used to determine the lineage/clade.;GENEPIO:0001501;String;Pangolin;Provide the name of the software used to determine the lineage/clade.;
lineage/clade analysis software version;Optional;The version of the software used to determine the lineage/clade.;GENEPIO:0001502;String;2.1.10;Provide the version of the software used ot determine the lineage/clade.;
variant designation;Optional;The variant classification of the lineage/clade i.e. variant, variant of concern.;GENEPIO:0001503;Enums;Variant of Concern (VOC) [GENEPIO:0100083];If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank.;['Variant of Interest (VOI) [GENEPIO:0100082]', 'Variant of Concern (VOC) [GENEPIO:0100083]', 'Variant Under Monitoring (VUM) [GENEPIO:0100279]']
variant evidence;Optional;The evidence used to make the variant determination.;GENEPIO:0001504;String;lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L);List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here.;
gene name 1;Optional;The name of the gene used in the diagnostic RT-PCR test.;GENEPIO:0001507;Enums;E gene (orf4) [GENEPIO:0100151];Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI;"['E gene (orf4) [GENEPIO:0100151]', 'M gene (orf5) [GENEPIO:0100152]', 'N gene (orf9) [GENEPIO:0100153]', 'Spike gene (orf2) [GENEPIO:0100154]', 'orf1ab (rep) [GENEPIO:0100155]', ' orf1a (pp1a) [GENEPIO:0100156]', ' nsp11 [GENEPIO:0100157]', ' nsp1 [GENEPIO:0100158]', ' nsp2 [GENEPIO:0100159]', ' nsp3 [GENEPIO:0100160]', ' nsp4 [GENEPIO:0100161]', ' nsp5 [GENEPIO:0100162]', ' nsp6 [GENEPIO:0100163]', ' nsp7 [GENEPIO:0100164]', ' nsp8 [GENEPIO:0100165]', ' nsp9 [GENEPIO:0100166]', ' nsp10 [GENEPIO:0100167]', ' RdRp gene (nsp12) [GENEPIO:0100168]', ' hel gene (nsp13) [GENEPIO:0100169]', ' exoN gene (nsp14) [GENEPIO:0100170]', ' nsp15 [GENEPIO:0100171]', ' nsp16 [GENEPIO:0100172]', 'orf3a [GENEPIO:0100173]', 'orf3b [GENEPIO:0100174]', 'orf6 (ns6) [GENEPIO:0100175]', 'orf7a [GENEPIO:0100176]', 'orf7b (ns7b) [GENEPIO:0100177]', 'orf8 (ns8) [GENEPIO:0100178]', 'orf9b [GENEPIO:0100179]', 'orf9c [GENEPIO:0100180]', 'orf10 [GENEPIO:0100181]', 'orf14 [GENEPIO:0100182]', ""SARS-COV-2 5' UTR [GENEPIO:0100183]"", 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
diagnostic pcr protocol 1;Optional;The name and version number of the protocol used for diagnostic marker amplification.;GENEPIO:0001508;String;PCREGene 2.0;The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.;
diagnostic pcr Ct value 1;Optional;The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.;GENEPIO:0001509;Int;21;Provide the CT value of the sample from the diagnostic RT-PCR test.;
gene name 2;Optional;The name of the gene used in the diagnostic RT-PCR test.;GENEPIO:0001510;Enums;RdRp gene (nsp12) [GENEPIO:0100168];Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI;"['E gene (orf4) [GENEPIO:0100151]', 'M gene (orf5) [GENEPIO:0100152]', 'N gene (orf9) [GENEPIO:0100153]', 'Spike gene (orf2) [GENEPIO:0100154]', 'orf1ab (rep) [GENEPIO:0100155]', ' orf1a (pp1a) [GENEPIO:0100156]', ' nsp11 [GENEPIO:0100157]', ' nsp1 [GENEPIO:0100158]', ' nsp2 [GENEPIO:0100159]', ' nsp3 [GENEPIO:0100160]', ' nsp4 [GENEPIO:0100161]', ' nsp5 [GENEPIO:0100162]', ' nsp6 [GENEPIO:0100163]', ' nsp7 [GENEPIO:0100164]', ' nsp8 [GENEPIO:0100165]', ' nsp9 [GENEPIO:0100166]', ' nsp10 [GENEPIO:0100167]', ' RdRp gene (nsp12) [GENEPIO:0100168]', ' hel gene (nsp13) [GENEPIO:0100169]', ' exoN gene (nsp14) [GENEPIO:0100170]', ' nsp15 [GENEPIO:0100171]', ' nsp16 [GENEPIO:0100172]', 'orf3a [GENEPIO:0100173]', 'orf3b [GENEPIO:0100174]', 'orf6 (ns6) [GENEPIO:0100175]', 'orf7a [GENEPIO:0100176]', 'orf7b (ns7b) [GENEPIO:0100177]', 'orf8 (ns8) [GENEPIO:0100178]', 'orf9b [GENEPIO:0100179]', 'orf9c [GENEPIO:0100180]', 'orf10 [GENEPIO:0100181]', 'orf14 [GENEPIO:0100182]', ""SARS-COV-2 5' UTR [GENEPIO:0100183]"", 'Not Applicable [GENEPIO:0001619]', 'Not Collected [GENEPIO:0001620]', 'Not Provided [GENEPIO:0001668]', 'Missing [GENEPIO:0001618]', 'Restricted Access [GENEPIO:0001810]']"
diagnostic pcr protocol 2;Optional;The name and version number of the protocol used for diagnostic marker amplification.;GENEPIO:0001511;String;PCRRdRpGene 3.0;The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.;
diagnostic pcr Ct value 2;Optional;The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.;GENEPIO:0001512;Int;36;Provide the CT value of the sample from the second diagnostic RT-PCR test.;
authors;Recommended;Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.;GENEPIO:0001517;String;Tejinder Singh, Fei Hu, Johnny Blogs;Include the first and last names of all individuals that should be attributed, separated by a comma.;