SARS-CoV-2.cl.1.0 SARS-CoV-2: clinical or host-associated; version 1.0 SARS-CoV-2: clinical or host-associated wgs_single;wgs_batch;wgs_diploid Use for SARS-CoV-2 samples that are relevant to public health. Required attributes include those considered useful for the rapid analysis and trace back of SARS-CoV-2 cases. # This is a submission template for batch deposit of 'SARS-CoV-2: clinical or host-associated; version 1.0' samples to the NCBI BioSample database (https://www.ncbi.nlm.nih.gov/biosample/). # Fields with an asterisk (*) are mandatory. Your submission will fail if any mandatory fields are not completed. If information is unavailable for any mandatory field, please enter 'not collected', 'not applicable' or 'missing' as appropriate. # All other fields are optional. Leave optional fields empty if no information is available. # You can add any number of custom fields to fully describe your BioSamples, simply include them in the table. # CAUTION: Be aware that Excel may automatically apply formatting to your data. In particular, take care with dates, incrementing autofills and special characters like / or -. Doublecheck that your text file is accurate before uploading to BioSample. # TO MAKE A SUBMISSION: # 1. Complete the template table (typically in Excel, or another spreadsheet application) # 2. Save the worksheet as a Text (Tab-delimited) file - use 'File, Save as, Save as type: Text (Tab-delimited)' # 3. Upload the file on the 'Attributes' tab of the BioSample Submission Portal at https://submit.ncbi.nlm.nih.gov/subs/biosample/. # 4. If you have any questions, please contact us at biosamplehelp@ncbi.nlm.nih.gov. collected by collected_by Name of persons or institute who collected the sample None collection date collection_date the date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format {timestamp} geographic location geo_loc_name Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" {term}:{term}:{text} host host The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens". None host disease host_disease Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh None isolate isolate identification or description of the specific individual from which this sample was obtained isolation source isolation_source Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. None antiviral treatment agent antiviral_treatment_agent What was the antiviral treatment agent? {text} collection device collection_device Instrument or container used to collect sample, e.g., swab {text} collection method collection_method Process used to collect the sample, e.g., bronchoalveolar lavage (BAL) {text} date of prior SARS-CoV-2 antiviral treatment date_of_prior_antiviral_treat Date of the SARS-CoV-2 antiviral treatment, e.g., 2021-03-30 {timestamp} date of prior SARS-CoV-2 infection date_of_prior_sars_cov_2_infection Date of the prior SARS-CoV-2 infection, e.g., 2021-03-30 {timestamp} date of SARS-CoV-2 vaccination date_of_sars_cov_2_vaccination Date of the 1st dose of the SARS-CoV-2 vaccine, e.g., 2021-03-30 {timestamp} exposure event exposure_event Event leading to exposure, e.g., mass gathering {text} geo loc exposure geo_loc_exposure The country where the host was likely exposed to the causative agent of the illness. 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, e.g., Canada {term}:{term}:{text} GISAID accession gisaid_accession The GISAID accession assigned to the sequence. GISAID Accession Numbers are used as unique and permanent identifiers for each virus beginning with the letters EPI and followed by numbers, to identify viruses and/or segments; https://www.gisaid.org/; e.g., EPI_ISL_1091361 {term} GISAID virus name gisaid_virus_name The full virus name submitted to GISAID (https://www.gisaid.org/), e.g., hCoV-19/Belgium/rega-3187/2021 {text} host age host_age Age of host at the time of sampling None host anatomical material host_anatomical_material Host anatomical material or substance produced by the body where the sample was obtained, e.g., stool, mucus, saliva {text} host anatomical part host_anatomical_part Anatomical part of the host organism (e.g. tissue) that was sampled, e.g., nasopharynx {text} host body product host_body_product substance produced by the host, e.g. stool, mucus, where the sample was obtained from {text} host disease outcome host_disease_outcome Final outcome of disease, e.g., death, chronic disease, recovery None host health state host_health_state Information regarding health state of the individual sampled at the time of sampling None host recent travel location host_recent_travel_loc The name of the country that was the destination of most recent travel. Specify the countries (and more granular locations if known) travelled, e.g., United Kingdom. Can include multiple travels; separate multiple travel events with a semicolon. {term}:{term}:{text} host recent travel return date host_recent_travel_return_date The date of a person's most recent return to some residence from a journey originating at that residence, e.g., 2021-03-30 {timestamp} host sex host_sex Gender or physical sex of the host male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected | not provided | restricted access male female pooled male and female neuter hermaphrodite intersex not determined missing not applicable not collected not provided restricted access host specimen voucher host_specimen_voucher Identifier for the physical specimen. 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. URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542; INSDC triplet example: UAM:Mamm:52179 {text} host subject id host_subject_id a unique identifier by which each subject can be referred to, de-identified, e.g. #131 {text} latitude and longitude lat_lon The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W {float} {float} passage method passage_method Description of how the organism was passaged. Provide a short description, e.g., 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. If not passaged, put ""not applicable"". {text} passage number passage_number The number of known passages, e.g., 3. If not passaged, put ""not applicable"". {integer}{text} prior SARS-CoV-2 antiviral treatment prior_sars_cov_2_antiviral_treat Has the host received SARS-CoV-2 antiviral treatment? no | yes no yes prior SARS-CoV-2 infection prior_sars_cov_2_infection Did the host have a prior SARS-CoV-2 infection? no | yes no yes prior SARS-CoV-2 vaccination prior_sars_cov_2_vaccination Has the host received a SARS-CoV-2 vaccination? no | yes - completed | yes - partially completed no yes - completed yes - partially completed purpose of sampling purpose_of_sampling the reason that the sample was collected, e.g., active surveillance in response to an outbreak, active surveillance not initiated by an outbreak, clinical trial, cluster investigation, environmental assessment, farm sample, field trial, for cause, industry internal investigation, market sample, passive surveillance, population based studies, research, research and development {text} purpose of sequencing purpose_of_sequencing The reason the sample was sequenced, e.g., baseline surveillance (random sampling) {text} SARS-CoV-2 diagnostic gene name 1 sars_cov_2_diag_gene_name_1 The name of the gene used in the first diagnostic SARS-CoV-2 RT-PCR test. E (orf4) | M (orf5) | N (orf9) | spike (orf2) | ORF1ab (rep) | ORF1a (pp1a) | nsp11 | nsp1 | nsp2 | nsp3 | nsp4 | nsp5 | nsp6 | nsp7 | nsp8 | nsp9 | nsp10 | nsp12 (RdRp) | nsp13 (Hel) | nsp14 (ExoN) | nsp15 | nsp16 | ORF3a | ORF3b | ORF6 (ns6) | ORF7a | ORF7b (ns7b) | ORF8 (ns8) | ORF9b | ORF9c | ORF10 | ORF14 E (orf4) M (orf5) N (orf9) spike (orf2) ORF1ab (rep) ORF1a (pp1a) nsp11 nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 nsp12 (RdRp) nsp13 (Hel) nsp14 (ExoN) nsp15 nsp16 ORF3a ORF3b ORF6 (ns6) ORF7a ORF7b (ns7b) ORF8 (ns8) ORF9b ORF9c ORF10 ORF14 SARS-CoV-2 diagnostic gene name 2 sars_cov_2_diag_gene_name_2 The name of the gene used in the second diagnostic SARS-CoV-2 RT-PCR test. E (orf4) | M (orf5) | N (orf9) | spike (orf2) | ORF1ab (rep) | ORF1a (pp1a) | nsp11 | nsp1 | nsp2 | nsp3 | nsp4 | nsp5 | nsp6 | nsp7 | nsp8 | nsp9 | nsp10 | nsp12 (RdRp) | nsp13 (Hel) | nsp14 (ExoN) | nsp15 | nsp16 | ORF3a | ORF3b | ORF6 (ns6) | ORF7a | ORF7b (ns7b) | ORF8 (ns8) | ORF9b | ORF9c | ORF10 | ORF14 E (orf4) M (orf5) N (orf9) spike (orf2) ORF1ab (rep) ORF1a (pp1a) nsp11 nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 nsp12 (RdRp) nsp13 (Hel) nsp14 (ExoN) nsp15 nsp16 ORF3a ORF3b ORF6 (ns6) ORF7a ORF7b (ns7b) ORF8 (ns8) ORF9b ORF9c ORF10 ORF14 SARS-CoV-2 diagnostic pcr Ct value 1 sars_cov_2_diag_pcr_ct_value_1 The cycle threshold (CT) value result from the first diagnostic SARS-CoV-2 RT-PCR test, e.g., 21 {integer} SARS-CoV-2 diagnostic pcr Ct value 2 sars_cov_2_diag_pcr_ct_value_2 The cycle threshold (CT) value result from the second diagnostic SARS-CoV-2 RT-PCR test, e.g., 36 {integer} sequenced by sequenced_by The name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention {text} vaccine received vaccine_received Which vaccine did the host receive, e.g., Pfizer-BioNTech COVID-19 vaccine {text} virus isolate of prior infection virus_isolate_of_prior_infection Specific isolate of SARS-CoV-2 in prior infection (if known), e.g., SARS-CoV-2/human/USA/CA-CDPH-001/2020 {text}