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<div class="res_logo"><h1 class="res_name"><a href="/biosample/" title="BioSample home">BioSample</a></h1><h2 class="res_tagline"></h2></div>
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<div class="search"><form method="get" action="/biosample/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="biosample" selected="selected">BioSample</option><option value="pubmed">PubMed</option><option value="books">Books</option><option value="clinvar" class="last">ClinVar</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search BioSample" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class=" inline_list searchlinks"><li>
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<div id="package"><h1>SARS-CoV-2: clinical or host-associated; version 1.0 Package</h1><p>You can download package details in <a href="?format=xml">xml format</a> or as an <a href="/biosample/docs/templates/packages/SARS-CoV-2.cl.1.0.xlsx">Excel spreadsheet</a>.</p><h2>Name</h2>SARS-CoV-2.cl.1.0<h2>Description</h2><p>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.</p><h2>Mandatory Attributes</h2><h4>collected by</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">collected_by</span></li><li><strong>Description</strong><span class="indent">Name of persons or institute who collected the sample</span></li></ul><h4>collection date</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">collection_date</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>geographic location</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">geo_loc_name</span></li><li><strong>Description</strong><span class="indent">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"</span></li></ul><h4>host</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host</span></li><li><strong>Description</strong><span class="indent">The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".</span></li></ul><h4>host disease</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_disease</span></li><li><strong>Description</strong><span class="indent">Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh</span></li></ul><h4>isolate</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">isolate</span></li><li><strong>Description</strong><span class="indent">identification or description of the specific individual from which this sample was obtained</span></li></ul><h4>isolation source</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">isolation_source</span></li><li><strong>Description</strong><span class="indent">Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.</span></li></ul><h2>Optional Attributes</h2><h4>antiviral treatment agent</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">antiviral_treatment_agent</span></li><li><strong>Description</strong><span class="indent">What was the antiviral treatment agent?</span></li></ul><h4>collection device</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">collection_device</span></li><li><strong>Description</strong><span class="indent">Instrument or container used to collect sample, e.g., swab</span></li></ul><h4>collection method </h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">collection_method</span></li><li><strong>Description</strong><span class="indent">Process used to collect the sample, e.g., bronchoalveolar lavage (BAL)</span></li></ul><h4>date of prior SARS-CoV-2 antiviral treatment</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">date_of_prior_antiviral_treat</span></li><li><strong>Description</strong><span class="indent">Date of the SARS-CoV-2 antiviral treatment, e.g., 2021-03-30</span></li></ul><h4>date of prior SARS-CoV-2 infection</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">date_of_prior_sars_cov_2_infection</span></li><li><strong>Description</strong><span class="indent">Date of the prior SARS-CoV-2 infection, e.g., 2021-03-30</span></li></ul><h4>date of SARS-CoV-2 vaccination</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">date_of_sars_cov_2_vaccination</span></li><li><strong>Description</strong><span class="indent">Date of the 1st dose of the SARS-CoV-2 vaccine, e.g., 2021-03-30</span></li></ul><h4>exposure event</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">exposure_event</span></li><li><strong>Description</strong><span class="indent">Event leading to exposure, e.g., mass gathering</span></li></ul><h4>geo loc exposure</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">geo_loc_exposure</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>GISAID accession</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">gisaid_accession</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>GISAID virus name</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">gisaid_virus_name</span></li><li><strong>Description</strong><span class="indent">The full virus name submitted to GISAID (https://www.gisaid.org/), e.g., hCoV-19/Belgium/rega-3187/2021</span></li></ul><h4>host age</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_age</span></li><li><strong>Description</strong><span class="indent">Age of host at the time of sampling</span></li></ul><h4>host anatomical material</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_anatomical_material</span></li><li><strong>Description</strong><span class="indent">Host anatomical material or substance produced by the body where the sample was obtained, e.g., stool, mucus, saliva</span></li></ul><h4>host anatomical part</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_anatomical_part</span></li><li><strong>Description</strong><span class="indent">Anatomical part of the host organism (e.g. tissue) that was sampled, e.g., nasopharynx</span></li></ul><h4>host body product</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_body_product</span></li><li><strong>Description</strong><span class="indent">substance produced by the host, e.g. stool, mucus, where the sample was obtained from</span></li></ul><h4>host disease outcome</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_disease_outcome</span></li><li><strong>Description</strong><span class="indent">Final outcome of disease, e.g., death, chronic disease, recovery</span></li></ul><h4>host health state</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_health_state</span></li><li><strong>Description</strong><span class="indent">Information regarding health state of the individual sampled at the time of sampling</span></li></ul><h4>host recent travel location</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_recent_travel_loc</span></li><li><strong>Description</strong><span class="indent">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.</span></li></ul><h4>host recent travel return date</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_recent_travel_return_date</span></li><li><strong>Description</strong><span class="indent">The date of a person's most recent return to some residence from a journey originating at that residence, e.g., 2021-03-30</span></li></ul><h4>host sex</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_sex</span></li><li><strong>Description</strong><span class="indent">Gender or physical sex of the host</span></li></ul><h4>host specimen voucher</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_specimen_voucher</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>host subject id</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">host_subject_id</span></li><li><strong>Description</strong><span class="indent">a unique identifier by which each subject can be referred to, de-identified, e.g. #131</span></li></ul><h4>latitude and longitude</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">lat_lon</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>passage method</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">passage_method</span></li><li><strong>Description</strong><span class="indent">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"".</span></li></ul><h4>passage number</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">passage_number</span></li><li><strong>Description</strong><span class="indent">The number of known passages, e.g., 3. If not passaged, put ""not applicable"".</span></li></ul><h4>prior SARS-CoV-2 antiviral treatment</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">prior_sars_cov_2_antiviral_treat</span></li><li><strong>Description</strong><span class="indent">Has the host received SARS-CoV-2 antiviral treatment?</span></li></ul><h4>prior SARS-CoV-2 infection</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">prior_sars_cov_2_infection</span></li><li><strong>Description</strong><span class="indent">Did the host have a prior SARS-CoV-2 infection?</span></li></ul><h4>prior SARS-CoV-2 vaccination</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">prior_sars_cov_2_vaccination</span></li><li><strong>Description</strong><span class="indent">Has the host received a SARS-CoV-2 vaccination? </span></li></ul><h4>purpose of sampling</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">purpose_of_sampling</span></li><li><strong>Description</strong><span class="indent">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</span></li></ul><h4>purpose of sequencing</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">purpose_of_sequencing</span></li><li><strong>Description</strong><span class="indent">The reason the sample was sequenced, e.g., baseline surveillance (random sampling)</span></li></ul><h4>SARS-CoV-2 diagnostic gene name 1</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">sars_cov_2_diag_gene_name_1</span></li><li><strong>Description</strong><span class="indent">The name of the gene used in the first diagnostic SARS-CoV-2 RT-PCR test.</span></li></ul><h4>SARS-CoV-2 diagnostic gene name 2</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">sars_cov_2_diag_gene_name_2</span></li><li><strong>Description</strong><span class="indent">The name of the gene used in the second diagnostic SARS-CoV-2 RT-PCR test.</span></li></ul><h4>SARS-CoV-2 diagnostic pcr Ct value 1</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">sars_cov_2_diag_pcr_ct_value_1</span></li><li><strong>Description</strong><span class="indent">The cycle threshold (CT) value result from the first diagnostic SARS-CoV-2 RT-PCR test, e.g., 21</span></li></ul><h4>SARS-CoV-2 diagnostic pcr Ct value 2</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">sars_cov_2_diag_pcr_ct_value_2</span></li><li><strong>Description</strong><span class="indent">The cycle threshold (CT) value result from the second diagnostic SARS-CoV-2 RT-PCR test, e.g., 36</span></li></ul><h4>sequenced by</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">sequenced_by</span></li><li><strong>Description</strong><span class="indent">The name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention</span></li></ul><h4>vaccine received</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">vaccine_received</span></li><li><strong>Description</strong><span class="indent">Which vaccine did the host receive, e.g., Pfizer-BioNTech COVID-19 vaccine</span></li></ul><h4>virus isolate of prior infection</h4><ul class="no_bullets"><li><strong>Harmonized name</strong><span class="indent">virus_isolate_of_prior_infection</span></li><li><strong>Description</strong><span class="indent">Specific isolate of SARS-CoV-2 in prior infection (if known), e.g., SARS-CoV-2/human/USA/CA-CDPH-001/2020</span></li></ul></div>
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