SARS-CoV-2: clinical or host-associated; version 1.0 Package

You can download package details in xml format or as an Excel spreadsheet.

Name

Description

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.

Mandatory Attributes

collected by

• Harmonized namecollected_by
• DescriptionName of persons or institute who collected the sample

collection date

• Harmonized namecollection_date
• Descriptionthe 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

geographic location

• Harmonized namegeo_loc_name
• DescriptionGeographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-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"

host

• Harmonized namehost
• DescriptionThe natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".

host disease

• Harmonized namehost_disease
• DescriptionName of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh

isolate

• Harmonized nameisolate
• Descriptionidentification or description of the specific individual from which this sample was obtained

isolation source

• Harmonized nameisolation_source
• DescriptionDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Optional Attributes

antiviral treatment agent

• Harmonized nameantiviral_treatment_agent
• DescriptionWhat was the antiviral treatment agent?

collection device

• Harmonized namecollection_device
• DescriptionInstrument or container used to collect sample, e.g., swab

collection method

• Harmonized namecollection_method
• DescriptionProcess used to collect the sample, e.g., bronchoalveolar lavage (BAL)

date of prior SARS-CoV-2 antiviral treatment

• Harmonized namedate_of_prior_antiviral_treat
• DescriptionDate of the SARS-CoV-2 antiviral treatment, e.g., 2021-03-30

date of prior SARS-CoV-2 infection

• Harmonized namedate_of_prior_sars_cov_2_infection
• DescriptionDate of the prior SARS-CoV-2 infection, e.g., 2021-03-30

date of SARS-CoV-2 vaccination

• Harmonized namedate_of_sars_cov_2_vaccination
• DescriptionDate of the 1st dose of the SARS-CoV-2 vaccine, e.g., 2021-03-30

exposure event

• Harmonized nameexposure_event
• DescriptionEvent leading to exposure, e.g., mass gathering

geo loc exposure

• Harmonized namegeo_loc_exposure
• DescriptionThe 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

GISAID accession

• Harmonized namegisaid_accession
• DescriptionThe 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

GISAID virus name

• Harmonized namegisaid_virus_name
• DescriptionThe full virus name submitted to GISAID (https://www.gisaid.org/), e.g., hCoV-19/Belgium/rega-3187/2021

host age

• Harmonized namehost_age
• DescriptionAge of host at the time of sampling

host anatomical material

• Harmonized namehost_anatomical_material
• DescriptionHost anatomical material or substance produced by the body where the sample was obtained, e.g., stool, mucus, saliva

host anatomical part

• Harmonized namehost_anatomical_part
• DescriptionAnatomical part of the host organism (e.g. tissue) that was sampled, e.g., nasopharynx

host body product

• Harmonized namehost_body_product
• Descriptionsubstance produced by the host, e.g. stool, mucus, where the sample was obtained from

host disease outcome

• Harmonized namehost_disease_outcome
• DescriptionFinal outcome of disease, e.g., death, chronic disease, recovery

host health state

• Harmonized namehost_health_state
• DescriptionInformation regarding health state of the individual sampled at the time of sampling

host recent travel location

• Harmonized namehost_recent_travel_loc
• DescriptionThe 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.

host recent travel return date

• Harmonized namehost_recent_travel_return_date
• DescriptionThe date of a person's most recent return to some residence from a journey originating at that residence, e.g., 2021-03-30

host sex

• Harmonized namehost_sex
• DescriptionGender or physical sex of the host

host specimen voucher

• Harmonized namehost_specimen_voucher
• DescriptionIdentifier 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

host subject id

• Harmonized namehost_subject_id
• Descriptiona unique identifier by which each subject can be referred to, de-identified, e.g. #131

latitude and longitude

• Harmonized namelat_lon
• DescriptionThe 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

passage method

• Harmonized namepassage_method
• DescriptionDescription 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"".

passage number

• Harmonized namepassage_number
• DescriptionThe number of known passages, e.g., 3. If not passaged, put ""not applicable"".

prior SARS-CoV-2 antiviral treatment

• Harmonized nameprior_sars_cov_2_antiviral_treat
• DescriptionHas the host received SARS-CoV-2 antiviral treatment?

prior SARS-CoV-2 infection

• Harmonized nameprior_sars_cov_2_infection
• DescriptionDid the host have a prior SARS-CoV-2 infection?

prior SARS-CoV-2 vaccination

• Harmonized nameprior_sars_cov_2_vaccination
• DescriptionHas the host received a SARS-CoV-2 vaccination?

purpose of sampling

• Harmonized namepurpose_of_sampling
• Descriptionthe 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

purpose of sequencing

• Harmonized namepurpose_of_sequencing
• DescriptionThe reason the sample was sequenced, e.g., baseline surveillance (random sampling)

SARS-CoV-2 diagnostic gene name 1

• Harmonized namesars_cov_2_diag_gene_name_1
• DescriptionThe name of the gene used in the first diagnostic SARS-CoV-2 RT-PCR test.

SARS-CoV-2 diagnostic gene name 2

• Harmonized namesars_cov_2_diag_gene_name_2
• DescriptionThe name of the gene used in the second diagnostic SARS-CoV-2 RT-PCR test.

SARS-CoV-2 diagnostic pcr Ct value 1

• Harmonized namesars_cov_2_diag_pcr_ct_value_1
• DescriptionThe cycle threshold (CT) value result from the first diagnostic SARS-CoV-2 RT-PCR test, e.g., 21

SARS-CoV-2 diagnostic pcr Ct value 2

• Harmonized namesars_cov_2_diag_pcr_ct_value_2
• DescriptionThe cycle threshold (CT) value result from the second diagnostic SARS-CoV-2 RT-PCR test, e.g., 36

sequenced by

• Harmonized namesequenced_by
• DescriptionThe name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention

vaccine received

• Harmonized namevaccine_received
• DescriptionWhich vaccine did the host receive, e.g., Pfizer-BioNTech COVID-19 vaccine

virus isolate of prior infection

• Harmonized namevirus_isolate_of_prior_infection
• DescriptionSpecific isolate of SARS-CoV-2 in prior infection (if known), e.g., SARS-CoV-2/human/USA/CA-CDPH-001/2020