TITLE: SOP for populating  NCBI submission  templates for SARS-CoV-2  (BioSample, SRA, and GenBank)
AUTHORS: Ruth Timme, Emma Griffiths, Duncan MacCannell, Stacia Wyman

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>Guidance on how to populate the three NCBI metadata submission templates for SARS-CoV-2 submissions, maximizing interoperability for COVID-19 surveillance. </span></div></div>

[STEPS]
?. [Three templates needed for NCBI SARS-CoV-2 submission]
Guidance for populating the three NCBI metadata templates for SARS-CoV-2 submission.  START HERE FIRST:  Read the PHA4GE contextual data specification BEFORE populating your submission templates!  Steps 3-4 help to map the NCBI submission template fields to the PHA4GE metadata specification, however, the primary PHA4GE guidance should be followed first to ensure the correct controlled vocabularies and ontology terms are used to populate these fields. Guidance included in this protocol:  Step 2) BioSample metadata template (modified for PHA4GE)Step 3) SRA metadata templateStep 4) GenBank source modifier template (modified for PHA4GE)Step 3) SRA metadata templateStep 4) GenBank source modifier template (modified for PHA4GE)
?. [BioSample metadata]
PHA4GE pathogen template for BioSample submissionDownload template here:
?. [SRA metadata]
Populate SRA’s batch metadata table:Download template here:ftp://ftp-trace.ncbi.nlm.nih.gov/sra/metadata_table/SRA_metadata.xlsxPRO TIPS:If you have sequences to submit that belong to more than one BioProject, create a separate submission + metadata table for each of your BioProjects. Entering fastq filenames in the spreadsheet: On a Mac, you can directly copy the file names from the folder into a spreadsheet. This is not possible on a PC using copy and paste but can be done with some command-line operation. Finally, it is important to develop a QA/QC step to make sure the files are associated with the correct sample name. For example, use a left function in excel to strip of the appended text in the file name and then use the exact match to make sure the name matches the sample name.
?. [SRA metadata]
ABC1FieldDescriptionExample2sample_nameInclude the same ID here as you entered for "sample_name" in the BioSample submission template.

Populate this field using the values in the PHA4GE specification for  "specimen collector sample ID".UT-123453library_IDThe library name should be a unique ID relevant to your workflow. It can be an autogenerated ID from your LIMS system or a modification of your sample_name.

Populate this field using the values in the PHA4GE specification for  "library_id".UT-12345.64TitleShort, free text description that identifies the data on public pages.

For Example:
{methodology} of {organism}: {sample_name}Amplicon-based sequencing of SARS-CoV-2: UT-123455library_strategyOverall sequencing strategy or approach. 
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. WGS, RNA-Seq, Amplicon)6library_sourcemolecule type used to make the librarySee NCBI SRA pick list. (e.g. viral RNA, metagenomic)7library_selectionLibrary capture methodSee NCBI SRA pick list. (e.g. random, PCR)8Library_layoutChoose from NCBI pick listSee NCBI SRA pick list. (single, paired)9platformSequencing platformSee NCBI SRA pick list. (e.g., Illumina, Oxford_nanopore, PacBio_SMRT).10instrument_modelName of the sequencing instrument. 

Populate this field using the values in the PHA4GE specification for "sequencing instrument"See NCBI SRA pick list. (e.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II)11Design_descriptionoptional field for free text description of methodsARTIC PCR-tiling of viral cDNA (V3), sequenced on Illumina MiSeq with DNA Flex library prep-kit. Only reads aligned to SARS-CoV-2 reference (NC_045512.2) retained12FiletypeFile format name for the raw sequence data
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. Fastq, OxfordNanopore_native, PacBio_HDF5)13Filenameinclude ALL of the files resulting from this library. **Add additional fields if there are more than two files (e.g. Filename3). 

Populate this field using the values in the PHA4GE specification for "r1 fastq filename".genome_r1.fastq (*must be exact)14Filename2genome_r2.fastq (*must be exact)

Populate this field using the values in the PHA4GE specification for  "r2 fastq filename".genome_r2.fastq (*must be exact)15Filename3-8list other fastq file names (e.g. for NextSeq data)Save the second sheet (SRA_data) as a TSV (tab-delimited file) for upload in the “SRA metadata” tab within the submission portal.*NCBI should also accept the original excel formatted file.
ABC1FieldDescriptionExample2sample_nameInclude the same ID here as you entered for "sample_name" in the BioSample submission template.

Populate this field using the values in the PHA4GE specification for  "specimen collector sample ID".UT-123453library_IDThe library name should be a unique ID relevant to your workflow. It can be an autogenerated ID from your LIMS system or a modification of your sample_name.

Populate this field using the values in the PHA4GE specification for  "library_id".UT-12345.64TitleShort, free text description that identifies the data on public pages.

For Example:
{methodology} of {organism}: {sample_name}Amplicon-based sequencing of SARS-CoV-2: UT-123455library_strategyOverall sequencing strategy or approach. 
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. WGS, RNA-Seq, Amplicon)6library_sourcemolecule type used to make the librarySee NCBI SRA pick list. (e.g. viral RNA, metagenomic)7library_selectionLibrary capture methodSee NCBI SRA pick list. (e.g. random, PCR)8Library_layoutChoose from NCBI pick listSee NCBI SRA pick list. (single, paired)9platformSequencing platformSee NCBI SRA pick list. (e.g., Illumina, Oxford_nanopore, PacBio_SMRT).10instrument_modelName of the sequencing instrument. 

Populate this field using the values in the PHA4GE specification for "sequencing instrument"See NCBI SRA pick list. (e.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II)11Design_descriptionoptional field for free text description of methodsARTIC PCR-tiling of viral cDNA (V3), sequenced on Illumina MiSeq with DNA Flex library prep-kit. Only reads aligned to SARS-CoV-2 reference (NC_045512.2) retained12FiletypeFile format name for the raw sequence data
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. Fastq, OxfordNanopore_native, PacBio_HDF5)13Filenameinclude ALL of the files resulting from this library. **Add additional fields if there are more than two files (e.g. Filename3). 

Populate this field using the values in the PHA4GE specification for "r1 fastq filename".genome_r1.fastq (*must be exact)14Filename2genome_r2.fastq (*must be exact)

Populate this field using the values in the PHA4GE specification for  "r2 fastq filename".genome_r2.fastq (*must be exact)15Filename3-8list other fastq file names (e.g. for NextSeq data)
?. [GenBank metadata]
Populate GenBank source modifier template:
?. [GenBank metadata]
ABC1Source modifierGuidanceExample2Sequence_IDID to link the fasta sequence to these source modifiers for a batch submission.  This ID must match the ID listed as the fasta file header. 

Suggested: use the sample_name submitted to BioSample, or the short lab ID contained within the full isolate name.

Populate this field using the values in the PHA4GE specification for "specimen collector sample ID".CA-CDPH-0013countryThis field can be populated by combining the PHA4GE fields "geo_loc name (country)" and "geo_loc name (state/province/region)". Put more country field first, followed by state/province/region, separated by a colon.USA: Virginia4hostThis field is only required for host-associated samples (Pathogen.cl specified in attribute_package).   Leave blank for environmental isolates. 

Populate this field using the values in the PHA4GE specification for "host (scientific name)".Homo sapiens5isolateFull name of the virus:

SARS-CoV-2/source/location/isolateID/year
Example: SARS-CoV-2/human/USA/CA-CDPH-001/2020

Populate this field using the values in the PHA4GE specification for "isolate".SARS-CoV-2/human/USA/CA-CDPH-001/20206collection-datethe date on which the sample was collected; 
"YYYY-mm-dd", "YYYY-mm", or "YYYY"

Populate this field using the values in the PHA4GE specification for "sample collection date".2020-06-047isolation-source"Clinical", "Animal", or "Environmental". 

Add the statement "See additional sample source fields for further information."clinical; See additional sample source fields for further information8BioSampleThe accession number of the BioSample registered for this sample. 

Populate this field using the values in the PHA4GE specification for "biosample accession".SAMN151871459BioProjectThe accession number of the BioProject(s) to which the BioSample belongs. 

Populate this field using the values in the PHA4GE specification for "bioproject accession".PRJNA625551
ABC1Source modifierGuidanceExample2Sequence_IDID to link the fasta sequence to these source modifiers for a batch submission.  This ID must match the ID listed as the fasta file header. 

Suggested: use the sample_name submitted to BioSample, or the short lab ID contained within the full isolate name.

Populate this field using the values in the PHA4GE specification for "specimen collector sample ID".CA-CDPH-0013countryThis field can be populated by combining the PHA4GE fields "geo_loc name (country)" and "geo_loc name (state/province/region)". Put more country field first, followed by state/province/region, separated by a colon.USA: Virginia4hostThis field is only required for host-associated samples (Pathogen.cl specified in attribute_package).   Leave blank for environmental isolates. 

Populate this field using the values in the PHA4GE specification for "host (scientific name)".Homo sapiens5isolateFull name of the virus:

SARS-CoV-2/source/location/isolateID/year
Example: SARS-CoV-2/human/USA/CA-CDPH-001/2020

Populate this field using the values in the PHA4GE specification for "isolate".SARS-CoV-2/human/USA/CA-CDPH-001/20206collection-datethe date on which the sample was collected; 
"YYYY-mm-dd", "YYYY-mm", or "YYYY"

Populate this field using the values in the PHA4GE specification for "sample collection date".2020-06-047isolation-source"Clinical", "Animal", or "Environmental". 

Add the statement "See additional sample source fields for further information."clinical; See additional sample source fields for further information8BioSampleThe accession number of the BioSample registered for this sample. 

Populate this field using the values in the PHA4GE specification for "biosample accession".SAMN151871459BioProjectThe accession number of the BioProject(s) to which the BioSample belongs. 

Populate this field using the values in the PHA4GE specification for "bioproject accession".PRJNA625551
?. [BioSample metadata]
ABC1attributesguidanceexample2sample_nameSample Name is a unique identifier for the sample (it cannot be left blank).

Populate with the same ID as "Isolate", or include just the lab ID:.

Populate this field using the values in the PHA4GE specification for "specimen collector sample ID".Example 1: SARS-CoV-2/human/USA/MI-MDHHS-SC20654/2020
Example 2: MI-MDHHS-SC206543bioproject_accessionThe accession number of the BioProject(s) to which the BioSample belongs (PRJNAxxxxxx). A valid BioProject accession has prefix PRJN, PRJE or PRJD. This cannot be left blank.

**Double-check that you are submitting to the correct data BioProject for your laboratory, and not the umbrella BioProject for the entire effort.

Populate this field using the values in the PHA4GE specification for "bioproject accession".PRJNA123454attribute_packageSpecify the pathogen type. 

"Pathogen.cl" (for clinical or host-associated pathogen) or "Pathogen.env" (for environmental, food or other pathogen). 

The value provided in this field drives validation of other fields.Pathogen.cl5organismPopulate this field using the values in the PHA4GE specification for "organism".Severe acute respiratory syndrome coronavirus 26isolateFull name of the virus:
SARS-CoV-2/source/location/isolateID/year

Populate this field using the values in the PHA4GE specification for "isolate".SARS-CoV-2/human/USA/CA-CDPH-001/20207collected_byFull name of laboratory or institute that collected the sample.

Populate this field using the values in the PHA4GE specification for "sample collected by".Utah Public Health Laboratory8collection_datethe date on which the sample was collected; 
"YYYY-mm-dd", "YYYY-mm", or "YYYY". Including the month or month/day of collection is extremely valuable for accessing seasonality in the database.

Populate this field using the values in the PHA4GE specification for "sample collection date".

If unknown, put "not collected", or other null value like "missing".2020-05-159geo_loc_nameGeographical 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 from more detailed information about the location, 

Populate this field combining the PHA4GE specification fields for "geo_loc name (country)" and "geo_loc name (state/province/region)". Put more country field first, followed by state/province/region, separated by a colon.

If unknown, put "not collected", or other null value like "missing".USA: Utah10isolation_sourceDescribe the sample as "Clinical", "Animal", or "Environmental". 

Add the statement "See additional sample source fields for further information".Clinical, see additional sample source fields for further information11lat_lonThe coordinates of the geographical location of sample or host collection.

If known, provide the geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in the format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W. 

Populate this field by combining the PHA4GE specification fields "geo_loc latitude" and "geo_loc_longitute"

**DO NOT PROVIDE LAT/LON OF THE INSTITUTION, NOR THE CENTER OF A CITY/REGION WHERE THE SAMPLE WAS COLLECTED. 

If unknown, put "not collected", or other null value like "missing".38.98 N 77.11 W

not collected12hostIf the combined attribute package is being used, this field can be left empty for Pathogen.ev isolates.

Populate this field using the values in the PHA4GE specification for "host (scientific name)". 

This field is only required for host-associated samples (Pathogen.cl specified in attribute_package).Homo sapiens13host_diseaseThis field is only required for host-associated samples (Pathogen.cl specified in attribute_package).  If the combined attribute package is being used, this field can be left empty for Pathogen.ev isolates. 

Populate this field using the values in the PHA4GE specification for "host_disease".

If the host is healthy or the information is unknown, put "missing"COVID-1914host_health_stateInformation regarding health state of the individual sampled at the time of sampling.

Populate this field using the values in the PHA4GE specification for "host health state".

If the information is unknown, or can not be shared, leave blank or provide a null value.asymptomatic15host_disease_outcomeFinal outcome of disease, e.g., death, chronic disease, recovery

Populate this field using the values in the PHA4GE specification for "host disease outcome". 

If the information is unknown, or can not be shared, leave blank or provide a null value.e.g., death, chronic disease, recovery16host_sexThe gender of the host at the time of sample collection.

Populate this field using the values in the PHA4GE specification for "host gender".

If the information is unknown, or can not be shared, leave blank or provide a null value.male17host_ageAge of host at the time of sampling

Populate this field using the values in the PHA4GE specification for "host age". Provide age in years. Age-binning is also acceptable.  

If the information is unknown or can not be shared, leave blank or provide a null value.3118host_subject_ida unique identifier by which each subject can be referred to, de-identified.

Populate this field using the values in the PHA4GE specification for "host subject ID".

If the information is unknown or can not be shared, leave blank or provide a null value.clincal12345619anatomical_materialProvide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. 

Populate this field using the values in the PHA4GE specification for "anatomical material".

If not applicable, leave blank.blood20anatomical_partAn anatomical part of an organism e.g. oropharynx. 

Populate this field using the values in the PHA4GE specification for "anatomical part".

If not applicable, leave blank.nasopharynx21body_productA substance excreted/secreted from an organism e.g. feces, urine, sweat.

Populate this field using the values in the PHA4GE specification for "body product".

If not applicable, leave blank.feces22passage_historyNumber of passages

Populate this field using the values in the PHA4GE specification for "passage number".

If not applicable, leave blank.323lab_hostName and description of the laboratory host used to propagate the organism or material from which the sample was obtained. 

This field can be populated by the PHA4GE field "lab_host".

If not applicable, leave blank.Vero E6 cell line24passage_methodPassage method.

Populate this field using the values in the PHA4GE specification for "passage method".

If not applicable, leave blank.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.25purpose_of_samplingThe reason that the sample was collected.

Populate this field using the values in the PHA4GE specification for "purpose of sampling".

If not applicable, leave blank.Select a value from the pick list in the template. (e.g. diagnostic testing)26environmental_materialA substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.

Populate this field using the values in the PHA4GE specification for "environmental material".

If not applicable, leave blank.face mask27environmental_siteAn environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.

Populate this field using the values in the PHA4GE specification for "environmental site".

If not applicable, leave blank.hospital room28collection_deviceThe instrument or container used to collect the sample e.g. swab.

Populate this field using the values in the PHA4GE specification for "collection device".

If not applicable, leave blank.swab29collection_methodThe process used to collect the sample e.g. phlebotomy, necropsy.

Populate this field using the values in the PHA4GE specification for "collection method".

If not applicable, leave blank.Bronchoalveolar lavage (BAL)30culture_collectionName of source institute and unique culture identifier for the organism (SARS-CoV-2). 

See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

If not applicable, leave blank.31host_specimen_voucherIdentifier for the physical host specimen.

Populate this field using the values in the PHA4GE specification for "host specimen voucher".

if not applicable, leave blank.URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, 

INSDC triplet example: UAM:Mamm:5217932descriptionOptional field for additional description of the sample.
ABC1attributesguidanceexample2sample_nameSample Name is a unique identifier for the sample (it cannot be left blank).

Populate with the same ID as "Isolate", or include just the lab ID:.

Populate this field using the values in the PHA4GE specification for "specimen collector sample ID".Example 1: SARS-CoV-2/human/USA/MI-MDHHS-SC20654/2020
Example 2: MI-MDHHS-SC206543bioproject_accessionThe accession number of the BioProject(s) to which the BioSample belongs (PRJNAxxxxxx). A valid BioProject accession has prefix PRJN, PRJE or PRJD. This cannot be left blank.

**Double-check that you are submitting to the correct data BioProject for your laboratory, and not the umbrella BioProject for the entire effort.

Populate this field using the values in the PHA4GE specification for "bioproject accession".PRJNA123454attribute_packageSpecify the pathogen type. 

"Pathogen.cl" (for clinical or host-associated pathogen) or "Pathogen.env" (for environmental, food or other pathogen). 

The value provided in this field drives validation of other fields.Pathogen.cl5organismPopulate this field using the values in the PHA4GE specification for "organism".Severe acute respiratory syndrome coronavirus 26isolateFull name of the virus:
SARS-CoV-2/source/location/isolateID/year

Populate this field using the values in the PHA4GE specification for "isolate".SARS-CoV-2/human/USA/CA-CDPH-001/20207collected_byFull name of laboratory or institute that collected the sample.

Populate this field using the values in the PHA4GE specification for "sample collected by".Utah Public Health Laboratory8collection_datethe date on which the sample was collected; 
"YYYY-mm-dd", "YYYY-mm", or "YYYY". Including the month or month/day of collection is extremely valuable for accessing seasonality in the database.

Populate this field using the values in the PHA4GE specification for "sample collection date".

If unknown, put "not collected", or other null value like "missing".2020-05-159geo_loc_nameGeographical 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 from more detailed information about the location, 

Populate this field combining the PHA4GE specification fields for "geo_loc name (country)" and "geo_loc name (state/province/region)". Put more country field first, followed by state/province/region, separated by a colon.

If unknown, put "not collected", or other null value like "missing".USA: Utah10isolation_sourceDescribe the sample as "Clinical", "Animal", or "Environmental". 

Add the statement "See additional sample source fields for further information".Clinical, see additional sample source fields for further information11lat_lonThe coordinates of the geographical location of sample or host collection.

If known, provide the geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in the format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W. 

Populate this field by combining the PHA4GE specification fields "geo_loc latitude" and "geo_loc_longitute"

**DO NOT PROVIDE LAT/LON OF THE INSTITUTION, NOR THE CENTER OF A CITY/REGION WHERE THE SAMPLE WAS COLLECTED. 

If unknown, put "not collected", or other null value like "missing".38.98 N 77.11 W

not collected12hostIf the combined attribute package is being used, this field can be left empty for Pathogen.ev isolates.

Populate this field using the values in the PHA4GE specification for "host (scientific name)". 

This field is only required for host-associated samples (Pathogen.cl specified in attribute_package).Homo sapiens13host_diseaseThis field is only required for host-associated samples (Pathogen.cl specified in attribute_package).  If the combined attribute package is being used, this field can be left empty for Pathogen.ev isolates. 

Populate this field using the values in the PHA4GE specification for "host_disease".

If the host is healthy or the information is unknown, put "missing"COVID-1914host_health_stateInformation regarding health state of the individual sampled at the time of sampling.

Populate this field using the values in the PHA4GE specification for "host health state".

If the information is unknown, or can not be shared, leave blank or provide a null value.asymptomatic15host_disease_outcomeFinal outcome of disease, e.g., death, chronic disease, recovery

Populate this field using the values in the PHA4GE specification for "host disease outcome". 

If the information is unknown, or can not be shared, leave blank or provide a null value.e.g., death, chronic disease, recovery16host_sexThe gender of the host at the time of sample collection.

Populate this field using the values in the PHA4GE specification for "host gender".

If the information is unknown, or can not be shared, leave blank or provide a null value.male17host_ageAge of host at the time of sampling

Populate this field using the values in the PHA4GE specification for "host age". Provide age in years. Age-binning is also acceptable.  

If the information is unknown or can not be shared, leave blank or provide a null value.3118host_subject_ida unique identifier by which each subject can be referred to, de-identified.

Populate this field using the values in the PHA4GE specification for "host subject ID".

If the information is unknown or can not be shared, leave blank or provide a null value.clincal12345619anatomical_materialProvide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. 

Populate this field using the values in the PHA4GE specification for "anatomical material".

If not applicable, leave blank.blood20anatomical_partAn anatomical part of an organism e.g. oropharynx. 

Populate this field using the values in the PHA4GE specification for "anatomical part".

If not applicable, leave blank.nasopharynx21body_productA substance excreted/secreted from an organism e.g. feces, urine, sweat.

Populate this field using the values in the PHA4GE specification for "body product".

If not applicable, leave blank.feces22passage_historyNumber of passages

Populate this field using the values in the PHA4GE specification for "passage number".

If not applicable, leave blank.323lab_hostName and description of the laboratory host used to propagate the organism or material from which the sample was obtained. 

This field can be populated by the PHA4GE field "lab_host".

If not applicable, leave blank.Vero E6 cell line24passage_methodPassage method.

Populate this field using the values in the PHA4GE specification for "passage method".

If not applicable, leave blank.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.25purpose_of_samplingThe reason that the sample was collected.

Populate this field using the values in the PHA4GE specification for "purpose of sampling".

If not applicable, leave blank.Select a value from the pick list in the template. (e.g. diagnostic testing)26environmental_materialA substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.

Populate this field using the values in the PHA4GE specification for "environmental material".

If not applicable, leave blank.face mask27environmental_siteAn environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.

Populate this field using the values in the PHA4GE specification for "environmental site".

If not applicable, leave blank.hospital room28collection_deviceThe instrument or container used to collect the sample e.g. swab.

Populate this field using the values in the PHA4GE specification for "collection device".

If not applicable, leave blank.swab29collection_methodThe process used to collect the sample e.g. phlebotomy, necropsy.

Populate this field using the values in the PHA4GE specification for "collection method".

If not applicable, leave blank.Bronchoalveolar lavage (BAL)30culture_collectionName of source institute and unique culture identifier for the organism (SARS-CoV-2). 

See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

If not applicable, leave blank.31host_specimen_voucherIdentifier for the physical host specimen.

Populate this field using the values in the PHA4GE specification for "host specimen voucher".

if not applicable, leave blank.URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, 

INSDC triplet example: UAM:Mamm:5217932descriptionOptional field for additional description of the sample.