TITLE: SOP for populating EBI submission  templates (ENA)
AUTHORS: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Guidance on how to populate the extended PHA4GE metadata package for SARS-CoV-2 submissions, maximizing interoperability for covid-19 surveillance. </div></div>

[STEPS]
?. [Three templates needed for NCBI SARS-CoV-2 submission]
Guidance for populating the three templates for SARS-CoV-2 submission to EBI.  This protocol helps to describe the fields needed to populate the ENA virus pathogen checklist, however, the primary PHA4GE guidance should be followed to ensure the controlled vocabularies and ontology terms are used to populate these fields. Link to PHA4GE SARS-CoV-2 metadata specification: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-SpecificationLink to PHA4GE SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject: https://www.protocols.io/private/BD4C35AC52C942B2D927E662ABC3D195Link to PHA4GE SARS-CoV2 EBI assembly submission protocol https://www.protocols.io/private/39BBC8E9B6F911EAA1530A58A9FEAC2A
?. [ENA virus pathogen reporting]
PHA4GE ENA virus pathogen reporting standard checklist for sample metadata:ENA submission spreadsheets are not tables with fields name in the first row, and specfics about each sample in subsequent rows. Instead the spreadsheet requires particular headers (denoted with "#"). e.g   ABCDEFG1#checklist_accessionERC0000332#unique_name_prefix3sample_nametax_idscientific_namehost ageorganismcollection dategeographic location (country and/or sea)4hCOV-sample-ENG-112697049Severe acute respiratory syndrome coronavirus 250Severe acute respiratory syndrome coronavirus 205/05/2020United Kingdom5#template6#unitsyearsAs described in the PHA4GE SARS-CoV-2 EBI submission protocol, there will be an oppotunity to download a template spreadsheet from ENA directly. We recommend that you add aditional fields as per the PHA4GE guidelines and keep a blank copy of this spreadsheet for subsequent submissions.
ABCDEFG1#checklist_accessionERC0000332#unique_name_prefix3sample_nametax_idscientific_namehost ageorganismcollection dategeographic location (country and/or sea)4hCOV-sample-ENG-112697049Severe acute respiratory syndrome coronavirus 250Severe acute respiratory syndrome coronavirus 205/05/2020United Kingdom5#template6#unitsyears
?. [ENA run metadata]
Populate ENA run metadata table:PRO TIPS:If you have sequences to submit that have drastically different metadata, create a separate submission + metadata table for each case. 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.
?. [ENA run metadata]
As described in the PHA4GE SARS-CoV-2 EBI submission protocol, there will be an oppotunity to download a template spreadsheet from ENA directly. There is a description of these fields in the table below.  ABC1FieldDescriptionExample2Sample referenceInclude the same ID here as you entered for "sample_name" in the BioSample submission template.

This field can be populated by the PHA4GE field "specimen collector sample ID".UT-123453Library nameThe 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.

This field can be populated by the PHA4GE field "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 liste.g. WGS, RNA-Seq, Amplicon6Library sourcemolecule type used to make the librarye.g. viral RNA, metagenomic7Library selectionLibrary capture methode.g. random, PCR8instrument modelName of the sequencing instrumente.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II9Design 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) retained10File nameIncludes files resulting from this library. This maybe named "First file name" if multiple files need to be submitted

This field can be populated by the PHA4GE field "r1 fastq filename".genome_r1.fastq (*must be exact)11Second file namegenome_r2.fastq (*must be exact)

This field can be populated by the PHA4GE field "r2 fastq filename". This field will only be shown for certain file types (i.e. paired FASTQ)genome_r2.fastq (*must be exact)12Filename3-8list other fastq file names (e.g. for NextSeq data)13(First/Second) MD5 ChecksumMD5 checksum of the file being submitted07182d8b0....
ABC1FieldDescriptionExample2Sample referenceInclude the same ID here as you entered for "sample_name" in the BioSample submission template.

This field can be populated by the PHA4GE field "specimen collector sample ID".UT-123453Library nameThe 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.

This field can be populated by the PHA4GE field "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 liste.g. WGS, RNA-Seq, Amplicon6Library sourcemolecule type used to make the librarye.g. viral RNA, metagenomic7Library selectionLibrary capture methode.g. random, PCR8instrument modelName of the sequencing instrumente.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II9Design 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) retained10File nameIncludes files resulting from this library. This maybe named "First file name" if multiple files need to be submitted

This field can be populated by the PHA4GE field "r1 fastq filename".genome_r1.fastq (*must be exact)11Second file namegenome_r2.fastq (*must be exact)

This field can be populated by the PHA4GE field "r2 fastq filename". This field will only be shown for certain file types (i.e. paired FASTQ)genome_r2.fastq (*must be exact)12Filename3-8list other fastq file names (e.g. for NextSeq data)13(First/Second) MD5 ChecksumMD5 checksum of the file being submitted07182d8b0....
?. [ENA virus pathogen reporting]
Guidlines to populate the sample metadata sheetThese fields are required for all ENA submission. They do not appear as part of the checklist. The description and guidance is tabulated below. Description of required fields  AB1ENA Required FieldsDefinition2sample_nameThe user-provided name of the sample.3tax_idThe NCBITaxon identifier for the organism being sequenced.4scientific_nameThe taxonomic name of the organism.5common_nameThe common name of the organism.6sample_descriptionFree text description of the sample.7instrument_model Name of the sequencing instrument.8library_source Molecule type used to make the library.9library_selection Library capture method.10library_strategy Overall sequencing strategy or approach.11library_layout Single or paired.12file_name Include ALL of the files resulting from this library. **Add additional fields if there are more than two files (e.g. Filename3) Guidance of required fields  ABC1ENA Required FieldsPHA4GE FieldPHA4GE Guidance2sample_namespecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID".3tax_idN/AUse "2697049" as the tad_id for SARS-CoV-2.4scientific_nameorganismThis field can be populated by the PHA4GE field "organism". Provide the full name "Severe acute respiratory syndrome coronavirus 2".5common_nameN/AThis field can be populated by the PHA4GE field "host (common name)". Provide "Sars-CoV-2".6sample_descriptionN/A7instrument_model N/ASee ENA SRA pick list. (e.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II)8library_source N/ASee ENA SRA pick list. (e.g. viral RNA, metagenomic)9library_selection N/ASee ENA SRA pick list. (e.g. random, PCR)10library_strategy N/ASee ENA SRA pick list. (e.g. WGS, RNA-Seq, Amplicon)11library_layout N/ASee ENA SRA pick list. (single, paired)12file_name r1 fastq filenameThis field can be populated by the PHA4GE field "r1 fastq filename".For SARSCov2 submission, ENA ask that the metadata comply with Checklist ERC000033: https://www.ebi.ac.uk/ena/browser/view/ERC000033. These fields below are drawn from the ENA Checklist, with description and mapping  to the respective PHA4GE field should help you transfer your metadata from the PHA4GE table to the something acceptable for ENA submission.  ABC1ENA Virus Checklist FieldENA DefinitionENA Requirement Status2subject exposure  Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild birdoptional3subject exposure durationDuration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 daysoptional4type exposureSetting within which the subject is exposed to animals, such as farm, slaughterhouse, food preparation. If multiple exposures are applicable, please state their type in the same order in which you reported the exposure in the field 'subject exposure'. Example: backyard flock; confined animal feeding operationoptional5personal protective equipmentUse of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: maskoptional6hospitalisationWas the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?optional7illness durationThe number of days the illness lasted. Example: 4optional8illness symptomsThe symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. If multiple exposures are applicabloptional 9collection dateThe date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.recommended10geographic location (country and/or sea)The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).mandatory11geographic location (latitude)The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 systemrecommended12geographic location (longitude)The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 systemrecommended13geographic location (region and locality)The geographical origin of the sample as defined by the specific region name followed by the locality name.recommended14sample capture statusReason for the sample collection.recommended15host disease outcomeDisease outcome in the host.recommended16host common namecommon name of the host, e.g. humanmandatory17host subject ida unique identifier by which each subject can be referred to, de-identified, e.g. #131mandatory18host ageage of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for treesrecommended19host health stateHealth status of the host at the time of sample collection.mandatory20host sexGender or sex of the host.mandatory21host scientific nameScientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.mandatory22virus identifierUnique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric charactersrecommended23collector nameName of the person who collected the specimen. Example: John Smithmandatory24collecting institutionName of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Addressmandatory25receipt dateDate on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.recommended26sample storage conditionsConditions at which sample was stored, usually storage temperature, duration and locationoptional27definition for seropositive sampleThe cut off value used by an investigatior in determining that a sample was seropositive.recommended28serotype (required for a seropositive sample)Serological variety of a species characterised by its antigenic properties. For Influenza, HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified and the NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format H5Nx or HxN1. Example: H1N1recommended29isolateindividual isolate from which the sample was obtainedmandatory30strainName of the strain from which the sample was obtained.optional31host habitatNatural habitat of the avian or mammalian host.recommended32isolation source host-associatedName of host tissue or organ sampled for analysis. Example: tracheal tissuerecommended33host descriptionOther descriptive information relating to the host.optional34gravidityWhether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.optional35host behaviourNatural behaviour of the host.recommended36isolation source non-host-associatedDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soilrecommended  ABC1ENA Virus Checklist FieldPHA4GE FieldPHA4GE Guidance2subject exposure  exposure eventThis field can be populated by the PHA4GE field "exposure event". Caution: this may be sensistive information. Consult the data steward before sharing. If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value.3subject exposure durationN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.4type exposureexposure eventThe PHA4GE field "exposure event" describes subject exposures and settings. Exposure information captured in the PHA4GE specification can be provided either in the ENA "subject exposure" or the "type exposure" field.5personal protective equipmentN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.6hospitalisationspecified as value under host health statusThis information can be found as values in the "host health status" field in the PHA4GE specification e.g. Hospitalized, Hospitalized (ICU), Hospitalized (Non-ICU). The ENA "hospitalisation" field requires yes/no values. Provide yes/no values for this field if submitting to ENA. If the information is unknown, or can not be shared, leave blank or provide a null value.   7illness durationN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.8illness symptomssigns and symptomsThis field can be populated by the PHA4GE field "signs and symptoms". If the information is unknown, not applicable, or not available, leave blank or provide a null value.9collection datesample collection dateThis field can be populated by the PHA4GE field "sample collection date". Caution: the sample collection date may be considered public health identifiable information. Consult the data steward before sharing. Acceptable formats are YYYY-MM-DD, YYYY-MM, or YYYY.10geographic location (country and/or sea)geo_loc (country)This field can be populated by the PHA4GE field "geo_loc name (country)". The values in the PHA4GE pick list are derived from the INSDC country list.11geographic location (latitude)geo_loc latitudeThis field can be populated by the PHA4GE field "geo_loc latitude". Caution: this is likely sensitive information. Consult the data steward before sharing. Do not provide latitude of the institution, nor the centre of the city/region where the sample was collected as this falsely implicates an existing location. If the information is unknown or can not be shared, leave blank or provide a null value. 12geographic location (longitude)geo_loc longitudeThis field can be populated by the PHA4GE field "geo_loc longitude". Caution: this is likely sensitive information. Consult the data steward before sharing. Do not provide longitude of the institution, nor the centre of the city/region where the sample was collected as this falsely implicates an existing location. If the information is unknown or can not be shared, leave blank or provide a null value.13geographic location (region and locality)geo_loc (state/province/region)This field can be populated by the PHA4GE field "geo_loc (state/province/region". Caution: this maye be sensitive information depending on the number of cases in this geographic area. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or provide a null value.14sample capture statuspurpose of samplingWhile the meanings of ENA's "sample capture status" and PHA4GE's "purpose of sampling" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. If the information is unknown or can not be shared, leave blank or provide a null value.15host disease outcomehost disease outcomeWhile the meanings of ENA's "host disease outcome" and PHA4GE's "host disease outcome" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. If the information is unknown or can not be shared, leave blank or provide a null value.16host common namehost (common name)This field can be populated by the PHA4GE field "host (common name)".17host subject idhost subject IDThis field can be populated by the PHA4GE field "host subject ID". Caution: the host subject ID may be considered public health identifiable information. Consult the data steward before sharing. If unknown or considered identifiable, provide an alternative ID or a null value.18host agehost ageThis field can be populated by the PHA4GE field "host age". Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or provide a null value.19host health statehost health stateWhile the meanings of the ENA and PHA4GE "host health state" fields overlap, ENA requires certain values in this field. If known, provide "diseased" or "healthy". If the information is unknown or can not be shared, provide a null value.20host sexhost genderWhile the meanings of ENA's "host sex" and PHA4GE's "host gender" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. Caution: the host gender may be considered public health identifiable information. Consult your data steward before sharing. If the information is unknown or can not be shared, provide a null value.21host scientific namehost (scientific name)This field can be populated by the PHA4GE field "host (scientific name)".22virus identifierspecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID". Caution: the sample ID may be considered sensitive information. Consult the data steward. You may need to provide an alternative ID.23collector nameN/AProvide the name of the person who collected the sample. If the information is unknown or can not be shared, provide a null value.24collecting institutionsample collected byThis field can be populated by the PHA4GE field "sample collected by". Caution: if the name of the lab reveals geographic information, this may be considered public health identifiable information. Consult the data steward before sharing. If information ca not be shared, provide a null value.25receipt datereceived dateThis field can be populated by the PHA4GE field "received date". If the information is unknown or can not be shared, leave blank or provide a null value.26sample storage conditionsN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.27definition for seropositive sampleN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.28serotype (required for a seropositive sample)N/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.29isolateisolateThis field can be populated by the PHA4GE field "isolate".  30strainN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.31host habitatN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.32isolation source host-associatedanatomical material; anatomical part; body productThis field can be populated by the PHA4GE fields "anatomical material", "anatomical part" and "body product". If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value.33host descriptionN/ACan be left blank.34gravidityN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.35host behaviourN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.36isolation source non-host-associatedenvironmental site; environmental materialThis field can be populated by the PHA4GE fields "environmental site" and "environmental material". If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value. There is extended guideance available at the PHA4GE SARS-CoV-2 metadata specification: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification
AB1ENA Required FieldsDefinition2sample_nameThe user-provided name of the sample.3tax_idThe NCBITaxon identifier for the organism being sequenced.4scientific_nameThe taxonomic name of the organism.5common_nameThe common name of the organism.6sample_descriptionFree text description of the sample.7instrument_model Name of the sequencing instrument.8library_source Molecule type used to make the library.9library_selection Library capture method.10library_strategy Overall sequencing strategy or approach.11library_layout Single or paired.12file_name Include ALL of the files resulting from this library. **Add additional fields if there are more than two files (e.g. Filename3)
ABC1ENA Required FieldsPHA4GE FieldPHA4GE Guidance2sample_namespecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID".3tax_idN/AUse "2697049" as the tad_id for SARS-CoV-2.4scientific_nameorganismThis field can be populated by the PHA4GE field "organism". Provide the full name "Severe acute respiratory syndrome coronavirus 2".5common_nameN/AThis field can be populated by the PHA4GE field "host (common name)". Provide "Sars-CoV-2".6sample_descriptionN/A7instrument_model N/ASee ENA SRA pick list. (e.g. Illumina MiSeq, iSeq 100, GridION, MinION, PacBio Sequel II)8library_source N/ASee ENA SRA pick list. (e.g. viral RNA, metagenomic)9library_selection N/ASee ENA SRA pick list. (e.g. random, PCR)10library_strategy N/ASee ENA SRA pick list. (e.g. WGS, RNA-Seq, Amplicon)11library_layout N/ASee ENA SRA pick list. (single, paired)12file_name r1 fastq filenameThis field can be populated by the PHA4GE field "r1 fastq filename".
ABC1ENA Virus Checklist FieldENA DefinitionENA Requirement Status2subject exposure  Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild birdoptional3subject exposure durationDuration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 daysoptional4type exposureSetting within which the subject is exposed to animals, such as farm, slaughterhouse, food preparation. If multiple exposures are applicable, please state their type in the same order in which you reported the exposure in the field 'subject exposure'. Example: backyard flock; confined animal feeding operationoptional5personal protective equipmentUse of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: maskoptional6hospitalisationWas the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?optional7illness durationThe number of days the illness lasted. Example: 4optional8illness symptomsThe symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. If multiple exposures are applicabloptional 9collection dateThe date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.recommended10geographic location (country and/or sea)The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).mandatory11geographic location (latitude)The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 systemrecommended12geographic location (longitude)The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 systemrecommended13geographic location (region and locality)The geographical origin of the sample as defined by the specific region name followed by the locality name.recommended14sample capture statusReason for the sample collection.recommended15host disease outcomeDisease outcome in the host.recommended16host common namecommon name of the host, e.g. humanmandatory17host subject ida unique identifier by which each subject can be referred to, de-identified, e.g. #131mandatory18host ageage of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for treesrecommended19host health stateHealth status of the host at the time of sample collection.mandatory20host sexGender or sex of the host.mandatory21host scientific nameScientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.mandatory22virus identifierUnique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric charactersrecommended23collector nameName of the person who collected the specimen. Example: John Smithmandatory24collecting institutionName of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Addressmandatory25receipt dateDate on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.recommended26sample storage conditionsConditions at which sample was stored, usually storage temperature, duration and locationoptional27definition for seropositive sampleThe cut off value used by an investigatior in determining that a sample was seropositive.recommended28serotype (required for a seropositive sample)Serological variety of a species characterised by its antigenic properties. For Influenza, HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified and the NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format H5Nx or HxN1. Example: H1N1recommended29isolateindividual isolate from which the sample was obtainedmandatory30strainName of the strain from which the sample was obtained.optional31host habitatNatural habitat of the avian or mammalian host.recommended32isolation source host-associatedName of host tissue or organ sampled for analysis. Example: tracheal tissuerecommended33host descriptionOther descriptive information relating to the host.optional34gravidityWhether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.optional35host behaviourNatural behaviour of the host.recommended36isolation source non-host-associatedDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soilrecommended
ABC1ENA Virus Checklist FieldPHA4GE FieldPHA4GE Guidance2subject exposure  exposure eventThis field can be populated by the PHA4GE field "exposure event". Caution: this may be sensistive information. Consult the data steward before sharing. If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value.3subject exposure durationN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.4type exposureexposure eventThe PHA4GE field "exposure event" describes subject exposures and settings. Exposure information captured in the PHA4GE specification can be provided either in the ENA "subject exposure" or the "type exposure" field.5personal protective equipmentN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.6hospitalisationspecified as value under host health statusThis information can be found as values in the "host health status" field in the PHA4GE specification e.g. Hospitalized, Hospitalized (ICU), Hospitalized (Non-ICU). The ENA "hospitalisation" field requires yes/no values. Provide yes/no values for this field if submitting to ENA. If the information is unknown, or can not be shared, leave blank or provide a null value.   7illness durationN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.8illness symptomssigns and symptomsThis field can be populated by the PHA4GE field "signs and symptoms". If the information is unknown, not applicable, or not available, leave blank or provide a null value.9collection datesample collection dateThis field can be populated by the PHA4GE field "sample collection date". Caution: the sample collection date may be considered public health identifiable information. Consult the data steward before sharing. Acceptable formats are YYYY-MM-DD, YYYY-MM, or YYYY.10geographic location (country and/or sea)geo_loc (country)This field can be populated by the PHA4GE field "geo_loc name (country)". The values in the PHA4GE pick list are derived from the INSDC country list.11geographic location (latitude)geo_loc latitudeThis field can be populated by the PHA4GE field "geo_loc latitude". Caution: this is likely sensitive information. Consult the data steward before sharing. Do not provide latitude of the institution, nor the centre of the city/region where the sample was collected as this falsely implicates an existing location. If the information is unknown or can not be shared, leave blank or provide a null value. 12geographic location (longitude)geo_loc longitudeThis field can be populated by the PHA4GE field "geo_loc longitude". Caution: this is likely sensitive information. Consult the data steward before sharing. Do not provide longitude of the institution, nor the centre of the city/region where the sample was collected as this falsely implicates an existing location. If the information is unknown or can not be shared, leave blank or provide a null value.13geographic location (region and locality)geo_loc (state/province/region)This field can be populated by the PHA4GE field "geo_loc (state/province/region". Caution: this maye be sensitive information depending on the number of cases in this geographic area. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or provide a null value.14sample capture statuspurpose of samplingWhile the meanings of ENA's "sample capture status" and PHA4GE's "purpose of sampling" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. If the information is unknown or can not be shared, leave blank or provide a null value.15host disease outcomehost disease outcomeWhile the meanings of ENA's "host disease outcome" and PHA4GE's "host disease outcome" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. If the information is unknown or can not be shared, leave blank or provide a null value.16host common namehost (common name)This field can be populated by the PHA4GE field "host (common name)".17host subject idhost subject IDThis field can be populated by the PHA4GE field "host subject ID". Caution: the host subject ID may be considered public health identifiable information. Consult the data steward before sharing. If unknown or considered identifiable, provide an alternative ID or a null value.18host agehost ageThis field can be populated by the PHA4GE field "host age". Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or provide a null value.19host health statehost health stateWhile the meanings of the ENA and PHA4GE "host health state" fields overlap, ENA requires certain values in this field. If known, provide "diseased" or "healthy". If the information is unknown or can not be shared, provide a null value.20host sexhost genderWhile the meanings of ENA's "host sex" and PHA4GE's "host gender" fields overlap in meaning, ENA provides a specific pick list of terms for populating the field. Use the ENA pick list if submitting to ENA. Caution: the host gender may be considered public health identifiable information. Consult your data steward before sharing. If the information is unknown or can not be shared, provide a null value.21host scientific namehost (scientific name)This field can be populated by the PHA4GE field "host (scientific name)".22virus identifierspecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID". Caution: the sample ID may be considered sensitive information. Consult the data steward. You may need to provide an alternative ID.23collector nameN/AProvide the name of the person who collected the sample. If the information is unknown or can not be shared, provide a null value.24collecting institutionsample collected byThis field can be populated by the PHA4GE field "sample collected by". Caution: if the name of the lab reveals geographic information, this may be considered public health identifiable information. Consult the data steward before sharing. If information ca not be shared, provide a null value.25receipt datereceived dateThis field can be populated by the PHA4GE field "received date". If the information is unknown or can not be shared, leave blank or provide a null value.26sample storage conditionsN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.27definition for seropositive sampleN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.28serotype (required for a seropositive sample)N/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.29isolateisolateThis field can be populated by the PHA4GE field "isolate".  30strainN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.31host habitatN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.32isolation source host-associatedanatomical material; anatomical part; body productThis field can be populated by the PHA4GE fields "anatomical material", "anatomical part" and "body product". If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value.33host descriptionN/ACan be left blank.34gravidityN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.35host behaviourN/AIf the information is unknown, not applicable, or not available, leave blank or provide a null value.36isolation source non-host-associatedenvironmental site; environmental materialThis field can be populated by the PHA4GE fields "environmental site" and "environmental material". If the information is unknown, not applicable, or can not be shared, leave blank or provide a null value.