TITLE: SARS-CoV2 GISAID submission protocol
AUTHORS: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides the steps needed to establish a new GISAID submission environment for your laboratory. Once established,  this protocol covers genome submission sample meta to GISAID.</div></div>

[STEPS]
?. [GISAID Submissions]
GISAID submissions require contextual information (metadata) and the COVID-19 consensus sequence or genome sequence. It is much simpler than other databases, as it has no hierachical structure. In GISAID, one set of contextual information links to one genome assembly.We advise that contextual inbformation should be in line with the PHA4GE metadata specification: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-SpecificationGISAID has its own extensive documentation, which is available once you have registered. You are encouraged to write to the GISAID curators if there are any issues.  This protocol, therefore, is a brief overview to help you get started.
?. [GISAID Submissions]
You can register on GISAID here: https://www.gisaid.org/registration/register/There are strict terms on your rights to your data, and how you can use other submitted data. Please read these terms carefully.  There will be a registration form to fill Once submitted, your registration will be moderated and you should recieve an email notification. Your registration request is manually inspected, so this may take some time.
?. [GISAID Submissions]
GISAID Submission methodsThere are two submission methods; Uploading single samples.Batch upload of multiple samples. In both cases, we advise that contextual infromation should be in line with the PHA4GE metadata specification. A brief overview of the fields and guidance are tabulated below. Extended description of the specification is available here: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-SpecificationThese fields below are drawn from the GISAID submission form, with description and mapping  to the respective PHA4GE field should help you transfer your metadata from the PHA4GE table to the something acceptable for GISAID submission.Description of GISAID fields   ABC1GISAID Batch Submission Headers (as of 2021-04-29)GISAID DefinitionGISAID Requirement Status2Submitterenter your GISAID-Usernamemandatory3FASTA filenamethe filename that contains the sequence without path (e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta)mandatory4Virus namee.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)mandatory5Typedefault must remain "betacoronavirus"mandatory6Passage details/historye.g. Original, Veromandatory7Collection dateDate in the format YYYY or YYYY-MM or YYYY-MM-DDmandatory8Locatione.g. Europe / Germany / Bavaria / Munichmandatory9Additional location informatione.g. Cruise Ship, Convention, Live animal market10Hoste.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etcmandatory11Additional host informatione.g. Patient infected while traveling in ….12Sampling strategye.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout
13GenderMale, Female, or unknownmandatory14Patient agee.g.  65 or 7 months, or unknownmandatory15Patient statuse.g.  Hospitalized, Released, Live, Deceased, or unknownmandatory16Specimen sourcee.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other17OutbreakDate, Location e.g. type of gathering, Family cluster, etc.18Last vaccinatedprovide details if applicable19TreatmentInclude drug name, dosage20Sequencing technologye.g.  Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc.mandatory21Assembly methode.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc.22Coveragee.g. 70x, 1,000x, 10,000x (average)23Originating labWhere the clinical specimen or virus isolate was first obtainedmandatory24Addressmandatory25Sample ID given by the sample provider26Submitting labWhere sequence data have been generated and submitted to GISAIDmandatory27Addressmandatory28Sample ID given by the submitting laboratory29Authorsa comma separated list of Authors with complete First followed by Last Name PHA4GE guidance on GISAID submission fields.  ABC1GISAID Batch Submission Headers (as of 2021-04-29)PHA4GE FieldPHA4GE Guidance2Submitter*user inputsThe submitter must acquire an account and provide their username in this field.3FASTA filenamefasta filenameThis field can be populated by the PHA4GE field "fasta filename".4Virus nameisolateWhile the meanings and structures of the GISAID field "Virus name" and the PHA4GE field "isolate" overlap, GISAID requires a slightly different structure for Virus name. e.g. PHA4GE structure: SARS-CoV-2/country/sapleID/2020, GISAID structure: hCov-19/country/sampleID/2020. Change "SARS-CoV-2" to "hCov-19" in the isolate name.5Type*should always be betacoronavirusProvide "betacoronavirus".6Passage details/historyspecimen processing; lab host; passage number; passage methodThis field can be populated by the PHA4GE fields "specimen processing", "lab host", "passage number" and "passage method". If the information is unknown or can not be shared, put "unknown".7Collection datesample collection dateThis field can be populated by the PHA4GE field "sample collection date". Caution: collection date may be considered public health identifiable information. If this date is considered identifiable, it is acceptable to add "jitter" to the collection date by adding or subtracting a calendar day (acceptable by GISAID). Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format "YYYY-MM-DD".8Locationgeo_loc_name (country)This field can be populated by the PHA4GE field "geo_loc name (country)". 9Additional location informationexposure eventThis field can be populated by the PHA4GE field "exposure event". Caution: this may be sensitive information. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or put "unknown".10Hosthost (scientific name)This field can be populated by the PHA4GE field "host (scientific name)". 11Sampling strategypurpose of samplingThis field can be populated by the PHA4GE field "purpose of sampling". 12Additional host informationN/AIf the information is unknown or can not be shared, leave blank.13Genderhost genderThis field can be populated by the PHA4GE field "host gender". Caution: the host gender may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put "unknown".14Patient agehost ageThis field can be populated by the PHA4GE field "host age". Provide age in years. Age-binning is not accepted. 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, put "unknown".  15Patient statushost health stateThis field can be populated by PHA4GE field "host health state". If the information is unknown, or can not be shared, put "unknown".16Specimen sourceanatomical material; anatomical part; body product; environmental material; environmental site; collection device; collection methodThis field can be populated by the PHA4GE fields "anatomical material", "anatomical part", "body product", "environmental material", "environmental site", "collection device" and "collection method". Separate the values using semi-colons. If the information is unknown or can not be shared, leave blank or put "unknown".17OutbreakN/AIf the information is unknown or can not be shared, leave blank.18Last vaccinatedN/AIf the information is unknown or can not be shared, leave blank.19TreatmentN/AIf the information is unknown or can not be shared, leave blank.20Sequencing technologysequencing instrumentThis field can be populated by the PHA4GE field "sequencing instrument". If the information is unknown or can not be shared, put "unknown".21Assembly methodconsensus sequence methodThis field can be populated by the PHA4GE field "consensus sequence method". If the information is unknown or can not be shared, leave blank or put "unknown".22Coverageassembly coverage depthThis field can be populated by the PHA4GE field "assembly coverage depth". If the information is unknown or can not be shared, leave blank or put "unknown".23Originating labsample 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 the information is unknown or can not be shared, leave blank or put "unknown".24Addresssample collector contact addressThis field can be populated by the PHA4GE field "sample collector contact address".25Sample ID given by the sample providerspecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID". Caution: the sample ID may be considered public health identifiable information. Consult your data steward before sharing. You may need to provide an alternative ID. 26Submitting labsequence submitted byThis field can be populated by the PHA4GE field "sequence submitted by". If information is unknown or can not be shared, leave blank or put "unknown".27Addresssequence submitter contact addressThis field can be populated by the PHA4GE field "sequence submitter contact address". If information is unknown or can not be shared, leave blank or put "unknown".28Sample ID given by the submitting laboratoryconsensus sequence IDThis field can be populated by the PHA4GE field "consensus sequence ID". If information is unknown or can not be shared, leave blank or put "unknown".29AuthorsauthorsThis field can be populated by the PHA4GE required field "authors". If information is unknown or can not be shared, leave blank or put "unknown".
ABC1GISAID Batch Submission Headers (as of 2021-04-29)GISAID DefinitionGISAID Requirement Status2Submitterenter your GISAID-Usernamemandatory3FASTA filenamethe filename that contains the sequence without path (e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta)mandatory4Virus namee.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)mandatory5Typedefault must remain "betacoronavirus"mandatory6Passage details/historye.g. Original, Veromandatory7Collection dateDate in the format YYYY or YYYY-MM or YYYY-MM-DDmandatory8Locatione.g. Europe / Germany / Bavaria / Munichmandatory9Additional location informatione.g. Cruise Ship, Convention, Live animal market10Hoste.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etcmandatory11Additional host informatione.g. Patient infected while traveling in ….12Sampling strategye.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout
13GenderMale, Female, or unknownmandatory14Patient agee.g.  65 or 7 months, or unknownmandatory15Patient statuse.g.  Hospitalized, Released, Live, Deceased, or unknownmandatory16Specimen sourcee.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other17OutbreakDate, Location e.g. type of gathering, Family cluster, etc.18Last vaccinatedprovide details if applicable19TreatmentInclude drug name, dosage20Sequencing technologye.g.  Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc.mandatory21Assembly methode.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc.22Coveragee.g. 70x, 1,000x, 10,000x (average)23Originating labWhere the clinical specimen or virus isolate was first obtainedmandatory24Addressmandatory25Sample ID given by the sample provider26Submitting labWhere sequence data have been generated and submitted to GISAIDmandatory27Addressmandatory28Sample ID given by the submitting laboratory29Authorsa comma separated list of Authors with complete First followed by Last Name
ABC1GISAID Batch Submission Headers (as of 2021-04-29)PHA4GE FieldPHA4GE Guidance2Submitter*user inputsThe submitter must acquire an account and provide their username in this field.3FASTA filenamefasta filenameThis field can be populated by the PHA4GE field "fasta filename".4Virus nameisolateWhile the meanings and structures of the GISAID field "Virus name" and the PHA4GE field "isolate" overlap, GISAID requires a slightly different structure for Virus name. e.g. PHA4GE structure: SARS-CoV-2/country/sapleID/2020, GISAID structure: hCov-19/country/sampleID/2020. Change "SARS-CoV-2" to "hCov-19" in the isolate name.5Type*should always be betacoronavirusProvide "betacoronavirus".6Passage details/historyspecimen processing; lab host; passage number; passage methodThis field can be populated by the PHA4GE fields "specimen processing", "lab host", "passage number" and "passage method". If the information is unknown or can not be shared, put "unknown".7Collection datesample collection dateThis field can be populated by the PHA4GE field "sample collection date". Caution: collection date may be considered public health identifiable information. If this date is considered identifiable, it is acceptable to add "jitter" to the collection date by adding or subtracting a calendar day (acceptable by GISAID). Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format "YYYY-MM-DD".8Locationgeo_loc_name (country)This field can be populated by the PHA4GE field "geo_loc name (country)". 9Additional location informationexposure eventThis field can be populated by the PHA4GE field "exposure event". Caution: this may be sensitive information. Consult the data steward before sharing. If the information is unknown or can not be shared, leave blank or put "unknown".10Hosthost (scientific name)This field can be populated by the PHA4GE field "host (scientific name)". 11Sampling strategypurpose of samplingThis field can be populated by the PHA4GE field "purpose of sampling". 12Additional host informationN/AIf the information is unknown or can not be shared, leave blank.13Genderhost genderThis field can be populated by the PHA4GE field "host gender". Caution: the host gender may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put "unknown".14Patient agehost ageThis field can be populated by the PHA4GE field "host age". Provide age in years. Age-binning is not accepted. 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, put "unknown".  15Patient statushost health stateThis field can be populated by PHA4GE field "host health state". If the information is unknown, or can not be shared, put "unknown".16Specimen sourceanatomical material; anatomical part; body product; environmental material; environmental site; collection device; collection methodThis field can be populated by the PHA4GE fields "anatomical material", "anatomical part", "body product", "environmental material", "environmental site", "collection device" and "collection method". Separate the values using semi-colons. If the information is unknown or can not be shared, leave blank or put "unknown".17OutbreakN/AIf the information is unknown or can not be shared, leave blank.18Last vaccinatedN/AIf the information is unknown or can not be shared, leave blank.19TreatmentN/AIf the information is unknown or can not be shared, leave blank.20Sequencing technologysequencing instrumentThis field can be populated by the PHA4GE field "sequencing instrument". If the information is unknown or can not be shared, put "unknown".21Assembly methodconsensus sequence methodThis field can be populated by the PHA4GE field "consensus sequence method". If the information is unknown or can not be shared, leave blank or put "unknown".22Coverageassembly coverage depthThis field can be populated by the PHA4GE field "assembly coverage depth". If the information is unknown or can not be shared, leave blank or put "unknown".23Originating labsample 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 the information is unknown or can not be shared, leave blank or put "unknown".24Addresssample collector contact addressThis field can be populated by the PHA4GE field "sample collector contact address".25Sample ID given by the sample providerspecimen collector sample IDThis field can be populated by the PHA4GE field "specimen collector sample ID". Caution: the sample ID may be considered public health identifiable information. Consult your data steward before sharing. You may need to provide an alternative ID. 26Submitting labsequence submitted byThis field can be populated by the PHA4GE field "sequence submitted by". If information is unknown or can not be shared, leave blank or put "unknown".27Addresssequence submitter contact addressThis field can be populated by the PHA4GE field "sequence submitter contact address". If information is unknown or can not be shared, leave blank or put "unknown".28Sample ID given by the submitting laboratoryconsensus sequence IDThis field can be populated by the PHA4GE field "consensus sequence ID". If information is unknown or can not be shared, leave blank or put "unknown".29AuthorsauthorsThis field can be populated by the PHA4GE required field "authors". If information is unknown or can not be shared, leave blank or put "unknown".
?. [GISAID Submissions]
Uploading single samplesYou can upload single sample through a web form shown below.
?. [GISAID Submissions]
Uploading multiple samples (Batch upload)You must first explictly request the batch upload feature from the curators. This will give you access to the batch upload page. Here you can upload mulitple samples (metadata and sequences). There is a link to detailed documentation and templates at the bottom left.