ERC000033 ENA virus pathogen reporting standard checklist Minimum information about a virus pathogen. A checklist for reporting metadata of virus pathogen samples associated with genomic data. This minimum metadata standard was developed by the COMPARE platform for submission of virus surveillance and outbreak data (such as Ebola) as well as virus isolate information. ENA sample collection: methods, storage and transport sample_storage_conditions Conditions at which sample was stored, usually storage temperature, duration and location. In soil context: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). optional single Human surveillance data subject_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 bird optional single type_exposure Setting 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 operation optional single personal_protective_equipment Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask optional single hospitalisation Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection? no yes optional single illness_duration The number of days the illness lasted. Example: 4 optional single illness_symptoms The 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 applicable, please state them separated by semicolon. optional single Collection event information collection_date The date the sample was collected with the intention of sequencing, 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. (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) mandatory single geographic_location_latitude The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) DD recommended single geographic_location_longitude The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) DD recommended single geographic_location_region_and_locality The geographical origin of the sample as defined by the specific region name followed by the locality name. recommended single internal environment subject_exposure_duration Duration 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 days week month year day optional single sample collection sample_capture_status Reason for the sample collection. active surveillance in response to outbreak active surveillance not initiated by an outbreak farm sample market sample other pet sample zoo sample recommended single Organism characteristics geographic_location_country_andor_sea The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html). Afghanistan Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia Aruba Ashmore and Cartier Islands Atlantic Ocean Australia Austria Azerbaijan Bahamas Bahrain Baker Island Baltic Sea Bangladesh Barbados Bassas da India Belarus Belgium Belize Benin Bermuda Bhutan Bolivia Borneo Bosnia and Herzegovina Botswana Bouvet Island Brazil British Virgin Islands Brunei Bulgaria Burkina Faso Burundi Cambodia Cameroon Canada Cape Verde Cayman Islands Central African Republic Chad Chile China Christmas Island Clipperton Island Cocos Islands Colombia Comoros Cook Islands Coral Sea Islands Costa Rica Cote d'Ivoire Croatia Cuba Curacao Cyprus Czechia Czech Republic Democratic Republic of the Congo Denmark Djibouti Dominica Dominican Republic Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Eswatini Ethiopia Europa Island Falkland Islands (Islas Malvinas) Faroe Islands Fiji Finland France French Guiana French Polynesia French Southern and Antarctic Lands Gabon Gambia Gaza Strip Georgia Germany Ghana Gibraltar Glorioso Islands Greece Greenland Grenada Guadeloupe Guam Guatemala Guernsey Guinea Guinea-Bissau Guyana Haiti Heard Island and McDonald Islands Honduras Hong Kong Howland Island Hungary Iceland India Indian Ocean Indonesia Iran Iraq Ireland Isle of Man Israel Italy Jamaica Jan Mayen Japan Jarvis Island Jersey Johnston Atoll Jordan Juan de Nova Island Kazakhstan Kenya Kerguelen Archipelago Kingman Reef Kiribati Kosovo Kuwait Kyrgyzstan Laos Latvia Lebanon Lesotho Liberia Libya Liechtenstein Line Islands Lithuania Luxembourg Macau Madagascar Malawi Malaysia Maldives Mali Malta Marshall Islands Martinique Mauritania Mauritius Mayotte Mediterranean Sea Mexico Micronesia, Federated States of Midway Islands Moldova Monaco Mongolia Montenegro Montserrat Morocco Mozambique Myanmar Namibia Nauru Navassa Island Nepal Netherlands New Caledonia New Zealand Nicaragua Niger Nigeria Niue Norfolk Island North Korea North Macedonia North Sea Northern Mariana Islands Norway Oman Pacific Ocean Pakistan Palau Palmyra Atoll Panama Papua New Guinea Paracel Islands Paraguay Peru Philippines Pitcairn Islands Poland Portugal Puerto Rico Qatar Republic of the Congo Reunion Romania Ross Sea Russia Rwanda Saint Barthelemy Saint Helena Saint Kitts and Nevis Saint Lucia Saint Pierre and Miquelon Saint Vincent and the Grenadines Samoa San Marino Saint Martin Sao Tome and Principe Saudi Arabia Senegal Serbia Seychelles Sierra Leone Singapore Sint Maarten Slovakia Slovenia Solomon Islands Somalia South Africa South Georgia and the South Sandwich Islands South Korea South Sudan Southern Ocean Spain Spratly Islands Sri Lanka State of Palestine Sudan Suriname Svalbard Sweden Switzerland Syria Taiwan Tajikistan Tanzania Tasman Sea Thailand Timor-Leste Togo Tokelau Tonga Trinidad and Tobago Tromelin Island Tunisia Turkey Turkmenistan Turks and Caicos Islands Tuvalu USA Uganda Ukraine United Arab Emirates United Kingdom Uruguay Uzbekistan Vanuatu Venezuela Viet Nam Wake Island Virgin Islands Wallis and Futuna West Bank Western Sahara Yemen Zambia Zimbabwe missing missing: control sample missing: data agreement established pre-2023 missing: endangered species missing: human-identifiable missing: lab stock missing: sample group missing: synthetic construct missing: third party data not applicable not collected not provided restricted access mandatory single host disorder host_disease_outcome Disease outcome in the host. dead recovered recovered with sequelae recommended single host description host_common_name common name of the host, e.g. human mandatory single host_subject_id a unique identifier by which each subject can be referred to, de-identified, e.g. #131 mandatory single host_age age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? centuries hours seconds months weeks minutes days decades years recommended single host_health_state Health status of the host at the time of sample collection. diseased healthy missing: control sample missing: data agreement established pre-2023 missing: endangered species missing: human-identifiable missing: lab stock missing: sample group missing: synthetic construct missing: third party data not applicable not collected not provided restricted access mandatory single host_sex Gender or sex of the host. female hermaphrodite male missing: control sample missing: data agreement established pre-2023 missing: endangered species missing: human-identifiable missing: lab stock missing: sample group missing: synthetic construct missing: third party data neuter not applicable not collected not provided other restricted access mandatory single lab_host scientific name of the laboratory host used to propagate the source organism from which the sample was obtained optional single host_scientific_name Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained. mandatory single Virus isolate information virus_identifier Unique 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 characters recommended single General collection event information collector_name Name of the person who collected the specimen. Example: John Smith mandatory single collecting_institution Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address mandatory single receipt_date Date 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. ^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$ recommended single Serology detection definition_for_seropositive_sample The cut off value used by an investigatior in determining that a sample was seropositive. recommended single serotype_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: H1N1 recommended single Infraspecies information isolate individual isolate from which the sample was obtained mandatory single strain Name of the strain from which the sample was obtained. optional single Associated host information host_habitat Natural habitat of the avian or mammalian host. domestic:free-range farm domestic:indoor farm domestic:live market domestic:semi-enclosed housing other wild:migratory wild:resident recommended single isolation_source_hostassociated Name of host tissue or organ sampled for analysis. Example: tracheal tissue recommended single host_description Other descriptive information relating to the host. optional single host details gravidity Whether 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. optional single host_behaviour Natural behaviour of the host. captive-wild (e.g. at zoo) domestic other wild recommended single Environmental information isolation_source_nonhostassociated Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soil recommended single