Kiri
| Dokumendiregister | Terviseamet |
| Viit | 8.1-2/24/5475-1 |
| Registreeritud | 27.05.2024 |
| Sünkroonitud | 28.05.2024 |
| Liik | Sissetulev dokument |
| Funktsioon | 8.1 Nakkushaiguste seire, ennetuse ja tõrje korraldamine |
| Sari | 8.1-2 Nakkushaiguste epidemioloogiaalane riigiväline kirjavahetus |
| Toimik | 8.1-2/2024 |
| Juurdepääsupiirang | Avalik |
| Juurdepääsupiirang | |
| Adressaat | ECDC respiratory viruses |
| Saabumis/saatmisviis | ECDC respiratory viruses |
| Vastutaja | Kärt Sõber (TA, Peadirektori asetäitja (1) vastutusvaldkond, Nakkushaiguste epidemioloogia osakond) |
| Originaal | Ava uues aknas |
Failid
|
Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu saatja korral palume linke ja faile mitte avada. |
To: Operational Contact Points for COVID-19 and Influenza
Cc: National Focal Points for Viral Respiratory Diseases, National Coordinators, Operational Contact Points for SARI
Dear colleagues,
Please find below the suggested updates to the metadata for the upcoming 2024/2025 season. Most of the proposed additions are minor updates. In addition, we are considering additional quantitative indicators for the metadata for 2024/2025. To finalize the proposal for the metadata, we would like to collect feedback from countries on the use of qualitative indicator, via an online survey : link by June 5. We kindly request that you coordinate with colleagues as required and make a single survey response for your country by June 5. The results will be presented and discussed at the network meeting EU/EEA Respiratory Virus Network meeting (12- 14 June) and will inform any subsequent proposals for metadata changes.
TESSY metadata updates
RESPISEVERE
- Add Influenza Type Subtype and RSV type variable to allow countries reporting aggregate data to include (sub)type information.
RESPISURV
- Align Respiratory support variable (RespiSupport) Coded values to align better with SARISURV. Adjust description to clarify the reporting of “OXYGEN”. Please see the attachment for further details.
INFLCLIN (Qualitative indicators)
- We are considering additional qualitative indicators for the metadata for 2024/2025 to allow qualitative assessment of all pathogens under surveillance. We suggest piloting any additional qualitative indicators during the next winter season. To finalize the proposal for the metadata, we would like to collect feedback from you, via an online survey: link by June 5.
- Further information on updates to Pandemic Influenza Severity Assessment (PISA) reporting will follow in the coming months and will be based on published guidance.
INFLZOO
- Two new codes have been added to the variable indicating species of animal exposure (AnimalExposure): R for 'cattle' and G for 'goat'. Please find an updated version of the reporting protocol for zoonotic influenza viruses attached.
Moving to new record types
All countries still reporting INFLVIRWAGGR, NCOVAGGR, NCOVTEST, INFLSARI need to switch to reporting the new record types by December 2024. The current reporting protocol provides a detailed list of the variables in each of the record types: Integrated respiratory reporting protocol (europa.eu). Please do not hesitate to contact us if you have any questions on reporting to the new record types. We can assist you by checking the data in the new format or working on a script to translate your data to the current submission format.
Do not hesitate to reach out to us in case you have any questions or concerns.
Kind regards,
The ECDC and WHO Europe respiratory virus surveillance teams
Confidentiality Notice
If you are not the intended recipient of this message, you are hereby kindly requested, to, consecutively, refrain from disclosing its content to any third party, delete it and inform its sender of the erroneous transmittal.
Minor changes to RESPISURV
Minor change in RespSupport in RESPISURV to align better with SARISURV
58
Respiratory support
Field: RespSupport
Coded value list: RespSupportSARI2
Coding:
Level of respiratory support given to patient. Please indicate the most invasive that applied.
[NEW for both RESPISURV & SARISURV]: If possible to distinguish between low-flow and high-flow oxygen support, please report low-flow oxygen into “O” and high-flow oxygen into “OXYGEN”.
If that is not possible, please report both low- and high-flow oxygen into “OXYGEN”.
Respiratory support
Field: RespSupport
Coded value list: RespSupportNCOV
Coding:
Level of respiratory support given to patient.
NONE = No respiratory support given
OXYGEN = High-flow oxygen therapy (non-invasive ventilation)
VENT = Invasive Ventilation
ECMO = Extra Corporeal Membrane Oxygenation
O = Other respiratory support
UNK = Respiratory support given unknown
Proposed, to match SARISURV: Current RESPISURV:
N = No
OXYGEN = Oxygen therapy
VENT = Ventilator including non-invasive positive pressure vent
ECMO = Extracorporeal membrane oxygenation
O = Other
UNK = Unknown
Zoonotic influenza virus reporting protocol May 2024
TESSy - The European Surveillance System
Zoonotic influenza virus Reporting Protocol
Version 2.2, May 2024
© ECDC May 2024 All rights reserved. Page 3 of 24
Contents How to use this document ..................................................................................................... 4
Finding further information .................................................................................................... 4
Copyright ............................................................................................................................. 4
Introduction ............................................................................................................... 5
Aim ...................................................................................................................................... 5
Objectives ............................................................................................................................ 5
Reporting to TESSy .................................................................................................... 6
When, what and how to report .............................................................................................. 6
Preparing data ...................................................................................................................... 6
Checking metadata ............................................................................................................... 6
Submitting your data ............................................................................................................ 7
Finalising your submission ..................................................................................................... 7
TESSy HelpDesk ................................................................................................................... 7
Annex – Zoonotic influenza virus metadata ................................................................... 8
Revisions of the zoonotic influenza virus metadata set ............................................................ 8
Metadata set ........................................................................................................................ 8
Current record type versions ............................................................................................. 8
INFLZOO metadata record type version 1 ............................................................................... 8
Common TESSy variables ...................................................................................................... 8
Epidemiological variables .................................................................................................. 9
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How to use this document This Reporting Protocol provides information for reporting countries’ data managers in three main sections:
• Reporting to TESSy – contains guidelines on how to prepare data for submission to TESSy, deadlines for data submission, subject-specific information (e.g. new changes to metadata), and links to further information.
• Annex – contains:
o The metadata sets for the subject(s) covered by this Reporting Protocol.
Finding further information Paragraphs denoted by the information icon tell where you can find further information.
Updated links to all the schedules, documentation and training materials mentioned in this Reporting Protocol are included in the TESSy Technical Guidelines & Tools (see the menu ‘Technical Guidelines and Tools’ when logged in TESSy), including:
• Metadata sets and history.
• Tutorials for data transformation using respectively Excel and Access.
• TESSy user documentation.
• CSV and XML transport protocols.
Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.
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Introduction An event of a human case infected with an influenza virus deriving from an animal source should be reported within 24 hours to EWRS which will cover the IHR notification for EU/EEA countries.
This reporting protocol describes the surveillance of the zoonotic influenza virus data in the EU/EEA and wider European Region. Aggregate data on zoonotic influenza (number of tested H5, number tested H7, number detected H5 and number detected H7) can be uploaded to INFLZOOAGGR . For the reporting of case-based data the record type INFLZOO should be used.
Aggregate data on number of tested and positive human cases enables the collection of denominator data as well as nominator data in case more human infections are occurring. For sporadic human infection a case-based reporting should be preferred to report information from people infected with a zoonotic influenza virus. The data aims to support situational risk assessment and trends over time. Case-based and aggregate data can be uploaded retrospectively when more information becomes available.
Aim To support the timely and complete reporting on number of samples tested, aggregate number of detected and of key information of zoonotic influenza cases in the EU/EEA and wider European Region.
Objectives • To collect denominator data on number of tested people. • To help assess the onset of the disease, confirmation of the subtype of infection and severity. • To provide information on exposure, treatment and outcome. • To provide additional contextual information to help understand the case identification. • To analyse trends over time.
Changes from last version Version 2.1: Inclusion of the aggregated record type INFLZOOAGGR and description of variables and coded value lists. Version 2.2: Inclusion of additional species under INFLZOO variable on exposure to animal species
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Reporting to TESSy
When, what and how to report Deadline for reporting: An event of a human infection with avian influenza virus should be reported within 24 hours to EWRS covering IHR for EU/EEA countries. If a suspected human case is under investigation, such information should be shared via EpiPulse with ECDC and other countries for awareness. Data for monitoring the event and assess trends should be reported to TESSy at least in the subsequent week following identification and confirmation.
Preparing data Data may be entered directly in TESSy for individual records (‘Manually create a record’). For any batch reporting by file upload (CSV or XML format) please note that once the data has been exported from your national database it needs to be in a format that TESSy can accept (see ‘checking metadata’).
Checking metadata The TESSy metadata define the fields and data formats that are valid as input to TESSy for a given subject. To ensure data can be saved correctly in TESSy, please check the data are correctly formatted according to the most recent metadata set.
It is especially important to focus on: • Field formats
Many fields require that data are formatted in a specific way. For example, dates must be in the YYYY-Www format (e.g 2021-W01); dates in any other format will be rejected.
• Coded values Some fields only permit the use of specific values (coded values). If any other value is used in the field, the upload will be rejected.
The metadata file contains all the definitions and rules you need to comply with to format your data correctly for every subject (usually a disease). The file can be downloaded as an Excel file from the TESSy documents website. By filtering the fields in the file by subject, you can see the fields required for your subject and the rules applying to these fields.
The Technical Annex provides an overview of how you work with the metadata file, and the TESSy user documentation provides in-depth details on metadata.
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Submitting your data Data are submitted through the TESSy web interface (go to Upload). Previously reported data can be found through the review tab (see below).
The Tessy User Guide provides an overview of how you submit files to TESSy, and the TESSy user documentation provides in-depth descriptions of all the upload methods.
Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. The result of your upload – i.e. rejected or validated – is displayed immediately after the conclusion of the check in the Validation details webpage. Please review the result carefully:
• If your file has been rejected, there will be a message explaining each instance of non- compliance with the metadata that you need to correct.
• If your file has been validated, there might be warnings and remarks relating to possible data quality issues or to potential overwriting of existing records that you should consider.
When you file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval – unapproved uploads can block for the approval of other uploads.
• The TESSy user documentation provides information on reviewing validation results and adjusting
reporting periods to avoid overwriting existing records.
• General training and guidance on reporting is available on the TESSy website. A training video on reporting COVID-19 data is available in the ECDC virtual academy.
TESSy HelpDesk Email: [email protected]
Telephone number: +46-(0)8-5860 1601
Availability:
9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC Holidays)
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Annex – Zoonotic influenza virus metadata
Revisions of the zoonotic influenza virus metadata set The most recent metadata set is available from the TESSy website under technical guidelines and tools tab (as shown below).
Zoonotic influenza virus record types and metadata sets
Current record type versions Table 1 shows the record type versions to be used when reporting zoonotic influenza virus case based (Record type: INFLZOO) or aggregated (Record-type: INFLZOOAGGR) data to TESSy.
Table 1: Zoonotic influenza virus record type versions
Record type Type of data Record type version
INFLZOO Case-based 1
INFLZOOAGGR Aggregated 1
INFLZOO metadata record type version 1
Common TESSy variables
Record identifier (mandatory)
Field: RecordId Coding: Text (max 80 characters) The record identifier is provided by the Member State. Enter a value that is unique for every record in the dataset with the format NUTS2 or countryregion_Www of cases (e.g. BE23_W23).
Record type (mandatory)
Field: RecordType Coding: INFLZOO The record type defines the structure and the format of the data reported.
Record type version
Field: RecordTypeVersion Coding: 1 The version of the record type defines the current structure of the data reported. The current version
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of the INFLZOO record type is 1. This variable is not mandatory as TESSy concludes the record type version from the metadataset indicated by default. However, the variable RecordTypeVersion can override this default.
Subject (mandatory) Field: Subject Coding: INFLZOO The subject describes the data to be reported.
Data source (mandatory)
Field: DataSource Coding: Pre-assigned as CountryCode-INFLZOO to each country; can be modified by National Coordinator The data source (surveillance system) that the record originates from.
Status (mandatory)
Field: Status Coding: NEW/UPDATE/DELETE The field ‘Status’ is used for updating data; the default is ‘New/Update’. By choosing ‘Delete’ the selected record (or batch of data) will remain in TESSy but be marked as inactive; this data can be used to reconstruct data for a given date in the past. Reporting country (mandatory) Field: ReportingCountry Coding: International organization for standardization (ISO) 3166-1-alpha-2, (two-letter code) This variable identifies the country reporting the case.
Date used for statistics (mandatory) Field: DateUsedForStatistics Coding: yyyy-Www The week reported cases were diagnosed.
Epidemiological variables
Date of onset (mandatory)
Field: DateOfOnset
Coding: yyyy-mm-dd, UNK
Date of onset of disease. Not applicable in asymptomatic cases. If not applicable, please use 'Unk'
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Date of notification (mandatory)
Field: DateOfNotification
Coding: yyyy-mm-dd
UNK
Date when the case is notified the first time to the place of notification
Place of notification
Field: PlaceOfNotification
Coding: NUTS/GAUL
Place of the first notification of the case to a regional authority. Select the most detailed NUTS level possible. Region should be provided at the NUTS 2 level. If the region is not in an EU/EEA country, then use GAUL nomenclature
Place of residence Field: PlaceOfResidence
Coding: NUTS/GAUL
Place of residence of patient at the time of disease onset. Select the most detailed NUTS(EU/EEA) or GAUL(non-EU/EEA) level possible
Imported
Field: Imported
Coding: N = No Y = Yes UNK = Unknown
Patient travelled outside the reporting country in the 14 days prior to symptom onset
Probable country of infection (repeatable)
Field: ProbableCountryOfInfection
Coding: International organization for standardization (ISO) 3166-1-alpha-2, (two-letter code) Country(ies) visited in the 2 weeks prior to onset of illness. If there is more than one country N/A should be used in the empty repeated fields.
EpiPulse ID (mandatory)
Field: EpiPulseID Coding: TEXT Link to EpiPulse through outbreak ID
Case classification Field: Classification Coding: CONF = Confirmed
POSS = Possible PROB = Probable
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UNK = Unknown Case classification according to EU case definition or national definition Laboratory method (repeatable) Field: LabMethod Coding: ANTIGEN = Antigen detection
GENOSEQ = Genotyping/Sequencing ISOV = Isolation of virus NEU = Neutralisation NUC = NAAT by RT-PCR, other or not specified O = Other, please specify SCONV = Seroconversion or fourfold titre rise SIGG = NCOV specific IgG-antibodies SIGM = NCOV specific IgM-antibodies SIGMG = NCOV specific IgM- and IgG antibodies UNK = Unknown
Laboratory method used to make diagnosis Surveillance system Field: SurvSys Coding: N = Non-sentinel patient
S = Sentinel patient Unk = Unknown
Surveillance system, sentinel or non-sentinel Setting Field: Setting Coding: C = Community
H = Hospital I = Investigation of outbreak NA = Not applicable OTH = other UNK = Unknown
Specification of the setting of diagnosis or case identification
Gender Field: Gender
Coding: F = Female M = Male O = Other (e.g., transsexual) UNK = Unknown Gender of the reported case.
Age (mandatory) Field: Age Coding: Numerical (0-120) UNK = Unknown Age of patient in years as reported in the national system at the time of disease onset.
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Age in months Field: AgeMonth Coding: Numerical (0-23) NA = Not applicable UNK = Unknown Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset. Virus Type (mandatory) Field: VirusType Coding: A = type A influenza virus
B = type B influenza virus C = type C influenza virus D= type D influenza virus
Virus type Virus HA subtype (mandatory) Field: HA Subtype Coding: H1 = A(H1)
H2 = A(H2) H3 = A(H3) H4 = A(H4) H5 = A(H5) H6 = A(H6) H7 = A(H7) H8 = A(H8) H9 = A(H9) H10 = A(H10) H11 = A(H11) H12 = A(H12) H13 = A(H13) H14 = A(H14) H15 = A(H15) H16 = A(H16) H17 = A(H17) H18 = A(H18) O = Other UNK = Unknown
Virus HA subtype Virus NA subtype (mandatory) Field: NA Subtype Coding: N1 = A(HxN1)
N2 = A(HxN2) N3 = A(HxN3) N4 = A(HxN4) N5 = A(HxN5) N6 = A(HxN6) N7 = A(HxN7) N8 = A(HxN8) N9 = A(HxN9) N10 = A(HxN10) N11 = A(HxN11) O = Other UNK = Unknown
Virus NA subtype
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Pathogen or subtype - Other Field: TypeOther Coding: TEXT
Details of pathogen or subtype, if coded as ‘other’, but is known.
Exposure to animal species (repeatable) Field: AnimalExposure Coding: A = avian (all species) if details or species unknown
B = bat C = chicken or other domesticated birds (poultry, turkey,…) F = ferret or mink G = goat P = pig R = cattle S = seal W = wild bird O = other
Unk = Unknown Exposure of the human case infected with a zoonotic flu virus to an animal Exposure to animal species, other species, describe Field: AnimalExposureOther Coding: TEXT
Exposure of the human case infected with a zoonotic flu virus to an animal species not listed
Viral coinfection (repeatable) Field: ViralCoinfection Coding: SARSCOV2 = SARS-CoV-2
INFL = seasonal influenza virus O = Other respiratory viral pathogen, please specify OTHCOR = Other coronavirus RSV = RSV (Respiratory syncytial virus) UNK = Unknown
Presence of viral co-infection Viral coinfection - Other Field: ViralCoinfectionOther Coding: TEXT Other viral coinfection not found in the list of possible values Clinical Presentation (repeatable) Field: ClinicalPresentation Coding: ASY = Asymptomatic CONJ = Conjunctival injection
COUGH = Dry or productive cough DIARR = Diarrhoea FEVER = History of fever/chills HEAD = Headache
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IRR = Irritability/confusion O = Other, please specify PAIN = Pain PAINABDO = Pain - abdominal PAINCHEST = Pain - chest PAINJOINT = Pain - joint PAINMUSC = Pain - muscular PAINOTH = Pain - other RUNOS = Runny nose SBREATH = Shortness of breath SORETHR = Sore throat UNK = Unknown VOMIT = Nausea/vomiting WEAK = General weakness
Clinical symptoms on onset
Clinical presentation – Other Field: ClinicalPresentationsOther Coding: Text UNK = Unknown Other reported clinical symptoms not found in the list of possible values Influenza Vaccination Field: InfluenzaVaccination Coding: N = No
Y = Yes UNK = Unknown
Current seasonal influenza vaccination Date of Vaccination Field: DateOfVacc Coding: yyyy-mm-dd, UNK Date of vaccination
Occupation Field: Occupation Coding: HCW = HealthCareWorker
VET = Veterinarian CUL = Culler COF = Commercial farmer BYF = Backyard or hobby farmer RIN = Bird ringer OTH = other UNK = unknown
Information on the occupation of the case
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Occupation– Other Field: OccupationOther Coding: TEXT Information on the occupation of the case not listed Precondition (repeatable field, mandatory) Field: Precondition Coding: ASPL = Asplenia
ASTH = Asthma CANC = Cancer, malignancy CARDIACDIS = Cardiac disorder, excluding hypertension DIAB = Diabetes HIV = HIV/other immune deficiency HYPERT = Hypertension KIDNEY = Kidney-related condition, renal disease LIVER = Liver-related condition, liver disease LUNG = Chronic lung disease, excluding asthma NEUROMUS = Neuromuscular disorder, chronic neurological NONE = None O = Other precondition, please specify OBES = Obesity PREG = Pregnancy, trimester is unknown PREG1 = Pregnancy, 1st trim, the 1st trim is from week 1 to the end of week 12 PREG2 = Pregnancy, 2nd trim, the 2nd trim is from week 13 to the end of week 26 PREG3 = Pregnancy, 3rd trim, the 3rd trim is from week 27 to the end of the pregnancy PREGPOST = Post-partum (<6 weeks) SMOKE = Current smoking TB = Tuberculosis UNK = Unknown precondition
Patient's underlying condition or conditions
Precondition –other Field: PreconditionOther Coding: Text Details of underlying conditions, if Precondition is coded as ‘other’, but is known.
Hospitalisation (mandatory) Field: Hospitalisation Coding: N = No UNK = Unknown Y = Yes Hospitalisation in the 4 weeks after onset of illness.
Date of Hospitalisation (mandatory) Field: DateOfHospitalisation Coding: yyyy-mm-dd
UNK= Unknown
If not applicable, please use 'UNK'. Date of Hospitalisation
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Intensive care (mandatory) Field: IntensiveCare Coding: N = No UNK = Unknown Y = Yes
Case required care in an intensive care unit or high dependency unit (unit with capabilities for more intensive observation, treatment and nursing care than can be provided on a regular ward). Date of admission to ICU or HDU Field: DateOfICUHDU Coding: yyyy-mm-dd Date of admission to intensive care unit or high dependency unit Number of days in ICU or HDU Field: NumberDaysICUHDU Coding: Numerical NA = Not applicable UNK = Unknown Total number of days patient spent in IDU or HDU Complications (repeatable) Field: Complications Coding: AKI = Acute renal/kidney injury
ARDS = Acute respiratory distress syndrome BRONCH = Bronchiolitis ENCEPH = Encephalitis HEARTFAIL = Heart failure MULTIFAIL = Multi-organ failure MYOCARD = Myocarditis NONE = None O = Other (please specify separately) OTHBAC = Other secondary bacterial infection PNEU = Bacterial pneumonia (secondary) SEPSIS = Sepsis/Multi-organ failure STILLBIRTH = Still birth as pregnancy outcome in a case UNK = Unknown
Complications at any time
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Respiratory support (mandatory, repeatable) Field: RespSupport Coding: ECMO = Extracorporeal membrane oxygenation
N = No NOTAVAIL = No respiratory support available NOTNEC = No respiratory support necessary O = Other, please specify OXYGEN = Oxygen therapy UNK = Unknown VENT = Ventilator including non-invasive positive pressure ventilation
Level of respiratory support given to patient. Respiratory support - Other Field: RespSupportOther Coding: Text UNK = Unknown
Other respiratory support not found in the list of possible values.
Outcome (mandatory)
Field: Outcome Coding: ALIVE = Alive, recovered, cured
DIEDINFLZOO = zoonotic influenza was main or contributing cause of death DIEDOTHER = Death not related to influenza infection DIEDUNK = Cause of death unknown STILLTREATMENT = Still on medical treatment (not recovered) UNK = Unknown outcome
Information on the outcome of the case in the 4 weeks after onset of illness Date of hospital discharge Field: DateOfDischarge Coding: yyyy-mm-dd UNK= Unknown Date of hospital discharge Date of death Field: DateOfDeath Coding: yyyy-mm-dd UNK= Unknown Date of death (exact date only)
Cause of death Field: CauseOfDeath Coding: INFLMAIN = The main cause of death was influenza
INFLUNDER = The underlying cause of death was influenza NOTINFL = Cause of death not influenza related.
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SECBACT = The cause of death was a secondary bacterial infection acquired in hospital
UNK = Cause of death was unknown Cause of Death Drug Used Prophylaxis (mandatory) Field: DrugUsedProphylaxis Coding: NONE = None
AMA = Amantadine BALO = Baloxavir Marboxil O = Other (or combinations with other) OSEL = Oseltamivir OSELZANA = Oseltamivir and Zanamivir UNK = Unknown ZANA = Zanamivir
Antivirals used as prophylaxis in the 14 days before onset of illness Drug Used Treatment (mandatory) Field: DrugUsedTreatment Coding: M2 = M2 inhibitors
NONE = None BALO = Baloxavir Marboxil O = Other (or combinations with other) OSEL = Oseltamivir OSELZANA = Oseltamivir and Zanamivir UNK = Unknown ZANA = Zanamivir
Antivirals used as prophylaxis in the 14 days before onset of illness Starting date of Treatment (mandatory) Field: DateOfTreatment Coding: yyyy-mm-dd UNK Starting date for antiviral treatment of the case during illness phase Resistance (mandatory, repeatable) Field: Resistance Coding: M2 = M2 inhibitors
NONE = None O = Other OSEL = Oseltamivir UNK = Unknown ZANA = Zanamivir BALO = Baloxavir Marboxil
Resistance to antiviral treatment as assessed by virologists. Report whether resistance has been detected to any antivirals in the coded value list.
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HA sequence aa resistance mutations Field: HAAAMutations Coding: TEXT Listing of amino acid substitution in HA, separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. E190D. M2 sequence aa resistance mutations Field: M2AAMutations Coding: TEXT Listing of amino acid substitution in M2 associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. S31N. NA sequence aa resistance mutations Field: NAAAMutations Coding: TEXT Listing of amino acid substitution in NA associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. H275Y. PA sequence aa resistance mutations Field: PAAAMutations Coding: TEXT Listing of amino acid substitution in PA associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. I38T or I38M or I38F Interpretation M2 Blocker Resistance Testing Field: InterprM2BlockerResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of M2BlockerResistanceTesting. Interpretation Baloxavir Marboxil Resistance Testing Field: InterprBaloxavirResistTest Coding: AARS = amino acid substitution in PA identified previously associated with reduced susceptibility for baloxavir
AANS = No amino acid substitution in PA previously associated with reduced susceptibility for baloxavir marboxil AAINP = Amino Acid substitution Interpretation not possible NA = Not applicable
Interpretation of Baloxavir Marboxil Resistance Testing.
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Interpretation Oseltamivir Resistance Testing Field: InterprOseltamivirResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of Oseltamivir Resistance Testing. Interpretation Zanamivir Resistance Testing Field: InterprZanamivirResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of Zanamivir Resistance Testing. ISD: HA sequence number Field: HAISD Coding: TEXT Accession number for sequence data HA, ISD or other. ISD: NA sequence number Field: NAISD Coding: TEXT Accession number for sequence data NA, ISD or other. ISD: M2 sequence number Field: M2ISD Coding: TEXT Accession number for sequence data M2, ISD or other. ISD: PA sequence number Field: PAISD Coding: TEXT Accession number for sequence data PA, ISD or other. ISD: HA sequence number Field: HAISD Coding: TEXT Accession number for sequence data HA, ISD or other. Wgs ENA identifier
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Field: WgsEnaId Coding: Text European Nucleotide Archive (ENA) run identifier, based on which the sequence read data can be retrieved. Starts with ERR or SRR, i.e. not the sample or experiment which ERS/ERX or SRS/SRX. Wgs Sequence RA identifier (repeatable) Field: WgsSequenceId Coding: Text Sequence identifier for whole genome or gene sequence, based on which the sequence read data can be retrieved from external database such as GISAID, GenBank or other db (except ENA). GISAID isolate sequence accession number should be reported in format EPI_ISL_402123, GenBank MK334047.1. Please report ENAId in WgsEnaId variable Comment Field: Comment Coding: Text Free comment on data, suggestion to fill in conclusion here.
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INFLZOOAGGR metadata record type version 1
Common TESSy variables Record ID Field: RecordId Coding: Text The record identifier is provided by the Member State. It must be unique within the national respiratory virus diseases surveillance system and anonymous. Record type Field: RecordType Coding: CV The record type defines the structure and the format of the data reported (case based reporting or aggregate reporting). The record types are defined by ECDC and are related to the subject. Only valid combinations of subject, record type and data source are accepted. Record type version Field: RecordTypeVersion Coding: NUM The version of the record type defines the current structure of the data reported. If no RecordTypeVersion is provided in the batch, it is set automatically with current version of the Record type. This variable is not mandatory as TESSy concludes the record type version from the metadata set indicated by default. However, RecordTypeVersion is required when no metadata set is provided at upload or when a RecordTypeVersion, other than the current one, needs to be used. Subject Field: Subject Coding: CV The subject describes the data to be reported. Status Field: Status Coding: CV Coded value list: [Statuses]:DELETE = Delete a previously reported record.NEW/UPDATE = Report a new or update a previously reported record (default). The field ‘Status’ is used for updating data; the default is NEW/UPDATE. By choosing DELETE the selected record (or batch of data) will remain in TESSy but be marked as inactive; this data can be used to reconstruct data for a given date in the past. Data Source Field: DataSource Coding: CV The data source specifies the source from which the data originates and is generated and revised/updated by the national contact point for surveillance in each Member State. If needed multiple data sources per country can be entered by different users to facilitate reporting. Reporting Country
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Field: ReportingCountry Coding: CV Coded value list: [Countries](see the coded values list) This variable identifies the country reporting the case. Date used for statistics Field: DateUsedForStatisticsWeek Coding: DATE The week for which the reported data refers. This is the date used by the national surveillance institute/organisation in reports and official statistics. The date used for statistics can vary from country to country but is it is preferably the date the sampling and/or testing has been performed or case was notified to the national health authorities (notification date). Pathogen: Field: Pathogen Coding: CV Coded value list: PathogenRESPI: INFL = Influenza virus MERS = MERS-CoV O = Other RSV = Respiratory syncytial virus SARSCOV2 = SARS-CoV-2 Pathogen associated with tests or detections. If selecting Other, please specify which pathogen in Pathogen – Other. Pathogen Other Field: PathogenOther Coding: Text Specified pathogen not captured in the coded values for Pathogen Influenza virus HA subtype Field: HASubtype Coding: CV Coded value list:InfluenzaVirusHASubType H1 = A(H1) H10 = A(H10) H11 = A(H11) H12 = A(H12) H13 = A(H13) H14 = A(H14) H15 = A(H15) H16 = A(H16) H17 = A(H17) H18 = A(H18) H2 = A(H2) H3 = A(H3) H4 = A(H4) H5 = A(H5) H6 = A(H6) H7 = A(H7)
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H8 = A(H8) H9 = A(H9) O = Other UNK = Unknown Influenza virus NA subtype Field: NASubtype: Coding: CV Coded value list: InfluenzaVirusNASubType N1 = A(HxN1) N10 = A(HxN10) N11 = A(HxN11) N2 = A(HxN2) N3 = A(HxN3) N4 = A(HxN4) N5 = A(HxN5) N6 = A(HxN6) N7 = A(HxN7) N8 = A(HxN8) N9 = A(HxN9) O = Other UNK = Unknown Number tested Field: NumTested Coding: NUM The number of samples tested per week Number detected Field: NumDetected Coding: NUM The number of samples testing positive per week Comment Field: Comment Coding: Text Free comment on data, suggestion to fill in conclusion here.
Minor changes to RESPISURV
Minor change in RespSupport in RESPISURV to align better with SARISURV
58
Respiratory support
Field: RespSupport
Coded value list: RespSupportSARI2
Coding:
Level of respiratory support given to patient. Please indicate the most invasive that applied.
[NEW for both RESPISURV & SARISURV]: If possible to distinguish between low-flow and high-flow oxygen support, please report low-flow oxygen into “O” and high-flow oxygen into “OXYGEN”.
If that is not possible, please report both low- and high-flow oxygen into “OXYGEN”.
Respiratory support
Field: RespSupport
Coded value list: RespSupportNCOV
Coding:
Level of respiratory support given to patient.
NONE = No respiratory support given
OXYGEN = High-flow oxygen therapy (non-invasive ventilation)
VENT = Invasive Ventilation
ECMO = Extra Corporeal Membrane Oxygenation
O = Other respiratory support
UNK = Respiratory support given unknown
Proposed, to match SARISURV: Current RESPISURV:
N = No
OXYGEN = Oxygen therapy
VENT = Ventilator including non-invasive positive pressure vent
ECMO = Extracorporeal membrane oxygenation
O = Other
UNK = Unknown
Zoonotic influenza virus reporting protocol May 2024
TESSy - The European Surveillance System
Zoonotic influenza virus Reporting Protocol
Version 2.2, May 2024
© ECDC May 2024 All rights reserved. Page 3 of 24
Contents How to use this document ..................................................................................................... 4
Finding further information .................................................................................................... 4
Copyright ............................................................................................................................. 4
Introduction ............................................................................................................... 5
Aim ...................................................................................................................................... 5
Objectives ............................................................................................................................ 5
Reporting to TESSy .................................................................................................... 6
When, what and how to report .............................................................................................. 6
Preparing data ...................................................................................................................... 6
Checking metadata ............................................................................................................... 6
Submitting your data ............................................................................................................ 7
Finalising your submission ..................................................................................................... 7
TESSy HelpDesk ................................................................................................................... 7
Annex – Zoonotic influenza virus metadata ................................................................... 8
Revisions of the zoonotic influenza virus metadata set ............................................................ 8
Metadata set ........................................................................................................................ 8
Current record type versions ............................................................................................. 8
INFLZOO metadata record type version 1 ............................................................................... 8
Common TESSy variables ...................................................................................................... 8
Epidemiological variables .................................................................................................. 9
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How to use this document This Reporting Protocol provides information for reporting countries’ data managers in three main sections:
• Reporting to TESSy – contains guidelines on how to prepare data for submission to TESSy, deadlines for data submission, subject-specific information (e.g. new changes to metadata), and links to further information.
• Annex – contains:
o The metadata sets for the subject(s) covered by this Reporting Protocol.
Finding further information Paragraphs denoted by the information icon tell where you can find further information.
Updated links to all the schedules, documentation and training materials mentioned in this Reporting Protocol are included in the TESSy Technical Guidelines & Tools (see the menu ‘Technical Guidelines and Tools’ when logged in TESSy), including:
• Metadata sets and history.
• Tutorials for data transformation using respectively Excel and Access.
• TESSy user documentation.
• CSV and XML transport protocols.
Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.
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Introduction An event of a human case infected with an influenza virus deriving from an animal source should be reported within 24 hours to EWRS which will cover the IHR notification for EU/EEA countries.
This reporting protocol describes the surveillance of the zoonotic influenza virus data in the EU/EEA and wider European Region. Aggregate data on zoonotic influenza (number of tested H5, number tested H7, number detected H5 and number detected H7) can be uploaded to INFLZOOAGGR . For the reporting of case-based data the record type INFLZOO should be used.
Aggregate data on number of tested and positive human cases enables the collection of denominator data as well as nominator data in case more human infections are occurring. For sporadic human infection a case-based reporting should be preferred to report information from people infected with a zoonotic influenza virus. The data aims to support situational risk assessment and trends over time. Case-based and aggregate data can be uploaded retrospectively when more information becomes available.
Aim To support the timely and complete reporting on number of samples tested, aggregate number of detected and of key information of zoonotic influenza cases in the EU/EEA and wider European Region.
Objectives • To collect denominator data on number of tested people. • To help assess the onset of the disease, confirmation of the subtype of infection and severity. • To provide information on exposure, treatment and outcome. • To provide additional contextual information to help understand the case identification. • To analyse trends over time.
Changes from last version Version 2.1: Inclusion of the aggregated record type INFLZOOAGGR and description of variables and coded value lists. Version 2.2: Inclusion of additional species under INFLZOO variable on exposure to animal species
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Reporting to TESSy
When, what and how to report Deadline for reporting: An event of a human infection with avian influenza virus should be reported within 24 hours to EWRS covering IHR for EU/EEA countries. If a suspected human case is under investigation, such information should be shared via EpiPulse with ECDC and other countries for awareness. Data for monitoring the event and assess trends should be reported to TESSy at least in the subsequent week following identification and confirmation.
Preparing data Data may be entered directly in TESSy for individual records (‘Manually create a record’). For any batch reporting by file upload (CSV or XML format) please note that once the data has been exported from your national database it needs to be in a format that TESSy can accept (see ‘checking metadata’).
Checking metadata The TESSy metadata define the fields and data formats that are valid as input to TESSy for a given subject. To ensure data can be saved correctly in TESSy, please check the data are correctly formatted according to the most recent metadata set.
It is especially important to focus on: • Field formats
Many fields require that data are formatted in a specific way. For example, dates must be in the YYYY-Www format (e.g 2021-W01); dates in any other format will be rejected.
• Coded values Some fields only permit the use of specific values (coded values). If any other value is used in the field, the upload will be rejected.
The metadata file contains all the definitions and rules you need to comply with to format your data correctly for every subject (usually a disease). The file can be downloaded as an Excel file from the TESSy documents website. By filtering the fields in the file by subject, you can see the fields required for your subject and the rules applying to these fields.
The Technical Annex provides an overview of how you work with the metadata file, and the TESSy user documentation provides in-depth details on metadata.
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Submitting your data Data are submitted through the TESSy web interface (go to Upload). Previously reported data can be found through the review tab (see below).
The Tessy User Guide provides an overview of how you submit files to TESSy, and the TESSy user documentation provides in-depth descriptions of all the upload methods.
Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. The result of your upload – i.e. rejected or validated – is displayed immediately after the conclusion of the check in the Validation details webpage. Please review the result carefully:
• If your file has been rejected, there will be a message explaining each instance of non- compliance with the metadata that you need to correct.
• If your file has been validated, there might be warnings and remarks relating to possible data quality issues or to potential overwriting of existing records that you should consider.
When you file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval – unapproved uploads can block for the approval of other uploads.
• The TESSy user documentation provides information on reviewing validation results and adjusting
reporting periods to avoid overwriting existing records.
• General training and guidance on reporting is available on the TESSy website. A training video on reporting COVID-19 data is available in the ECDC virtual academy.
TESSy HelpDesk Email: [email protected]
Telephone number: +46-(0)8-5860 1601
Availability:
9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC Holidays)
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Annex – Zoonotic influenza virus metadata
Revisions of the zoonotic influenza virus metadata set The most recent metadata set is available from the TESSy website under technical guidelines and tools tab (as shown below).
Zoonotic influenza virus record types and metadata sets
Current record type versions Table 1 shows the record type versions to be used when reporting zoonotic influenza virus case based (Record type: INFLZOO) or aggregated (Record-type: INFLZOOAGGR) data to TESSy.
Table 1: Zoonotic influenza virus record type versions
Record type Type of data Record type version
INFLZOO Case-based 1
INFLZOOAGGR Aggregated 1
INFLZOO metadata record type version 1
Common TESSy variables
Record identifier (mandatory)
Field: RecordId Coding: Text (max 80 characters) The record identifier is provided by the Member State. Enter a value that is unique for every record in the dataset with the format NUTS2 or countryregion_Www of cases (e.g. BE23_W23).
Record type (mandatory)
Field: RecordType Coding: INFLZOO The record type defines the structure and the format of the data reported.
Record type version
Field: RecordTypeVersion Coding: 1 The version of the record type defines the current structure of the data reported. The current version
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of the INFLZOO record type is 1. This variable is not mandatory as TESSy concludes the record type version from the metadataset indicated by default. However, the variable RecordTypeVersion can override this default.
Subject (mandatory) Field: Subject Coding: INFLZOO The subject describes the data to be reported.
Data source (mandatory)
Field: DataSource Coding: Pre-assigned as CountryCode-INFLZOO to each country; can be modified by National Coordinator The data source (surveillance system) that the record originates from.
Status (mandatory)
Field: Status Coding: NEW/UPDATE/DELETE The field ‘Status’ is used for updating data; the default is ‘New/Update’. By choosing ‘Delete’ the selected record (or batch of data) will remain in TESSy but be marked as inactive; this data can be used to reconstruct data for a given date in the past. Reporting country (mandatory) Field: ReportingCountry Coding: International organization for standardization (ISO) 3166-1-alpha-2, (two-letter code) This variable identifies the country reporting the case.
Date used for statistics (mandatory) Field: DateUsedForStatistics Coding: yyyy-Www The week reported cases were diagnosed.
Epidemiological variables
Date of onset (mandatory)
Field: DateOfOnset
Coding: yyyy-mm-dd, UNK
Date of onset of disease. Not applicable in asymptomatic cases. If not applicable, please use 'Unk'
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Date of notification (mandatory)
Field: DateOfNotification
Coding: yyyy-mm-dd
UNK
Date when the case is notified the first time to the place of notification
Place of notification
Field: PlaceOfNotification
Coding: NUTS/GAUL
Place of the first notification of the case to a regional authority. Select the most detailed NUTS level possible. Region should be provided at the NUTS 2 level. If the region is not in an EU/EEA country, then use GAUL nomenclature
Place of residence Field: PlaceOfResidence
Coding: NUTS/GAUL
Place of residence of patient at the time of disease onset. Select the most detailed NUTS(EU/EEA) or GAUL(non-EU/EEA) level possible
Imported
Field: Imported
Coding: N = No Y = Yes UNK = Unknown
Patient travelled outside the reporting country in the 14 days prior to symptom onset
Probable country of infection (repeatable)
Field: ProbableCountryOfInfection
Coding: International organization for standardization (ISO) 3166-1-alpha-2, (two-letter code) Country(ies) visited in the 2 weeks prior to onset of illness. If there is more than one country N/A should be used in the empty repeated fields.
EpiPulse ID (mandatory)
Field: EpiPulseID Coding: TEXT Link to EpiPulse through outbreak ID
Case classification Field: Classification Coding: CONF = Confirmed
POSS = Possible PROB = Probable
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UNK = Unknown Case classification according to EU case definition or national definition Laboratory method (repeatable) Field: LabMethod Coding: ANTIGEN = Antigen detection
GENOSEQ = Genotyping/Sequencing ISOV = Isolation of virus NEU = Neutralisation NUC = NAAT by RT-PCR, other or not specified O = Other, please specify SCONV = Seroconversion or fourfold titre rise SIGG = NCOV specific IgG-antibodies SIGM = NCOV specific IgM-antibodies SIGMG = NCOV specific IgM- and IgG antibodies UNK = Unknown
Laboratory method used to make diagnosis Surveillance system Field: SurvSys Coding: N = Non-sentinel patient
S = Sentinel patient Unk = Unknown
Surveillance system, sentinel or non-sentinel Setting Field: Setting Coding: C = Community
H = Hospital I = Investigation of outbreak NA = Not applicable OTH = other UNK = Unknown
Specification of the setting of diagnosis or case identification
Gender Field: Gender
Coding: F = Female M = Male O = Other (e.g., transsexual) UNK = Unknown Gender of the reported case.
Age (mandatory) Field: Age Coding: Numerical (0-120) UNK = Unknown Age of patient in years as reported in the national system at the time of disease onset.
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Age in months Field: AgeMonth Coding: Numerical (0-23) NA = Not applicable UNK = Unknown Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset. Virus Type (mandatory) Field: VirusType Coding: A = type A influenza virus
B = type B influenza virus C = type C influenza virus D= type D influenza virus
Virus type Virus HA subtype (mandatory) Field: HA Subtype Coding: H1 = A(H1)
H2 = A(H2) H3 = A(H3) H4 = A(H4) H5 = A(H5) H6 = A(H6) H7 = A(H7) H8 = A(H8) H9 = A(H9) H10 = A(H10) H11 = A(H11) H12 = A(H12) H13 = A(H13) H14 = A(H14) H15 = A(H15) H16 = A(H16) H17 = A(H17) H18 = A(H18) O = Other UNK = Unknown
Virus HA subtype Virus NA subtype (mandatory) Field: NA Subtype Coding: N1 = A(HxN1)
N2 = A(HxN2) N3 = A(HxN3) N4 = A(HxN4) N5 = A(HxN5) N6 = A(HxN6) N7 = A(HxN7) N8 = A(HxN8) N9 = A(HxN9) N10 = A(HxN10) N11 = A(HxN11) O = Other UNK = Unknown
Virus NA subtype
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Pathogen or subtype - Other Field: TypeOther Coding: TEXT
Details of pathogen or subtype, if coded as ‘other’, but is known.
Exposure to animal species (repeatable) Field: AnimalExposure Coding: A = avian (all species) if details or species unknown
B = bat C = chicken or other domesticated birds (poultry, turkey,…) F = ferret or mink G = goat P = pig R = cattle S = seal W = wild bird O = other
Unk = Unknown Exposure of the human case infected with a zoonotic flu virus to an animal Exposure to animal species, other species, describe Field: AnimalExposureOther Coding: TEXT
Exposure of the human case infected with a zoonotic flu virus to an animal species not listed
Viral coinfection (repeatable) Field: ViralCoinfection Coding: SARSCOV2 = SARS-CoV-2
INFL = seasonal influenza virus O = Other respiratory viral pathogen, please specify OTHCOR = Other coronavirus RSV = RSV (Respiratory syncytial virus) UNK = Unknown
Presence of viral co-infection Viral coinfection - Other Field: ViralCoinfectionOther Coding: TEXT Other viral coinfection not found in the list of possible values Clinical Presentation (repeatable) Field: ClinicalPresentation Coding: ASY = Asymptomatic CONJ = Conjunctival injection
COUGH = Dry or productive cough DIARR = Diarrhoea FEVER = History of fever/chills HEAD = Headache
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IRR = Irritability/confusion O = Other, please specify PAIN = Pain PAINABDO = Pain - abdominal PAINCHEST = Pain - chest PAINJOINT = Pain - joint PAINMUSC = Pain - muscular PAINOTH = Pain - other RUNOS = Runny nose SBREATH = Shortness of breath SORETHR = Sore throat UNK = Unknown VOMIT = Nausea/vomiting WEAK = General weakness
Clinical symptoms on onset
Clinical presentation – Other Field: ClinicalPresentationsOther Coding: Text UNK = Unknown Other reported clinical symptoms not found in the list of possible values Influenza Vaccination Field: InfluenzaVaccination Coding: N = No
Y = Yes UNK = Unknown
Current seasonal influenza vaccination Date of Vaccination Field: DateOfVacc Coding: yyyy-mm-dd, UNK Date of vaccination
Occupation Field: Occupation Coding: HCW = HealthCareWorker
VET = Veterinarian CUL = Culler COF = Commercial farmer BYF = Backyard or hobby farmer RIN = Bird ringer OTH = other UNK = unknown
Information on the occupation of the case
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Occupation– Other Field: OccupationOther Coding: TEXT Information on the occupation of the case not listed Precondition (repeatable field, mandatory) Field: Precondition Coding: ASPL = Asplenia
ASTH = Asthma CANC = Cancer, malignancy CARDIACDIS = Cardiac disorder, excluding hypertension DIAB = Diabetes HIV = HIV/other immune deficiency HYPERT = Hypertension KIDNEY = Kidney-related condition, renal disease LIVER = Liver-related condition, liver disease LUNG = Chronic lung disease, excluding asthma NEUROMUS = Neuromuscular disorder, chronic neurological NONE = None O = Other precondition, please specify OBES = Obesity PREG = Pregnancy, trimester is unknown PREG1 = Pregnancy, 1st trim, the 1st trim is from week 1 to the end of week 12 PREG2 = Pregnancy, 2nd trim, the 2nd trim is from week 13 to the end of week 26 PREG3 = Pregnancy, 3rd trim, the 3rd trim is from week 27 to the end of the pregnancy PREGPOST = Post-partum (<6 weeks) SMOKE = Current smoking TB = Tuberculosis UNK = Unknown precondition
Patient's underlying condition or conditions
Precondition –other Field: PreconditionOther Coding: Text Details of underlying conditions, if Precondition is coded as ‘other’, but is known.
Hospitalisation (mandatory) Field: Hospitalisation Coding: N = No UNK = Unknown Y = Yes Hospitalisation in the 4 weeks after onset of illness.
Date of Hospitalisation (mandatory) Field: DateOfHospitalisation Coding: yyyy-mm-dd
UNK= Unknown
If not applicable, please use 'UNK'. Date of Hospitalisation
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Intensive care (mandatory) Field: IntensiveCare Coding: N = No UNK = Unknown Y = Yes
Case required care in an intensive care unit or high dependency unit (unit with capabilities for more intensive observation, treatment and nursing care than can be provided on a regular ward). Date of admission to ICU or HDU Field: DateOfICUHDU Coding: yyyy-mm-dd Date of admission to intensive care unit or high dependency unit Number of days in ICU or HDU Field: NumberDaysICUHDU Coding: Numerical NA = Not applicable UNK = Unknown Total number of days patient spent in IDU or HDU Complications (repeatable) Field: Complications Coding: AKI = Acute renal/kidney injury
ARDS = Acute respiratory distress syndrome BRONCH = Bronchiolitis ENCEPH = Encephalitis HEARTFAIL = Heart failure MULTIFAIL = Multi-organ failure MYOCARD = Myocarditis NONE = None O = Other (please specify separately) OTHBAC = Other secondary bacterial infection PNEU = Bacterial pneumonia (secondary) SEPSIS = Sepsis/Multi-organ failure STILLBIRTH = Still birth as pregnancy outcome in a case UNK = Unknown
Complications at any time
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Respiratory support (mandatory, repeatable) Field: RespSupport Coding: ECMO = Extracorporeal membrane oxygenation
N = No NOTAVAIL = No respiratory support available NOTNEC = No respiratory support necessary O = Other, please specify OXYGEN = Oxygen therapy UNK = Unknown VENT = Ventilator including non-invasive positive pressure ventilation
Level of respiratory support given to patient. Respiratory support - Other Field: RespSupportOther Coding: Text UNK = Unknown
Other respiratory support not found in the list of possible values.
Outcome (mandatory)
Field: Outcome Coding: ALIVE = Alive, recovered, cured
DIEDINFLZOO = zoonotic influenza was main or contributing cause of death DIEDOTHER = Death not related to influenza infection DIEDUNK = Cause of death unknown STILLTREATMENT = Still on medical treatment (not recovered) UNK = Unknown outcome
Information on the outcome of the case in the 4 weeks after onset of illness Date of hospital discharge Field: DateOfDischarge Coding: yyyy-mm-dd UNK= Unknown Date of hospital discharge Date of death Field: DateOfDeath Coding: yyyy-mm-dd UNK= Unknown Date of death (exact date only)
Cause of death Field: CauseOfDeath Coding: INFLMAIN = The main cause of death was influenza
INFLUNDER = The underlying cause of death was influenza NOTINFL = Cause of death not influenza related.
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SECBACT = The cause of death was a secondary bacterial infection acquired in hospital
UNK = Cause of death was unknown Cause of Death Drug Used Prophylaxis (mandatory) Field: DrugUsedProphylaxis Coding: NONE = None
AMA = Amantadine BALO = Baloxavir Marboxil O = Other (or combinations with other) OSEL = Oseltamivir OSELZANA = Oseltamivir and Zanamivir UNK = Unknown ZANA = Zanamivir
Antivirals used as prophylaxis in the 14 days before onset of illness Drug Used Treatment (mandatory) Field: DrugUsedTreatment Coding: M2 = M2 inhibitors
NONE = None BALO = Baloxavir Marboxil O = Other (or combinations with other) OSEL = Oseltamivir OSELZANA = Oseltamivir and Zanamivir UNK = Unknown ZANA = Zanamivir
Antivirals used as prophylaxis in the 14 days before onset of illness Starting date of Treatment (mandatory) Field: DateOfTreatment Coding: yyyy-mm-dd UNK Starting date for antiviral treatment of the case during illness phase Resistance (mandatory, repeatable) Field: Resistance Coding: M2 = M2 inhibitors
NONE = None O = Other OSEL = Oseltamivir UNK = Unknown ZANA = Zanamivir BALO = Baloxavir Marboxil
Resistance to antiviral treatment as assessed by virologists. Report whether resistance has been detected to any antivirals in the coded value list.
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HA sequence aa resistance mutations Field: HAAAMutations Coding: TEXT Listing of amino acid substitution in HA, separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. E190D. M2 sequence aa resistance mutations Field: M2AAMutations Coding: TEXT Listing of amino acid substitution in M2 associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. S31N. NA sequence aa resistance mutations Field: NAAAMutations Coding: TEXT Listing of amino acid substitution in NA associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. H275Y. PA sequence aa resistance mutations Field: PAAAMutations Coding: TEXT Listing of amino acid substitution in PA associated with antiviral resistance (WHO table) separated by semi colon. Format for reporting composition ALL relevant amino acid positions: e.g. I38T or I38M or I38F Interpretation M2 Blocker Resistance Testing Field: InterprM2BlockerResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of M2BlockerResistanceTesting. Interpretation Baloxavir Marboxil Resistance Testing Field: InterprBaloxavirResistTest Coding: AARS = amino acid substitution in PA identified previously associated with reduced susceptibility for baloxavir
AANS = No amino acid substitution in PA previously associated with reduced susceptibility for baloxavir marboxil AAINP = Amino Acid substitution Interpretation not possible NA = Not applicable
Interpretation of Baloxavir Marboxil Resistance Testing.
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Interpretation Oseltamivir Resistance Testing Field: InterprOseltamivirResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of Oseltamivir Resistance Testing. Interpretation Zanamivir Resistance Testing Field: InterprZanamivirResistTest Coding: AAHRI = Amino acid substitution previously associated with highly reduced inhibition
AAINP = Genotypic interpretation not possible AANI = No amino acid substitution prev assoc. with (highly)reduced inhibition AARI = Amino acid substitution previously associated with reduced inhibition HRI = Highly reduced inhibition NA = Not applicable NI = Normal inhibition RI = Reduced inhibition
Interpretation of Zanamivir Resistance Testing. ISD: HA sequence number Field: HAISD Coding: TEXT Accession number for sequence data HA, ISD or other. ISD: NA sequence number Field: NAISD Coding: TEXT Accession number for sequence data NA, ISD or other. ISD: M2 sequence number Field: M2ISD Coding: TEXT Accession number for sequence data M2, ISD or other. ISD: PA sequence number Field: PAISD Coding: TEXT Accession number for sequence data PA, ISD or other. ISD: HA sequence number Field: HAISD Coding: TEXT Accession number for sequence data HA, ISD or other. Wgs ENA identifier
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Field: WgsEnaId Coding: Text European Nucleotide Archive (ENA) run identifier, based on which the sequence read data can be retrieved. Starts with ERR or SRR, i.e. not the sample or experiment which ERS/ERX or SRS/SRX. Wgs Sequence RA identifier (repeatable) Field: WgsSequenceId Coding: Text Sequence identifier for whole genome or gene sequence, based on which the sequence read data can be retrieved from external database such as GISAID, GenBank or other db (except ENA). GISAID isolate sequence accession number should be reported in format EPI_ISL_402123, GenBank MK334047.1. Please report ENAId in WgsEnaId variable Comment Field: Comment Coding: Text Free comment on data, suggestion to fill in conclusion here.
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INFLZOOAGGR metadata record type version 1
Common TESSy variables Record ID Field: RecordId Coding: Text The record identifier is provided by the Member State. It must be unique within the national respiratory virus diseases surveillance system and anonymous. Record type Field: RecordType Coding: CV The record type defines the structure and the format of the data reported (case based reporting or aggregate reporting). The record types are defined by ECDC and are related to the subject. Only valid combinations of subject, record type and data source are accepted. Record type version Field: RecordTypeVersion Coding: NUM The version of the record type defines the current structure of the data reported. If no RecordTypeVersion is provided in the batch, it is set automatically with current version of the Record type. This variable is not mandatory as TESSy concludes the record type version from the metadata set indicated by default. However, RecordTypeVersion is required when no metadata set is provided at upload or when a RecordTypeVersion, other than the current one, needs to be used. Subject Field: Subject Coding: CV The subject describes the data to be reported. Status Field: Status Coding: CV Coded value list: [Statuses]:DELETE = Delete a previously reported record.NEW/UPDATE = Report a new or update a previously reported record (default). The field ‘Status’ is used for updating data; the default is NEW/UPDATE. By choosing DELETE the selected record (or batch of data) will remain in TESSy but be marked as inactive; this data can be used to reconstruct data for a given date in the past. Data Source Field: DataSource Coding: CV The data source specifies the source from which the data originates and is generated and revised/updated by the national contact point for surveillance in each Member State. If needed multiple data sources per country can be entered by different users to facilitate reporting. Reporting Country
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Field: ReportingCountry Coding: CV Coded value list: [Countries](see the coded values list) This variable identifies the country reporting the case. Date used for statistics Field: DateUsedForStatisticsWeek Coding: DATE The week for which the reported data refers. This is the date used by the national surveillance institute/organisation in reports and official statistics. The date used for statistics can vary from country to country but is it is preferably the date the sampling and/or testing has been performed or case was notified to the national health authorities (notification date). Pathogen: Field: Pathogen Coding: CV Coded value list: PathogenRESPI: INFL = Influenza virus MERS = MERS-CoV O = Other RSV = Respiratory syncytial virus SARSCOV2 = SARS-CoV-2 Pathogen associated with tests or detections. If selecting Other, please specify which pathogen in Pathogen – Other. Pathogen Other Field: PathogenOther Coding: Text Specified pathogen not captured in the coded values for Pathogen Influenza virus HA subtype Field: HASubtype Coding: CV Coded value list:InfluenzaVirusHASubType H1 = A(H1) H10 = A(H10) H11 = A(H11) H12 = A(H12) H13 = A(H13) H14 = A(H14) H15 = A(H15) H16 = A(H16) H17 = A(H17) H18 = A(H18) H2 = A(H2) H3 = A(H3) H4 = A(H4) H5 = A(H5) H6 = A(H6) H7 = A(H7)
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H8 = A(H8) H9 = A(H9) O = Other UNK = Unknown Influenza virus NA subtype Field: NASubtype: Coding: CV Coded value list: InfluenzaVirusNASubType N1 = A(HxN1) N10 = A(HxN10) N11 = A(HxN11) N2 = A(HxN2) N3 = A(HxN3) N4 = A(HxN4) N5 = A(HxN5) N6 = A(HxN6) N7 = A(HxN7) N8 = A(HxN8) N9 = A(HxN9) O = Other UNK = Unknown Number tested Field: NumTested Coding: NUM The number of samples tested per week Number detected Field: NumDetected Coding: NUM The number of samples testing positive per week Comment Field: Comment Coding: Text Free comment on data, suggestion to fill in conclusion here.