Page 1 Inclusion

08.12.2021 11:08 projectredcap.org

ConfidentialHospital-based surveillance of COVID-19, Influenza & Respiratory diseases in Switzerland {BASEC 2020-00827} [2020+]

Page 1

Inclusion

Record ID__________________________________

Hospital based surveillance of Influenza and COVID-19 cases in Switzerland

Each new record is a distinct COVID-19 OR Influenza Episode related to a patient.

In case a patient undergoes one Influenza episode and one COVID-19 episode, please createtwo separate records: one for influenza, and one for COVID-19.

A new episode is defined as a new hospitalisation separated by at minimum 30 days from theprevious hospitalisation. In case a specific patient undergoes more than one episode, pleasecreate a new record to report each additional episode.

Whenever possible, make sure that you fill the Inclusion, Demography, Case Declaration, andAdmission forms within 48h. The other forms can be filled later but ASAP.Is this another episode of the same virus (COVID-19 or Influenza) from a same patient ?

No (this is the patient's first episode)Yes (the first episode record has been already reported)Still to be confirmed

ID of first episode of this patient__________________________________

ID is the number on the right of the full CenterID-ID ([0-9999])identifier, e.g. 123-456

Was the first episode of this patient recorded in theold COVID-19 database?

Yes No

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Center (or consortium) where the first episode wascreated

CHUV (Lausanne) EOC (Lugano)HFR (Fribourg) Hirslanden AG ZH

(Zurich) Hirslanden Klinik St. Anna(Luzern) Hopital VS (Sion)

HUG (Geneva) Inselspital (Bern)UKBB (Kinderspital Basel)KISPI (Zurich) KSA (Aarau)KSGR (Graubuenden)KSNW (Niedwalden) KSSG (St.Gallen) &

consortium KSW (Winterthur)LUKS (Luzern) OKS (St.Gallen)Spitaeler SH (Schaffhausen)STGAG KSM (Muensterlingen)USB (Basel) USZ (Zurich)

(your current center: [user-dag-label])

Center (or consortium) where the first episode wascreated - Old Database

CHUV (Lausanne) EOC (Lugano)HFR (Fribourg) Hirslanden AG ZH

(Zurich) Hopital VS (Sion)HUG (Geneva) Inselspital (Bern)KISPI (Basel) KISPI (Zurich)KSA (Aarau) KSGR (Graubuenden)KSNW (Niedwalden) KSSG (St.Gallen) &

consortium KSW (Winterthur)LUKS (Luzern) OKS (St.Gallen)Spitaeler SH (Schaffhausen)STGAG KSM (Muensterlingen)USB (Basel) USZ (Zurich)

(your current center: [user-dag-label])

Checking inclusion criteriaThis entry reports: A laboratory-confirmed Influenza diagnosis

A laboratory-confirmed COVID-19 diagnosis (e.g.RT-PCR/Antigenic test)A clinical COVID-19 diagnosis (e.g.CT-scan/radio/serology)

Hospitalised for more than 24 hours Yes No

Patient's inclusionConfirm inclusion ? Yes (include patient)

If the inclusion cannot be confirmed, please do not report this episode: either have the PI delete the entry, or replaceit with an episode that fulfills the inclusion criteria.

Inclusion date__________________________________

ID of user checking the inclusion__________________________________




Page 3

Demography

DemographyYear of birth

__________________________________

Is the patient a child (< 18 years) YesNo

Is the patient 6 years old or less ? YesNo

Birth Month__________________________________

Gender Male Female Other

Height, Weight and BMI will be evaluated during each individual hospitalisation event




Page 4

Case Declaration

Starting date of symptoms__________________________________

Exposure factorsType of exposure Community acquired

Nosocomial (> 5 days) from this hospitalNosocomial (> 5 days) from another institutionUnknown

Type of exposure Community acquiredNosocomial (> 3 days) from this hospitalNosocomial (> 3 days) from another institutionUnknown

Where was the patient exposed? HouseholdSchool / Kindergarten / DaycareFamily / Friends circleOther contactUnknown

Employed in a healthcare facility at time of Noinfection? Yes

Unknown

Employed in a microbiology laboratory at time of Noinfection? Yes

Unknown

Was the infection acquired abroad? NoYesUnknown



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In which country was the infection most probably Afghanistancontracted? Åland Islands

AlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua and BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBosnia and HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, The Democratic Republic of TheCook IslandsCosta RicaCote D'ivoireCroatiaCubaCyprusCzechiaDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopia


Falkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-bissauGuyanaHaitiHeard Island and Mcdonald IslandsHoly See (Vatican City State)HondurasHong KongHungaryIcelandIndiaIndonesiaIran, Islamic Republic ofIraqIrelandIsle of ManIsraelItalyJamaicaJapanJerseyJordanKazakhstanKenyaKiribatiKorea, Democratic People's Republic ofKorea, Republic ofKosovoKuwaitKyrgyzstanLao People's Democratic RepublicLatviaLebanonLesothoLiberiaLibyan Arab JamahiriyaLiechtensteinLithuaniaLuxembourgMacaoMacedonia, The Former Yugoslav Republic ofMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMartiniqueMauritania

MauritiusMayotteMexicoMicronesia, Federated States ofMoldova, Republic ofMonacoMongoliaMontenegroMontserratMoroccoMozambiqueMyanmarNamibiaNauruNepalNetherlandsNetherlands AntillesNew CaledoniaNew ZealandNicaraguaNigerNigeriaNiueNorfolk IslandNorthern Mariana IslandsNorwayOmanPakistanPalauPalestinian Territory, OccupiedPanamaPapua New GuineaParaguayPeruPhilippinesPitcairnPolandPortugalPuerto RicoQatarReunionRomaniaRussian FederationRwandaSaint HelenaSaint Kitts and NevisSaint LuciaSaint Pierre and MiquelonSaint Vincent and The GrenadinesSamoaSan MarinoSao Tome and PrincipeSaudi ArabiaSenegalSerbiaSeychellesSierra LeoneSingaporeSlovakiaSloveniaSolomon IslandsSomaliaSouth AfricaSouth Georgia and The South Sandwich IslandsSpainSri LankaSudanSurinameSvalbard and Jan MayenSwazilandSweden

SwitzerlandSyrian Arab RepublicTaiwan, Province of ChinaTajikistanTanzania, United Republic ofThailandTimor-lesteTogoTokelauTongaTrinidad and TobagoTunisiaTurkeyTurkmenistanTurks and Caicos IslandsTuvaluUgandaUkraineUnited Arab EmiratesUnited KingdomUnited StatesUnited States Minor Outlying IslandsUruguayUzbekistanVanuatuVenezuelaViet NamVirgin Islands, BritishVirgin Islands, U.S.Wallis and FutunaWestern SaharaYemenZambiaZimbabwe

First positive diagnosis methodDate and time of collection of diagnosis method(CT scan/Serology/Lab sample) __________________________________

...check if date/time may NOT be exact exact date and timeexact date / estimated timeestimated date and time

Type of sample Nasal swabThroat swabNasopharyngeal swabTracheal aspirationBroncho-alveolar lavageOther...

...please, specify sample type__________________________________


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In which service was the diagnosis method made/ sample Medicinetaken ? Geriatrics

Intensive CareSurgeryPaediatricsEmergency RoomNICU/PICUObstetricsGeneral practitionerOther...

...please, specify where__________________________________

Confirmation method PCR (RT-PCR/POCT-PCR)CT Scan or radiology compatible with COVID-19diagnosisSerology compatible with COVID-19 diagnosisAntigenic testOther...

Confirmation method PCR (RT-PCR/POCT-PCR)Antigenic Rapid Flu testViral cultureImmunofluorescenceOther

...please, specify confirmation method__________________________________

Influenza virus type ABUnknown

Influenza virus sub-type__________________________________

Was the patient's sample sequenced? NoYesUnknown



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Canton in which the patient resides, given by "XX" in ZHthe GISAID number BE

LUhCoV-19/Switzerland/XX-ZZZZZZZZ/YYYY UR

SZOWNWGLZGFRSOBSBLSHARAISGGRAGTGTIVDVSNEGEJUUN

(UN = Unknown)

Number associated to the sample, given by "ZZZZZZZZ"in the GISAID number __________________________________

hCoV-19/Switzerland/XX-ZZZZZZZZ/YYYY

Year in which the sample was sequenced, given by 2020"YYYY" in the GISAID number 2021

hCoV-19/Switzerland/XX-ZZZZZZZZ/YYYY



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COVID-19 virus type Common variant/Mutation but no VOCA.23.1AY.1AY.4AY.4.1AY.4.2AY.5AY.6AY.7AY.7.2AY.9AY.12AY.25AY.26AY.33AY.39AY.42AY.43AY.46AY.46.6AY.51AY.102AY.103AY.121AY.122B.1B.1.1B.1.1.7 - AlphaB.1.1.29B.1.1.39B.1.1.70B.1.1.189B.1.1.222B.1.1.296B.1.1.318B.1.1.529 - OmicronB.1.36B.1.36.1B.1.111-E484KB.1.146B.1.160B.1.160.16B.1.160.20B.1.177B.1.214B.1.214.2B.1.221B.1.258B.1.258.17B.1.351 - BetaB.1.367B.1.427/B.1.429 - EpsilonB.1.525 - EtaB.1.526 - IotaB.1.617B.1.617.1 - KappaB.1.617.2 - DeltaB.1.617.3B.1.620B.1.621 - MuC.1.2C.16C.36.3C.37 - LambdaP.1 - GammaP.1.2P.2 - ZetaP.3 - ThetaPh-B.1.1.28


N501Y Mutation - no sequencing availableOtherUnknown

(The options for this field will be updatedregularly)

... please specify__________________________________

Was a multiplex PCR used? NoYesUnknown

Were concomitant viruses identified? NoYesUnknown

Which concomitant viruses were identified ? AdenovirusCoronavirus 229ECoronavirus HKU1Coronavirus OC43Coronavirus NL63Mers-CoVSARS-CoV-2Human MetapneumovirusHuman RhinovirusHuman EnterovirusInfluenza AInfluenza BParainfluenza 1Parainfluenza 2Parainfluenza 3Parainfluenza 4RSVBocavirusOther

Previous SARS-CoV-2/COVID-19 infectionsBased on the information in the patient files, was the Nopatient already previously infected by YesSARS-CoV-2/COVID-19? Unknown

Based on the information in the patient files, is Nothere proof of a previous infection (e.g. available Yesresults of a PCR/antigenic test)?

Based on the information in the patient's files, please give the date of diagnostic (even if just __________________________________approximated) for this previous infection



Page 13

Admission

Please confirm that the patient is rehospitalised same episodefollowing complications of this same episode!

Entry date into the hospital__________________________________

The difference between this first hospitalisation and the sample date is more than 14 days: please make sure this isaccurate!

I confirm that the Hospital Entry Date and the Sample confirmedDate are correct because this hospitalisation iseither:

a follow-up of an hospitalisation due toCOVID-19/Influenza, or an hospitalisation due tocomplications of COVID-19/InfluenzaA nosocomial case

Patient's admissionWhere was the patient hospitalised ? Medicine

GeriatricsIntensive CareSurgeryPaediatricsEmergency RoomNICU/PICUObstetricsOther...

...please, specify where the patient was hospitalised__________________________________

Was the patient hospitalised in an unit dedicated to Nothe reported infection? Yes

Unknown

[Only applicable for hospital consortia] 12

Please provide the ID of the hospital in your 3consortium. 4

56789

((optional))

...code of Unit/Building__________________________________(optional)



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Origin (pre-hospitalisation) DomicileLong term careOther hospitalOther...

...please, specify origin__________________________________

Was the patient in contact with a healthcare personnel Yesprior to hospitalisation (by phone or consultation) ? No

Unknown

Height and Weight during hospitalisationHeight

__________________________________previously reported height (if applicable): ([cm])[height][previous-instance]

Weight__________________________________([kg])

BMI__________________________________([kg/m2])

Obesity No Yes Unknown

This is only a warning message:the BMI calculation and obesity status do not match. Please check the given values. Note that the WHO classification based on BMI is lacking subtleties, so this warning is only present to raiseawareness on a possible error. It does not imply that there is indeed an error.

SymptomsSeverity (CURB-65 score) Confusion (abbreviated Mental Test Score < 9)

Urea (BUN > 19 mg/dL or 7 mmol/L)Respiratory rate > 30 per minuteBlood pressure: diastolic < 60 or systeolic < 90mmHgAge >= 65 yearsNone of the above

Severity (for children) Respiratory distressOxygen saturation < 92%Evidence of severe clinical dehydration orclinical shockAltered conscious levelNone of the above

Total score (each choice counts for 1)__________________________________(0-1 points: low risk >1 points: high risk)



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Additional symptoms CoughRhinitisDiarrhoeaFeverLoss of smellLoss of tasteSore throatMyalgiaHeadacheDyspnoeNone of the above

What was the highest temperature recorded atadmission? __________________________________

(in degrees celsius)

Vaccination status AT ADMISSIONVaccinated against COVID-19 No

YesUnknown

Vaccine name Comirnaty©ModernaAstra-ZenecaJanssen (J&J)UnknownOther...

... please specify vaccine name__________________________________

First injection date (COVID-19)__________________________________

...estimated date ? estimated day, exact monthestimated month and day

((optional))

Had the second dose of COVID-19 vaccine No Yes Unknown



Second injection date (COVID-19)__________________________________


((optional))



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Had the booster dose of COVID-19 vaccine No Yes Unknown



Booster injection date (COVID-19)__________________________________


((optional))

Vaccinated for the current influenza season NoYesUnknown

Vaccination date (influenza)__________________________________

Had the second dose of influenza vaccine NoYesNot applicable (patient >9 years old)Unknown

Vaccination date for second dose (influenza)__________________________________(Only applicable for children < 9 years)

Vaccine name Agrippal®Influvac®Fluad®Mutagrip®Fluarix Tetra®Vaxigrip Tetra®UnknownOther

Was the mother immunized against influenza during this Nochild's pregnancy? Yes

Not applicable (patient >6 months old)Unknown




Page 17

Clinical Complementary Information

Co-morbiditiesDoes the patient have comorbidities?

No Yes

Chronic respiratory disease No Yes Unknown

... please specify__________________________________

Asthma No Yes Unknown

Diabetes No Yes Unknown

Hypertension No Yes Unknown

Chronic cardiovascular disease No Yes Unknown

Chronic renal disease No Yes Unknown

Chronic liver disease No Yes Unknown

Chronic neurological impairment No Yes Unknown

Hematological pathology with immuno-suppression No Yes Unknown

Oncological pathologies No Yes Unknown

Rheumatological and auto-immune pathology withimmuno-suppression

No Yes Unknown

Dementia No Yes Unknown

Transplant (solid organs) No Yes Unknown

HIV-positive No Yes Unknown

Immuno-suppressive treatment No Yes Unknown

History of prematurity No Yes Unknown

Tuberculosis No Yes Unknown

Others No Yes Unknown

.... please specify__________________________________



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Other risk factorsPregnancy No Yes Unknown

Postpartum < 4 weeks No Yes Unknown(Women who gave birth in the 4 weeks before theepisode)

Premature < 24 months No Yes Unknown(Premature children aged < 24 months)

...please specify the gestational week the child wasborn in __________________________________

(Number between 0 and 38)

...please specify weight at birth__________________________________(in kg)

Smoking No Yes Unknown

Is the patient under an ACE inhibitor? No Yes Unknown

Charlson Comorbidity Index (CCI) Please report the SCORE, not the percentage nor the __________________________________estimated risk

[PMID CACI Calculator]

Charlson M, Szatrowski TP, Peterson J, Gold J.Validation of a combined comorbidity index. J ClinEpidemiol. 1994;47(11):1245-51. PMID: 7722560

Antiviral treatment (against Influenza/COVID-19)Prophylactic treatment No Yes Unknown

Treatment of confirmed infection No Yes Unknown

Name of the treatment ChloroquineInterferonLopinavir/RitonavirRemdesivirTenofovirRibavirinDexamethason (PLEASE REPORT DEXAMETHASON UNDERCORTICO-STEROID TREATMENTS, NOT HERE)Other...

Name of the treatment OseltamivirZanamivirBaloxavirOther...



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...please, specify (name of treatment)__________________________________

Start date of Chloroquine treatment__________________________________((if available))

End date of Chloroquine treatment__________________________________((if available))

Start date of Interferon treatment__________________________________((if available))

End date of Interferon treatment__________________________________((if available))

Start date of Lopinovir/Ritonavir treatment__________________________________((if available))

End date of Lopinovir/Ritonavir treatment__________________________________((if available))

Start date of Remdesivir treatment__________________________________((if available))

End date of Remdesivir treatment__________________________________((if available))

Start date of Tenofovir treatment__________________________________((if available))

End date of Tenofovir treatment__________________________________((if available))

Start date of Ribavirin treatment__________________________________((if available))

End date of Ribavirin treatment__________________________________((if available))

Start date of Oseltamivir treatment__________________________________((if available))



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End date of Oseltamivir treatment__________________________________((if available))

Start date of Zanamivir treatment__________________________________((if available))

End date of Zanamivir treatment__________________________________((if available))

Start date of Baloxavir treatment__________________________________((if available))

End date of Baloxavir treatment__________________________________((if available))

Start date of Other treatment__________________________________((if available))

End date of Other treatment__________________________________((if available))

Antibody treatments (against COVID-19)Antibody treatment against confirmed infection No Yes Unknown

Name of the antibody treatment Bamlanivimab/EtesevimabCasirivimab/ImdevimabTocilizumab/ActemraPlasma therapySotrovimabOther...

...please, specify (name of antibody treatment)__________________________________

Start date of Bamlanivimab/Etesevimab treatment__________________________________((if available))

End date of Bamlanivimab/Etesevimab treatment__________________________________((if available))

Start date of Casirivimab/Imdevimab treatment__________________________________((if available))



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End date of Casirivimab/Imdevimab treatment__________________________________((if available))

Start date of Tocilizumab/Actemra treatment__________________________________((if available))

End date of Tocilizumab/Actemra treatment__________________________________((if available))

Start date of Plasma Therapy__________________________________((if available))

End date of Plasma Therapy__________________________________((if available))

Start date of Sotrovimab treatment__________________________________((if available))

End date of Sotrovimab treatment__________________________________((if available))

Start date of Other antibody treatment__________________________________((if available))

End date of Other antibody treatment__________________________________((if available))

Cortico-steroids treatment (against COVID-19)WARNING - If the cortico-steroids are prescribed against COMPLICATIONS, please do not enter them here, but belowin section "Additional treatments (against complications)"

Was the patient treated with cortico-steroids against NoCOVID-19? Yes

Unknown

Name of the cortico-steroid treatment DexamethasonPrednisoneBudesonidOther...

...please, specify (name of cortico-steroid treatment)__________________________________



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Start date of Dexamethason treatment__________________________________((if available))

End date of Dexamethason treatment__________________________________((if available))

Start date of Prednisone treatment__________________________________((if available))

Ending date of Prednisone treatment__________________________________((if available))

Start date of Budesonid treatment__________________________________((if available))

End date of Budesonid treatment__________________________________((if available))

Start date of other cortico-steroids treatment__________________________________((if available))

End date of cortico-steroids treatment__________________________________((if available))

Stay in Intermediate careDid the patient stay in intermediate care ?

No Yes Unknown

Intermediate care (first stay)Intermediate care entry date

__________________________________((if available))

Intermediate care exit date__________________________________((if available))

Non-invasive ventilation No Yes Unknown

Any additional stay in intermediate care to report ? No Yes



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Intermediate care (second stay)Intermediate care entry date

__________________________________((if available))



Any additional stay in intermediate care to report ? No Yes

Intermediate care (third stay)Intermediate care entry date

__________________________________((if available))



Stay in Intensive careDid the patient stay in intensive care ?

No Yes Unknown

Intensive care (first stay)Intensive care entry date

__________________________________((if available))

Intensive care exit date__________________________________((if available))


Invasive ventilation No Yes Unknown

Extra-Corporeal Membrane Oxygenation (ECMO) No Yes Unknown

Any additional stay in intensive care to report ? No Yes



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Intensive care (second stay)Intensive care entry date

__________________________________((if available))





Any additional stay in intensive care to report ? No Yes

Intensive care (third stay)Intensive care entry date

__________________________________((if available))





Complications(probably related to Influenza/COVID-19)Did the patient have any complications ?

No Yes Unknown

Ear/Nose/Throat (ENT) diseases No Yes Unknown

Acute Otitis Media No Yes Unknown

Respiratory diseases No Yes Unknown

Acute respiratory distress syndrome No Yes Unknown



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Pneumonia No Yes Unknown

...pneumonia code[see pneumonia classification]

PN1 PN2 PN3PN4 PN5

...lobar pneumonia No Yes Unknown

...was the pneumonia associated with the reportedinfection?

No Yes Unknown

Paediatric Multisystem Inflammatory Syndrome(PIMS/PMIS)

No Yes Unknown

Cardiac disease No Yes Unknown

Digestive disease No Yes Unknown

Liver disease No Yes Unknown

Renal disease No Yes Unknown

Neurological impairment No Yes Unknown

Encephalitis/Encephalopathy No Yes Unknown

Febrile convulsion No Yes Unknown

Psychiatric alteration No Yes Unknown

Deconditioning syndrome No Yes Unknown

Osteo-articular disease No Yes Unknown

Thrombosis/Embolism No Yes Unknown

Other bacterial infections (excepted pneumonia) No Yes Unknown

Other non-bacterial infections No Yes Unknown

Other complications... No Yes

...please, specify (complications)__________________________________



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Additional treatments (against complications)Antibiotic treatment taken (against complications) No Yes Unknown

Code of given antibiotics (main)[see list of AB codes] __________________________________

([code required - 0 if n/a])

Code of given antibiotics (additional)__________________________________([optional])









Antifungal treatment taken (against complications) No Yes Unknown

Cortico-steroids treatment taken (againstcomplications)

No Yes Unknown

Immunomodulator treatment taken (againstcomplications)

No Yes Unknown




Page 27

Patient Follow Up

TransfersWas the patient transferred during hospitalisation? Yes No Unknown

... the patient was transferred in MedicineGeriatricsIntensive CareSurgeryPaediatricsNICU/PICUObstetricsOthers...

... please specify (one item only)__________________________________

Patient's destinationDeceased Yes No Unknown

... death occured during hospitalisationafter being discharged

Date of death__________________________________

Was the death caused by Influenza/COVID-19? No Yes Unknown

Destination DomicileLTC FacilityAnother hospitalRehabilitationOtherUnknown

... please specify destination__________________________________

Was the patient transferred to an hospital Noparticipating to this surveillance system? Yes



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In which participating hospital was the patient CHUV (Lausanne)transferred? EOC (Lugano)

HFR (Fribourg)Hirslanden AG ZH (Zurich)

Make sure you give the patient ID to the hospital Hirslanden Klinik St. Anna (Luzern)he/she is being transferred to in order to ease the Hopital VS (Sion)follow-up process! HUG (Geneva)

Inselspital (Bern)UKBB (Kinderspital Basel)KISPI (Zurich)KSA (Aarau)KSGR (Graubuenden)KSNW (Niedwalden)KSSG (St.Gallen) & consortiumKSW (Winterthur)LUKS (Luzern)OKS (St.Gallen)Spitaeler SH (Schaffhausen)STGAG KSM (Muensterlingen)USB (Basel)USZ (Zurich)

Why was the patient transferred to another hospital? Lack of spaceFavourable evolution (the patient was put inrecovery care)Unfavourable evolution (the patient needed to beput in intensive care)Unknown

Discharging date from hospital__________________________________

Did the patient leave with any sequelae requiringpost-discharge treatment?

Yes No Unknown

CommentsComments

__________________________________


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