Finnish National Infectious Diseases Register

This page has been last updated for R14.

The Finnish National Infectious Diseases Register data file was introduced in Data Release 14. It covers all notifiable diseases and microbes reported the Finnish Institute for Health and Welfare (THL). It also includes COVID-19 infections, replacing the COVID-19 data file released up to DF11.

Sandbox directory

The data is available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/

Please refer to the sandbox readme for the full variable list and coding.

Description

The Finnish National Infectious Diseases Register (Tartuntatautirekisteri) is maintained by the Finnish Institute for Health and Welfare (THL) under the Communicable Diseases Act and Decree. It is based on mandatory notifications submitted by physicians and laboratories, with data collected since 1995. Register data is used for the prevention, control and research of infectious diseases. The microbes and diseases captured are those defined as notifiable under Finnish law; see THL's list of notifiable diseases and microbes. More general information on the register is available on the THL Infectious Diseases pages.

In FinnGen, data from this register is provided as two datasets: the original COVID-19 dataset, and a newer complete dataset covering all notifiable diseases and microbes (including COVID-19). For release-specific details on file contents and variables, always refer to the readme in the sandbox directory.

For general information on the register, see the THL Infectious Diseases pages.

VARIABLE	DESCRIPTION	VALUES
FINNGENID	FINNGENID
Gender	Gender	1 = male 2 = female 0 = no information
Age_in_years	Age in years
Year_of_birth	Birth year
Category_of_citizenship	Category of citizenship	1 = Finnish 2 = foreigner 0 = no information
Healthcare_worker	Healthcare worker	1 = yes 2 = no 0 = no information
Hospital_district	Hospital district	coded *
Country_of_contraction	Country of of contraction	coded *
Category_of_country_of_contraction	Category of country of contraction	1 = domestic 2 = from abroad
Origin_of_patient	Origin of patient	1 = Finnish 2 = foreigner 0 = no information
Origin_of_patients_geographical_location	Origin of patient's geographical location	coded*
Travel_abroad	Travel abroad	1 = yes 2 = no trips 0 = information could not be obtained
Approx_sampling_day	Date of sampling, approximate (randomized +/- 1-15 days from the exact date)
Approx_starting_date_symptoms	Starting date of symptoms, approximate (randomized +/- 1-15 days from the exact date)
Time_passed_between_compiling_statistics_and_death	Time passed between compiling statistics and death (2= 0-7 days, 3=30 days)	2 = 0-7 days 3 = 30 days
Disease	Disease	coded *
Diagnosis_code	Diagnosis code for the clinical diagnosis, as reported by the physician.	coded *
Microbe	The microbe finding reported on the laboratory's infectious disease notification.	coded *
Microbe_genera	The reported microbe together with all of its ancestors in the taxonomic tree. Derived within the register rather than reported directly.	coded *
Microbe_class	Microbe class	1 = bacterium 2 = virus 3 = fungus 4 = parasite 5 = general finding
Microbial_characteristics	Microbial characteristics	coded *
Type_of_microbial_characteristic	Type of microbial characteristic	1 = type 2 = biotype 3 = serotype 5 = drug susceptibility 6 = toxin production
COVID_19_virus_variant	Virus variant of the COVID-19 finding	coded *
Close_contact_with_a_COVID_19_case_or_suspect	Close contact with a confirmed or suspected COVID-19 case	1 = close contact with a family member 2 = close contact at work place 3 = close contact in healthcare 4 = close contact somewhere else 0 = no information
Type_of_sample	Type of sample	coded *
Method_of_detection	Method of detection of the laboratory finding	1 = direct microscopy 2 = antigen detection 3 = PCR or other nucleic acid detection 4 = culture 5 = antibodies 0 = other
Laboratory_type	Laboratory type	coded *
Sample_in_culture_collection	Sample in culture collection.	1 = yes 2 = no
Reason_for_sampling_physician_report	Reason for sampling from the physician notification	1 = symptoms suggestive of coronavirus infection 2 = examination of an asymptomatic person 0 = no information
Reason_for_sampling_lab_report	Reason for sampling from laboratory notification	1 = suspected epidemic 2 = travel or contact abroad 3 = follow-up 4 = border test 7 = symptoms 8 = screening 0 = no information
Symptoms_of_the_disease	Symptoms of the disease	1 = yes 2 = no 0 = no information
Chronic_disease	Long-term illness	coded *
Hospital_treatment	Hospital treatment	1 = yes 2 = no 0 = no information
Intensive_care	Intensive care (COVID-19)	1 = yes 2 = no 0 = no information
Respiratory_support	Respiratory support given (COVID-19)	1 = extracorporeal membrane oxygenation 2 = no given respiratory support 3 = other oxygen therapy 4 = ventilation incl. non-invasive ventilation 0 = no information
Treatment_outcome_status	Patient's treatment outcome / status (COVID-19)	1 = alive/recovered/cured 2 = patient still in treatment, not recovered 3 = died of COVID-19 coronavirus infection 4 = died of other cause 5 = cause of death unknown 0 = not known
Type_of_report	Type of report	1 = Doctor's report 2 = Laboratory's report
Reporting_group	The infectious diseases register's tree-structured finding classification. Each subgroup also implies its parent group, and only one group can occur per parallel level of the tree for a given case.	coded *
Reporting_group_tree	The higher, more general level of the reporting classification, sitting above Reporting_group.	coded *
Target_of_monitoring_the_history_also	Target of monitoring, incl. history	coded *

*See value descriptions from the infectious disease register value dictionary in the sandbox.