> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/what-phenotype-files-are-available-in-sandbox-1/other-registers/finnish-national-infectious-diseases-register.md).

# Finnish National Infectious Diseases Register

This page has been last updated for R14.

{% hint style="info" %}
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 ](/finngen-data-specifics/red-library-data-individual-level-data/what-phenotype-files-are-available-in-sandbox-1/other-registers/infectious-disease-registry-covid-19.md)released up to DF11.
{% endhint %}

### 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](https://thl.fi/ohjeita-ammattilaisille/laakarin-tartuntatauti-ilmoitus/ilmoitettavat-taudit-ja-mikrobit#laakarin-tartuntatauti-ilmoitus-ilmoitettavat-taudit-ja-mikrobit). More general information on the register is available on the [THL Infectious Diseases pages](https://thl.fi/en/data-and-statistics/infectious-diseases).

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.

{% hint style="info" %}
For general information on the register, see the [THL Infectious Diseases pages](https://thl.fi/en/data-and-statistics/infectious-diseases). 
{% endhint %}

| VARIABLE                                                 | DESCRIPTION                                                                                                                                                                                           | VALUES                                                                                                                                                                                                                                                                                   |
| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| FINNGENID                                                | FINNGENID                                                                                                                                                                                             |                                                                                                                                                                                                                                                                                          |
| Gender                                                   | Gender                                                                                                                                                                                                | <p><code>1</code> = male<br><code>2</code> = female<br><code>0</code> = no information</p>                                                                                                                                                                                               |
| Age\_in\_years                                           | Age in years                                                                                                                                                                                          |                                                                                                                                                                                                                                                                                          |
| Year\_of\_birth                                          | Birth year                                                                                                                                                                                            |                                                                                                                                                                                                                                                                                          |
| Category\_of\_citizenship                                | Category of citizenship                                                                                                                                                                               | <p><code>1</code> = Finnish<br><code>2</code> = foreigner<br><code>0</code> = no information</p>                                                                                                                                                                                         |
| Healthcare\_worker                                       | Healthcare worker                                                                                                                                                                                     | <p><code>1</code> = yes<br><code>2</code> = no<br><code>0</code> = no information</p>                                                                                                                                                                                                    |
| Hospital\_district                                       | Hospital district                                                                                                                                                                                     | coded \*                                                                                                                                                                                                                                                                                 |
| Country\_of\_contraction                                 | Country of of contraction                                                                                                                                                                             | coded \*                                                                                                                                                                                                                                                                                 |
| Category\_of\_country\_of\_contraction                   | Category of country of contraction                                                                                                                                                                    | <p><code>1</code> = domestic<br><code>2</code> = from abroad</p>                                                                                                                                                                                                                         |
| Origin\_of\_patient                                      | Origin of patient                                                                                                                                                                                     | <p><code>1</code> = Finnish<br><code>2</code> = foreigner<br><code>0</code> = no information</p>                                                                                                                                                                                         |
| Origin\_of\_patients\_geographical\_location             | Origin of patient's geographical location                                                                                                                                                             | coded\*                                                                                                                                                                                                                                                                                  |
| Travel\_abroad                                           | Travel abroad                                                                                                                                                                                         | <p><code>1</code> = yes<br><code>2</code> = no trips<br><code>0</code> = information could not be obtained</p>                                                                                                                                                                           |
| 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)                                                                                                                           | <p><code>2</code> = 0-7 days<br><code>3</code> = 30 days</p>                                                                                                                                                                                                                             |
| 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                                                                                                                                                                                         | <p><code>1</code> = bacterium<br><code>2</code> = virus<br><code>3</code> = fungus<br><code>4</code> = parasite<br><code>5</code> = general finding</p>                                                                                                                                  |
| Microbial\_characteristics                               | Microbial characteristics                                                                                                                                                                             | coded \*                                                                                                                                                                                                                                                                                 |
| Type\_of\_microbial\_characteristic                      | Type of microbial characteristic                                                                                                                                                                      | <p><code>1</code> = type<br><code>2</code> = biotype<br><code>3</code> = serotype<br><code>5</code> = drug susceptibility<br><code>6</code> = toxin production </p>                                                                                                                      |
| 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                                                                                                                                             | <p><code>1</code> = close contact with a family member<br><code>2</code> = close contact at work place<br><code>3</code> = close contact in healthcare<br><code>4</code> = close contact somewhere else<br><code>0</code> = no information</p>                                           |
| Type\_of\_sample                                         | Type of sample                                                                                                                                                                                        | coded \*                                                                                                                                                                                                                                                                                 |
| Method\_of\_detection                                    | Method of detection of the laboratory finding                                                                                                                                                         | <p><code>1</code> = direct microscopy<br><code>2</code> = antigen detection<br><code>3</code> = PCR or other nucleic acid detection<br><code>4</code> = culture<br><code>5</code> = antibodies<br><code>0</code> = other</p>                                                             |
| Laboratory\_type                                         | Laboratory type                                                                                                                                                                                       | coded \*                                                                                                                                                                                                                                                                                 |
| Sample\_in\_culture\_collection                          | Sample in culture collection.                                                                                                                                                                         | <p><code>1</code> = yes<br><code>2</code> = no</p>                                                                                                                                                                                                                                       |
| Reason\_for\_sampling\_physician\_report                 | Reason for sampling from the physician notification                                                                                                                                                   | <p><code>1</code> = symptoms suggestive of coronavirus infection<br><code>2</code> = examination of an asymptomatic person<br><code>0</code> = no information</p>                                                                                                                        |
| Reason\_for\_sampling\_lab\_report                       | Reason for sampling from laboratory notification                                                                                                                                                      | <p><code>1</code> = suspected epidemic<br><code>2</code> = travel or contact abroad<br><code>3</code> = follow-up<br><code>4</code> = border test<br><code>7</code> = symptoms<br><code>8</code> = screening<br><code>0</code> = no information</p>                                      |
| Symptoms\_of\_the\_disease                               | Symptoms of the disease                                                                                                                                                                               | <p><code>1</code> = yes<br><code>2</code> = no<br><code>0</code> = no information</p>                                                                                                                                                                                                    |
| Chronic\_disease                                         | Long-term illness                                                                                                                                                                                     | coded \*                                                                                                                                                                                                                                                                                 |
| Hospital\_treatment                                      | Hospital treatment                                                                                                                                                                                    | <p><code>1</code> = yes<br><code>2</code> = no<br><code>0</code> = no information</p>                                                                                                                                                                                                    |
| Intensive\_care                                          | Intensive care (COVID-19)                                                                                                                                                                             | <p><code>1</code> = yes<br><code>2</code> = no<br><code>0</code> = no information</p>                                                                                                                                                                                                    |
| Respiratory\_support                                     | Respiratory support given (COVID-19)                                                                                                                                                                  | <p><code>1</code> = extracorporeal membrane oxygenation<br><code>2</code> = no given respiratory support <br><code>3</code> = other oxygen therapy <br><code>4</code> = ventilation incl. non-invasive ventilation<br><code>0</code> = no information</p>                                |
| Treatment\_outcome\_status                               | Patient's treatment outcome / status (COVID-19)                                                                                                                                                       | <p><code>1</code> = alive/recovered/cured<br><code>2</code> = patient still in treatment, not recovered<br><code>3</code> =  died of COVID-19 coronavirus infection<br><code>4</code> = died of other cause<br><code>5</code> = cause of death unknown<br><code>0</code> = not known</p> |
| Type\_of\_report                                         | Type of report                                                                                                                                                                                        | <p><code>1</code> = Doctor's report<br><code>2</code> = Laboratory's report</p>                                                                                                                                                                                                          |
| 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.