Estonia National SARS-CoV-2 Sequencing cohort

Study profile

Description

The Estonia National SARS-CoV-2 Sequencing cohort study (KoroGeno–EST Study) was to sequence and analyse the complete genomes of SARS-CoV-2 in Estonia. The study carried out the determination of SARS-CoV-2 variants, described the changes in the distribution of SARS-CoV-2 Pango lineages and performed a molecular epidemiological analysis to support the Estonian Health Board in monitoring and managing the outbreaks. Data of the study have been used to conduct in depth analyses of SARS-CoV-2 epidemic in Estonia during 2020 and 2023.

Countries involved: Estonia

Sample size: 2,630 children and 23,031 adults

Related publications:

Soeorg H, Päll T, Abroi A, et al. The effect of policy measures, school holidays and travel on the incidence of SARS-CoV-2 infection in children and adults in Estonia from 2021 to 2022. PLoS One. 2025;20(7):e0327719. Published 2025 Jul 3. doi:10.1371/journal.pone.0327719
Soeorg H, Abroi A, Päll T, et al. Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022. PLoS One. 2024;19(12):e0316213. Published 2024 Dec 20. doi:10.1371/journal.pone.0316213

Metadata collected

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	Data collected?
Demographics
Date of birth (full or MM/YY)	✅
Age at contact	✅
Sex / gender	✅
Country of birth
Ethnic group / race / population sector	✅
Income level
Employment / occupation
Other socio-economic status proxy
Education level
Civil status (‘marital’)
Locality (of health care provision)	✅
Locality (of residence)	✅
Household size
Household composition

Hospitalisation
Admission / discharge dates or duration	✅
Episode dates	✅
Episode type (e.g., general; birth)
Diagnosis (e.g., codes)	✅
Procedures (e.g., codes)	✅
Procedures dates	✅
Dispensed medications	?
ICU admission	✅
Admission type (planned/emergency)
Hospitalisation for COVID-19	✅

Primary care, outpatient care
Date of visit / contact	?
Diagnosis codes
Dispensed medications codes
Dispensed medications date
Primary care utilisation summary

Health status and exposures
Height
Weight
Date of anthropometrics
Chronic / co-morbid conditions~
Medications for chronic conditions
Smoker in household
Current smoker
~ can include obesity

Vaccines
COVID-19 vaccine (timing, doses)	✅
Type of COVID-19 vaccine	✅
Other vaccinations / vaccination history

COVID-19 symptoms & contacts
COVID-19 episodes
COVID-19 symptoms (type, severity, duration)	✅
Influenza-like symptoms (type, timing, duration)
COVID-19 health-seeking behaviour
COVID-19 contacts in household
Medications during C-19 episode

Pregnancy & birth
Date of delivery	✅
Length of gestation	✅
Birthweight	✅
Maternal age at delivery	✅
Pregnancy complications	✅
Smoking pre-pregnancy
Vaccines in pregnancy (non-COVID-19)	✅
Parity / nulliparity	✅
Pre-pregnancy body mass index
Pregnancy outcome (e.g. miscarriage)	✅
Mode of delivery
Sex of baby	✅
Congenital anomalies	✅
Other newborn complications	✅
Placental weight
Antenatal care usage
Currently pregnant

Death
Date of / age at death	✅
Cause of death	✅

COVID-19 laboratory tests
Sample type tested
Sample / specimen collection date	✅
SARS-CoV-2 PCR test date	✅
SARS-CoV-2 PCR pos / neg result	✅
SARS-CoV-2 PCR Ct Value	✅
SARS-CoV-2 LFT test date
SARS-CoV-2 LFT test result
Serology test date
Serology test results
SARS- COV-2 genomic test results
SARS- COV-2 variant/ lineage	✅
Other lab tests

COVID-19 sample collection / storage
Sample type collected
Sample collection date
Sample collection time
Sample processing
Sample quality
Consent to use research sample
Consent to share research sample

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