Western Cape Province Study

Study profile

Description

This study is a population-level cohort study linking clinic data and genomic surveillance data to monitor SARS-CoV-2 outcomes, vaccination, and variant trends in the Western Cape Province, South Africa. The study utilises electronic health records and integrates data across various sources, including COVID-19 diagnoses, clinical outcomes, admissions, mortality data, and vaccination records.

Countries involved: South Africa

Sample size: 1.2 million children and adolescents aged <20 years and ~120,000 pregnancies per year

Related publications:

Hussey H, Davies MA, Heekes A, et al. Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis. Int J Infect Dis. 2022;118:150-154. doi:10.1016/j.ijid.2022.02.051
Davies MA, Morden E, Rousseau P, et al. Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa. Int J Infect Dis. 2023;127:63-68. doi:10.1016/j.ijid.2022.11.024
Davies MA, Kassanjee R, Rousseau P, et al. Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa. Trop Med Int Health. 2022;27(6):564-573. doi:10.1111/tmi.13752
Kassanjee R, Davies MA, Ngwenya O, et al. COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa. J Int AIDS Soc. 2023;26(6):e26104. doi:10.1002/jia2.26104
Kehoe K, Morden E, Zinyakatira N, et al. Lower respiratory tract infection admissions and deaths among children under 5 years in public sector facilities in the Western Cape Province, South Africa, before and during the COVID-19 pandemic (2019 – 2021). S Afr Med J. 2024;114(3):e1560. Published 2024 Mar 18. doi:10.7196/SAMJ.2024.v114i3.1560
Kassanjee R, Davies MA, Heekes A, et al. COVID-19 vaccine uptake and effectiveness by time since vaccination in the Western Cape province, South Africa: An observational cohort study during 2020-2022. Preprint. medRxiv. 2024;2024.01.24.24301721. Published 2024 Jan 25. doi:10.1101/2024.01.24.24301721
Kehoe K, Morden E, Zinyakatira N, et al. Diarrhoeal admissions among children aged <5 years in public sector facilities in Western Cape Province, South Africa, before and during the COVID-19 pandemic (2019 – 2021). S Afr Med J. 2025;115(7):e2726. Published 2025 Aug 1. doi:10.7196/SAMJ.2025.v115i7.2726

Metadata collected

Click to view

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

✅

# subset

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

✅

^if results in hospitalisation

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

Access metadata