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Determining the epidemiological parameters of Covid-19 through a household transmission study in a rural area of South Africa and Kenya

Acronym: COREP

Coordinator: Prof. Till Winfred Bärnighausen

Funding:  The European & Developing Countries Clinical Trials Partnership (EDCTP; Grant RIA2020EF-3026)

Participating Organisations: 

Fundación Privada Instituto de Salud Global Barcelona (ISGLobal), Spain

The Aga Khan University (AKU) - Kenya, Kenya

Department of Health, Kilifi County-Kenya, Kenya

Wits Reproductive Health and HIV Institute (WRHI), South Africa

Burnet Institute, Australia

University of Washington, United States

List of the other investigators

  1. Prof. Stanley Luchters, Aga Khan University, Nairobi, Kenya.
  2. Prof. Matthew F. Chersich, Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, South Africa.
  3. Prof Gijs Walraven, Aga Khan Development Network
  4. Prof. Emilio Letang, Fundación Privada Instituto de Salud Global Barcelona (ISGLobal), Spain
  5. Professor David Anderson, Burnet Institute, Australia.
  6. Prof. Jennifer Balkus, University of Washington, United States.
  7. A/Prof Anthony Ngugi, Aga Khan University, Nairobi, Kenya.
  8. A/Prof Shaheen Sayed, Aga Khan University, Nairobi, Kenya.
  9. Dr Gloria Maimela, Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, South Africa.
  10. Dr Alain Vandormael, Heidelberg University Medical School, Germany.
  11. Dr Julia Katherine Rohr, Harvard University, United States.
  12. Mrs Evaline Lang'at, Department of Health, Kilifi County, Kenya.

Research team members

  1. Dr Maureen Kimani, Kenya Ministry of Health, Department of Community Health Sciences, Kenya
  2. Dr John Kiiru, Kenya Ministry of Health, Department of Laboratory Sciences, Kenya
  3. Dr Francis Ndungu, KEMRI Kilifi, Kenya
  4. Mr Ben Kitole, Kilifi County Health Department, Kenya
  5. Mrs Caroline Gichuki, Aga Khan University, Kenya
  6. Mrs Eunice Irungu, Aga Khan University, Kenya
  7. Ms. Joy Mauti, Heidelberg University, Germany
  8. Dr Catherine Martin, Wits Reproductive and HIV Institute, Faculty of Health Sciences, University of Witwatersrand
  9. Ms. Dieyna Drame, Harvard University, USA


The epidemiological parameters of SARS-CoV-2 infection in sub-Saharan Africa are largely unknown and require population-, and household- and individual-level enquiry. Similarly, strategies for decentralised diagnostic testing for SARS-CoV-2 need adaptation and evaluation. This project addressed research gaps in the natural history and epidemiological parameters of SARS-CoV-2 infection using serologic-surveillance methodologies and household-cluster investigations, as per WHO COVID-19 study protocols. Secondarily, the project aimed to identify efficient, feasible, cost-effective approaches to the decentralized diagnosis of SARS-CoV-2 infection in rural areas.  Finally, managing topics around risk factors infection and transmission during the implementation of the project anecdotal vaccine uptake and hesitancy were observed. 
To address this, four major studies were developed in two Sub-Saharan countries from September 2020 to April 2022. Both countries established the project in rural areas.  In Kenya, in the Kaloleni and Rabai sub-counties of Kilifi where the age distribution is as follows: 0-4=12.9%, 5-11=16.6%, 12-17=15.9%, 18-34=26.5%, 35-49=12.2%, 50-64=7.6%, and >=65+ years=8.3%.  In South Africa, in the Thabong sub-district, Lejweleputswa in the Free State province where the age distribution is as follows: <15=26.5%, 15-64=68.4%  and ≥65=5.1%.
In South Africa a household-cluster investigation was conducted where 26 index cases and 95 household contacts were enrolled. Of these, 3 index cases and their household contacts withdrew consent for participation; resulting in 23 index cases and 83 household contacts being followed up for 28 days and included in all analyses. The main results found that of the 83 household contacts, 20 from 11 households had a positive SARS-CoV-2 PCR at enrolment. These were classified as coprimary cases. During follow-up, of the 63 contacts who were SARS-CoV-2 PCR negative at enrolment, a further 5 became PCR positive – 4 on day 7 and 1 on day 28. In addition to the 5 who were PCR positive, a further 5 household contacts had SARS-CoV-2 antibodies detected during the follow-up period. Cumulatively, 10 contacts (16%) had incident SARS-CoV-2 infection; 5 on day 7 and 5 on the day 28 visit. These incident cases originated from 9 (39%) households. The incidence rate was estimated as 5.8 per 1,000 person-days (95% CI 3.14 – 11.95).
In Kenya, three studies were conducted within a demographic and health information registry:  Kaloleni/Rabai Community Health and Demographic Surveillance System (KR-HDSS). There are approximately 310 community health volunteers in KR-HDSS (+/-30/cluster, and 60 households per community health volunteer). Community health volunteers collect KR-HDSS data 6 monthly from each house in their allocated area. The volunteers provide health services to the households, according to national guidelines and have established close relationships with the community (community health volunteers are referred to as community health workers hereafter).
The first study was a household-transmission study where 47 participants from 11 households were enrolled. These included 11 primary cases, and 36 household members. There were 5 households with a co-primary case (based on PCR), and all households had a co-primary case based on the Wantai Antibody test. At baseline among the 36 contacts, 17 at-risk participants were either PCR plus antibody-negative or they were negative on one test with the other result missing. Among these 17, only 1 participant became antibody positive at day 7 (PCR negative).
The second study was on Sero-surveillance where 524 eligible households were enrolled. Over 24 weeks, repeated serosurveys were conducted with symptom screening and collected Dried Plasma Spots (VL Plasma®) from finger-prick specimens which were then tested for ELISA serology (both dimeric IgA and IgG). In total, 5 rounds of data and sample collection were conducted. In each round, the following number of participants took part: Round 1 (baseline; 446 households with 1,649 participants); round 2 (370 households with 1,744 participants); round 3 (394 households with 1,863 participants), round 4 (393 households with 1,862 participants), and round 5 (391 households with 1,759 participants).
Thirdly, a vaccine hesitancy qualitative study was conducted in, Kenya. In total, 18 in-depth interviews and 6 focus group discussions were conducted. The primary analyses of the results of all studies are currently being prepared.


Duration: 20 months – completed 30.04.2022

Contact Person: Joy Mauti (joy.mauti(at)uni-heidelberg.de)