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Surveillance and epidemiologic evaluation of COVID-19, DFID-2019 Serosurveillance Project

Kenya, 2021
Health and Well-Being (HaW)
African Population and Health Research Center, KEMRI Wellcome Trust - Kilifi,
Last modified December 08, 2022 Page views 39195 Metadata DDI/XML JSON

Identification

IDNO
APHRC-KEN-SEECK-2021-v1.0
Title
Surveillance and epidemiologic evaluation of COVID-19, DFID-2019 Serosurveillance Project
Subtitle
DFID-2019 Serosurveillance Project
Country
Name Country code
Kenya KEN
Abstract
With more than 10 million confirmed SARS-CoV-2 infections, 500,000 deaths reported by 1st July 2020 and enormous costs to the global economy, the coronavirus disease 2019 (COVID-19) pandemic ranks among the most urgent crises in recent history. While
high-income countries appear to be approaching their first epidemic peak, most Lowand Middle-Income Countries (LMICs) are anticipating an exponential increase in cases. In Kenya, over 6,000 cases have been confirmed among more than 170,000
individuals tested and close to 150 deaths reported as of 1st July 2020. The national COVID-19 response is led by the National Emergency Response Committee overseeing the Emergency Operation Centre (EOC). EOC coordinates technical activities at
national level and with counties through Rapid Response Teams implementing case identification, contact tracing and isolation.

RT-PCR assays from nasopharyngeal (NP) and oropharyngeal (OP) samples remain the molecular test of choice for the aetiologic diagnosis of SARS-CoV-2 infection currently taking place at six laboratories across the country (including KEMRI Centre for
Geographic Medicine, Coast). The sudden increase in demand for nasopharyngeal swabs and viral transport medium generated by the pandemic has exerted pressure on global supply chains for these supplies and hampered mass testing in the country.
The government has instituted measures to slow the progression of the pandemic in Kenya, including promotion of hand hygiene, cough etiquette, and wearing of face masks in public areas, limiting social gatherings, suspension of international passenger
flights into and out of Kenya, extended school and workplace closures, introducing a nationwide curfew, restricting travel into and out of “hotspot” counties, and mandatory quarantine for suspected cases. These interventions are aimed at “flattening the
epidemic curve” to avert deaths arising from a surge in demand for services exceeding the capacity of the health system. However, these measures are also associated with substantial economic and societal costs. Governments are therefore faced with the
dilemma of choosing between minimizing deaths arising directly from COVID-19 and the negative secondary impact of the mitigation measures. The optimal solution to this dilemma relies on the availability of accurate and timely surveillance data to inform
planning while strengthening health service delivery.

KEMRI-CGMR-C has a longstanding partnership with the Ministry of Health providing technical support through research, policy engagement and capacity building through its four scientific departments, including well-established high quality clinical surveillance
across various health facilities participating in the Clinical Investigation Network (CIN),the Childhood Acute Illness and Nutrition Network (CHAIN) and at the Kilifi County Hospital. This protocol describes a series of clinical and seroepidemiological surveillance and research activities aimed primarily at providing evidence to support the national COVID-19 response in Kenya. Specifically, we aim to (i) undertake surveillance to describe the clinical, demographic, and genomic profile, trends, clinical course and outcomes of patients with acute respiratory illness including COVID-19 and including
post-COVID-19 multisystem inflammatory syndrome, (ii) use serological assays to estimate the seroprevalence of SARS-CoV-2 antibodies among target populations in Kenya, (iii) to determine the quantity, duration and contribution to transmission of faecal shedding of SARS-CoV-2 in settings where risk of faecal-oral contamination is high (iv) examine the availability and utilization of resources and organization of health services for the management of COVID-19 and (v) describe the secondary effects of COVID-19
on essential routine health services.The surveillance work proposed here will provide complementary data on COVID-19 in
the Kenyan population, organization of available resources for clinical management, and how these change over time to refine existing models of the projected course of the epidemic. The findings will ultimately inform contextualised recommendations on where,
among whom, and when existing control strategies should be modified and to inform planning for the possible escalation of the epidemic in Kenya

Version

Version Date
2021-06-17
Version Notes
This is the first complete version.

Scope

Keywords
Keyword
Serocurveillance
General population

Coverage

Geographic Coverage
National coverage
Unit of Analysis
This study analyzed data from blood samples from sociodemographic data from Individual respondents who are residents of Korogocho and Viwandani
Universe
The survey covered all the DSS household members (usual residents) from three urban settings - Nairobi, Kilifi and Kisumu

Producers and sponsors

Authoring entity/Primary investigators
Agency Name
African Population and Health Research Center
KEMRI Wellcome Trust - Kilifi
Producers
Name Affiliation Role
Ministry of Health Collaborator implementing partner
Funding Agency/Sponsor
Name Abbreviation
Department for International Development DFID
Other Identifications/Acknowledgments
Name Affiliation Role
DFID Funder Funded project activities
Korogocho and Viwandani administration Community Sensitization and community mobilization
Koch FM and Reuben FM Community Sensitization

Sampling

Sampling Procedure
This study was conducted on a randomly selected population of 850 adults and children living within the health and demographic surveillance system area (HDSS) run by APHRC. We used the Nairobi Urban Health and Demographic Surveillance System (NUHDSS) database as the sampling frame. We collect a single blood sample from each participant (5ml from adults and 2ml from
children) and analysed for SARS-CoV-2 antibodies.
Deviations from the Sample Design
There was no sample for under - one year old participants, because the NUHDSS register had not been updated for one year, occasioned by COVID-19. We engaged Community Health Volunteers/Mobilizers to come up with a list of children born in the last one year and this served as our sampling frame for the under-one year age group.
Response Rate
100%
Weighting
na

Data Collection

Dates of Data Collection (YYYY/MM/DD)
Start date End date
2021-01-21 2021-05-18
Mode of data collection
Face-to-face [f2f]
Supervision
The data was collected by a team of 11 field staff - including 9 field interviewers, 1 supervisor and 1 lab Tech. This team was coordinated by a reseach officer. Overal oversight for the project was provided by the PI.
The Field interviewers were divided into mobilizers (who conducted consenting at household level) and interviewers who conducted interviews at the site office. Lab activities were conducted by the Lab Tech.
Type of Research Instrument
The study used a participants' questionnaire (SARS COV-2 Sero-survey - Questionnaire) to collect information from the participants. The questionnaire was developed in English, and translated to swahili.
Information captured in the questionnaire included:

Sociodemographic information: Participants name, ethnicity, education, religion, age, gender, place of residence.

Health information: Access to prevention services, risk of exposure to COVID 19, outmigration and inmigration information, vaccination status of children participants, laboratory information including blood sample collection and blood grouping.

Data collection was conducted electronicallay. Participants were assigned unique numbers which were used to label blood samples.

Data Processing

Cleaning Operations
There was no data entry because the study questionnaire was uploaded to an online platform. Discrepancies realized in the generated database were resolved through concensus in data review meetings. Consultations were made with the PI and the larger KEMRI team on a needs basis.
Other Processing
The blood Samples were centrifuged and serum separated onsite, stored at -80°C at the main office for transportation to the Kilifi Wellcome Trust Research Program (KWTRP) laboratories for COVID-19 IgM and IgG antibody analysis.

Data Appraisal

Estimates of Sampling Error
For each HDSS location, the population register was used to select a random sample of residents across all age groups targeting 800 persons in an age-stratified sample as 50 in each 5-year age band between 15-64 years and above and 100 in 5-year band from 0-14 years. This target sample size wouldl yield 300 participants <15 years which would be enough to estimate 1% seroprevalence with a 2% margin of error. It would also give 500 participants in the 15-64-year-age group which would be enough to estimate a seroprevalence of 3-5% with <5% error margin.

Data access

Contact
Name Email URI
African Population and Health Research Center info@aphrc.org www.aphrc.org
Conditions
APHRC data access condition

All non-APHRC staff seeking to use data generated at the Center must obtain written approval to use the data from the Director of Research.
This form is developed to assess applications for data use and facilitate responsible sharing of data with external partners/collaborators/researchers. By entering into this agreement, the undersigned agrees to use these data only for the purpose for which they were obtained and to abide by the conditions outlined below:

1.Data Ownership:
The data remain the property of APHRC; any unauthorized reproduction and sharing of the data is strictly prohibited. The user will, therefore, not release nor permit others to use or release the data to any other person without the written authorization from the Center.

2.Purpose:
The provided data must be used for the purpose specified in the Data Request Form; any other use not specified in the form must receive additional or separate authorization.

3.Respondent Identifiers:
The Center is committed to protecting the identity of the respondents who provide information in its research. All analytical data sets (both qualitative and quantitative) released by the Data Unit MUST are stripped of respondent identifiers to protect the identity of the respondents. By accepting to use APHRC data, the user is pledging that he/she will not, under any circumstance, regenerate the identifiers or permit others to use the data to learn the identity of any individual, household or community included in any data set.

4.Confidentiality pledge:
The user will not use nor permit others to use the data to report any information in the data sets that could identify, directly or by inference, individuals or households.

5.Reporting of errors or inconsistencies:
The user will promptly notify the Head of the Statistics and Survey Unit any errors discovered in the data as soon as the errors are discovered.

6.Publications resulting from APHRC data:
The Center requires external collaborators to work with APHRC staff on all publications resulting from its data. In order to facilitate this, lead authors should send a detailed concept note of the paper (including the background, rationale, data, analytical methods, and preliminary findings) to the Principle Investigator (or Theme Leader) for the project (with a copy to the Director of Research), who will circulate the abstract to concerned researchers for possible expression of interest in participating in the publication as co-authors. Any exception to the involvement of APHRC staff should be approved by the Director of Research, APHRC.

7.Security:
The user will take responsibility for the security of the data by ensuring that the data are used and stored in a secure environment where access is password protected. This will ensure that non-authorized people should not have access to the data.

8.Loss of privilege to use data:
In the event that APHRC determines that the data user is in violation of the conditions for using the data, or if the user wishes to cancel this agreement, the user will destroy the data files provided to him/her. APHRC retains the right to revoke this agreement or informs publishers to withhold publication of any work based wholly or in part on its data if the conditions for using the data are violated.

9.Acknowledgement:
Any work/reports from this data must acknowledge APHRC as the source of these data. For example, the suggested acknowledgement for NUHDSS data is:
"This research uses livelihoods data collected under the longitudinal Nairobi Urban Health and Demographic Surveillance System (NUHDSS) since 2006. The NUHDSS is carried out by the African Population and Health Research Center in two slums settlements (Korogocho and Viwandani) in Nairobi City."Additionally all funders, the study communities that provided the data, and staff who collected and analyzed or processed the data should be acknowledged.

10.Deposit of Reports/Papers:
The user should submit electronic and paper copies of all publications generated using APHRC data to the Policy Engagement and Communications Department, with copies to the Director of Research.

11.Change of contact details:
The user will promptly inform the Director of Research of any change in your personal details as contained on this data request form.
Citation requirement
Use of the dataset must be acknowledged using a citation which would include:
- the Identification of the Primary Investigator
- the title of the survey (including country, acronym and year of implementation)
- the survey reference number
- the source and date of download

Metadata production

Document ID
APHRC-KEN-SEECK-2021-v1.0
Producers
Name Abbreviation Affiliation Role
African Population and Health Research Center APHRC KEMRI Funder
Date of Production
2021-06-17
Document version
Version 1.0(June 2021)