Surveillance, modeling and epidemiological evaluation of COVID-19 in Kenya

The KWTRP research teams are conducting a series of surveillance and epidemiological evaluation activities to improve the understanding of COVID-19 in Kenya and support the national and counties’ emergency response.

What questions are we trying to answer?

The researchers aim is to collect and analyse data to help understand various aspects of COVID-19, including:

• The pattern of COVID-19 cases,
• The pattern of exposure to SARS-CoV-2 among different groups
• Individual characteristics that may increase or lower the risk of severe COVID-19
• The impact of COVID-19 on health care services

They will apply this knowledge to guide national planning to limit the negative effects of the pandemic in Kenya. They will investigate questions such as:

• How common is COVID-19 infection in children and adults admitted to hospital and healthy adults such as healthcare workers?
• What proportion of the general population has been exposed to SARS-CoV-2?
• How does COVID-19 affect patients that are undernourished or that have vitamin D/iron deficiency or that are infected with HIV?
• How have hospitals tried to provide routine and COVID-19 related care?

The team is doing this work in several different groups of people across 18 Kenyan Counties.

What does the surveillance and modeling involve?

Clinical surveillance of COVID-19

They will draw on hospital documentation collected routinely for non-research purposes and national/ County COVID-19 surveillance documents to establish the rate of all suspected and confirmed COVID-19 cases (the burden of COVID-19) and to describe the presentation, course, outcomes and risk factors for outcomes.

They will also collect blood and stool samples at admission, discharge and at several timepoints after admission to understand the presentation, course and outcomes of SARS-CoV-2 infection in clinically vulnerable patients – such as severely malnourished children, individuals with micronutrient deficiencies, and adults with immunodeficiency or chronic non-communicable conditions – as well as the role of fecal shedding.

Surveillance for SARS-CoV-2 infection

They also aim to determine the rate of active and past SARS-CoV-2 infection in several groups in the Kenyan population including:

• Healthcare workers (approximately 1500)
• Other non-healthcare frontline workers, i.e., workers likely to be at high risk of being exposed to SARS-CoV-2 or working in jobs important for the functioning of the economy (approximately 700)
• Residents of the Kilifi Health and Demographic Surveillance System (HDSS) and two other HDSS in Kenya, in Nairobi and Kisumu. This will represent the general population (approximately 800 from each HDSS)
• Antenatal clinic (ANC) clients (approximately 135 per month)
• Blood donors (approximately 300-500 per month).

Surveillance for past SARS-CoV-2 infection identified from antibodies in blood (serosurveillance) will entail collection of blood samples in healthcare workers, other non-healthcare frontline workers and HDSS residents. Each healthcare worker will provide samples at four timepoints over one year while each non-healthcare frontline worker will be sampled three times over 6 months. Serosurveillance in ANC clients and blood donors will use residual (leftover) blood from routine activities.

We will investigate antibody responses and waning by collecting blood samples from asymptomatic and symptomatic SARS-CoV-2 infected individuals at a number of sampling points through the year following positive diagnosis.  Blood samples will be collected from approximately 200 asymptomatic children and adults, and all symptomatic children and adults at 2 weeks, 4 weeks, 6 weeks, 8 weeks, 3 months, 6 months, 9 months and 12 months after diagnosis.

Understanding the effect of COVID-19 on health services

Hospital managers, senior and junior clinicians (doctors, nurses, pharmacists) will be interviewed about their experiences of the changes made in hospitals to help provide care for COVID-19 cases (e.g. use of new equipment or reorganizing of wards) and how they have managed to sustain routine services. Health care capacity monitoring will also be performed at pre-determined intervals.

Surveillance of Mortality

To understand the impact of COVID-19 on health outcomes, we are conducting mortality surveillance at the Kilifi health and demographic surveillance system (HDSS). This will provide information that will shed some light on the true health impact of the pandemic.

Modeling the COVID-19 pandemic

We are carrying out epidemiological modeling of the pandemic to provide predictions on the transmission, health impacts, and intervention and health services impacts of the pandemic. These predictions are used by the government to inform decisions about intervention selection and implementation and resource planning. Our modeling team is part of the Kenya COVID-19 modeling technical working group of the ministry of health.

Other surveillance and epidemiologic evaluation studies

We will also conduct micronutrient testing, genetic testing and studies of how SARS-CoV-2 infection affects how cells function.  These studies will not directly enroll participants but will use samples collected through other studies and activities.