COVID-19 has emerged as global pandemic during the past few months, with an unprecedented impact on public health, and society more generally. Virus epidemiology is poorly understood, as are factors influencing the diverse clinical picture. To date most cases have been seen in high income countries and consequently COVID-19 diagnostics and research have mainly been set-up in these settings. Outstanding questions include an understanding of how the virus spreads and how it causes pathology. A particular gap in current knowledge is the effect of HIV and tuberculosis (TB) on the outcomes of COVID-19 disease as these two conditions impair the host immune response to other infectious disease. Understanding how these three pandemics interact is crucial. We have developed a proposal that will answer critical questions concerning COVID-19 disease epidemiology in the context of low resource countries with high burden of poverty, and in the presence of high rates of TB and HIV, namely, Namibia and Botswana. Given that there are currently few cases of COVID-19 diagnosed in both countries, the project will document how the virus spreads within susceptible populations. The development of this proposal is highly collaborative and interdisciplinary, with investigators from Namibia and Botswana working closely with colleagues in Europe. We will also work with an NGO in Namibia, Health Poverty Action, to support rapid implementation.

The project includes two studies that will be conducted sequentially. The first study will follow the WHO protocol for household transmission investigations in the context of COVID-19. It will explore transmission frequency and describe the clinical spectrum of disease. Samples collected will also serve as basis for COVID-19 molecular epidemiology and host immunological response. The second study will evaluate the presentation, diagnosis and clinical characteristics of individuals presenting to sentinel health facilities in both countries. The project will have a strong laboratory strengthening component which will enhance COVID-19 laboratory and research capacity. This will include the development of skills and knowledge for diagnostic testing and COVID-19 sequencing and will build scientific and research capacity.

The findings from this project will provide robust data to assist in guiding national responses to COVID-19 in both countries as well as assisting with our understanding of the pathogenesis of the virus in the context of TB and HIV, in turn providing vital information on how to deliver clinical care and how to design therapeutics and vaccines.

Inclusion Criteria:

• Household contact study: all household members of Covid-19 index cases in selected areas
• Healthcare facility study: all attendees of selected primary healthcare facilities

Exclusion Criteria:

• Household contact study: non-household members of Covid-19 index cases in selected areas; individuals not giving consent
• Healthcare facility study: individuals not giving consent

Household contact study: household members of Covid-19 index cases in one urban and one rural region of Namibia and Botswana, respectively.

Healthcare facility study: facility attendees at one urban and one rural primary healthcare facility in Namibian and Botswana, respectively.