Replication Data for: Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data

This is a replication dataset for the submitted manuscript "Revealing the extent of the…".

The related study was conducted to estimate the SARS-CoV-2 pandemic peak and COVID-19 disease burden including reported severe cases and deaths in the major urban counties in Kenya. National surveillance PCR tests, serological surveys, and mobility data were used to develop and fit a county-specific transmission model in the country.

These datasets presented contain the number of positive PCR-confirmed swab tests for each county by date of sample collection (21st Feb to 6th August), the number of positive and negative serological results for each county by date of sample collection (21st Feb to 6th August), number of deaths with a PCR-confirmed swab test for each county by recorded date of death (21st Feb to 6th August), the total number of swab samples collected in Mombasa county, and analyzed at Kemri-Wellcome Research Program testing center (21st Feb – 27th June), and summary data of Kenyan epidemic, including reported total number of test performed. The datasets are used for COVID-19 forecasts.

Data Analysis Code Avaialbility The code used to simulate transmission in Kenyan counties and is fitted to the data provided here is available in the open access Github repository github.com . This includes a sequence of notebooks which outline each step of the analysis to aid reproducibility.