Estimating excess mortality during the COVID-19 pandemic from a population-based infectious disease surveillance in two diverse populations in Kenya, March 2020-December 2021

Robust data on the impact of the COVID-19 pandemic on mortality in Africa are relatively scarce. Using data from two well-characterized populations in Kenya we aimed to estimate excess mortality during the COVID-19 pandemic period. The mortality data arise from an ongoing population-based infectious disease surveillance (PBIDS) platform, which has been operational since 2006 in rural western Kenya (Asembo, Siaya County) and an urban informal settlement (Kibera, Nairobi County), Kenya. PBIDS participants were regularly visited at home (2–3 times a year) by field workers who collected demographic data, including deaths. In addition, verbal autopsy (VA) interviews for all identified deaths are conducted. We estimated all-cause and cause-specific mortality rates before and during the height of the COVID-19 pandemic, and we compared associated mortality rates between the periods using incidence rate ratios. Excess deaths during the COVID-19 period were also estimated by modelling expected deaths in the absence of COVID-19 by applying a negative binomial regression model on historical mortality data from January 2016. Overall and monthly excess deaths were determined using the P-score metric. Spearman correlation was used to assess whether there is a relationship between the generated P-score and COVID-19 positivity rate. The all-cause mortality rate was higher during the COVID-19 period compared to the pre-COVID-19 period in Asembo [9.1 (95% CI, 8.2–10.0) vs. 7.8 (95% CI, 7.3–8.3) per 1000 person-years of observation, pyo]. In Kibera, the all-cause mortality rate was slightly lower during the COVID-19 period compared to the pre-COVID-19 period [2.6 (95% CI, 2.2–3.2 per 1000 pyo) vs. 3.1; 95% CI, 2.7–3.4 per 1000 pyo)]. An increase in all-cause mortality was observed (incidence rate ratio, IRR, 1.16; 95% CI, 1.04–1.31) in Asembo, unlike in Kibera (IRR, 0.88; 95% CI, 0.71–1.09). The notable increase in mortality rate in Asembo was observed among persons aged 50 to 64 years (IRR, 2.62; 95% CI, 1.95–3.52), persons aged ...