JMIR Publications

ABSTRACT

Background:

Little is known about levels of co-circulation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and their impact on disease severity in sub-Saharan Africa.

Objective:

We aimed to describe influenza and SARS-CoV-2 co-circulation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance.

Methods:

We used epidemic curves and the Pearson's r to describe the correlation between SARS-CoV-2 positivity in data from eight influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data obtained from the Kenya Ministry of Health. We used a logistic regression model to assess association between influenza and SARS-CoV-2 co-infection with severe clinical illness. Severe clinical illness was defined as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit (ICU)/High Dependance Unit (HDU), mechanical ventilation, or a report of any danger sign (for children <5 years) among hospitalized patients.

Results:

We enrolled 7,349 patients from influenza sentinel surveillance sites during April 2020 through Mar 2022 and 76.3% were aged <5 years. We detected any influenza (A or B) in 8.7% (629/7,224), SARS-CoV-2 in 10.7% (768/7,199), and co-infection in 0.9% (63/7,165) samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% of the number tested in the universal national surveillance (60/week vs 36,000/week), SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson's r=0.58, p<.001). The odds of clinical severe illness among participants with co-infection were similar to those of patients with influenza only (aOR: 0.91; 95% CI: 0.47–1.79) and SARS-CoV-2 only (aOR: 0.92; 95% CI: 0.47–1.82).

Conclusions:

Influenza substantially co-circulated with SARS-CoV-2 in Kenya. We found significant correlation of SARS-CoV-2 positivity in the data from eight influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings highlight the utility of influenza sentinel surveillance system as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance.