Prospective clinical surveillance for severe acute respiratory illness and COVID-19 vaccine effectiveness in Kenyan hospitals during the COVID-19 pandemic
Authors: Lucinde Ruth Khadembu , Gathuri Henry , Isaaka Lynda , Ogero Morris , Mumelo Livingstone , Kimego Dennis , Mbevi George , Wanyama Conrad , Otieno Edwin Onyango , Mwakio Stella , Saisi Metrine , Isinde Elizabeth , Oginga Irene Njeri , Wachira Alvin , Manuthu Evans , Kariuki Hazel , Nyikuli Jared , Wekesa Cyprian , Otedo Amos , Bosire Hannah , Okoth Steve Biko , Ongalo Winston , Mukabi David , Lusamba Wilber , Muthui Beatrice , Adembesa Isaac , Mithi Caroline , Sood Mohammed , Ahmed Nadia , Gituma Bernard , Giabe Matiko , Omondi Charles , Aman Rashid , Amoth Patrick , Kasera Kadondi , Were Fred , Nganga Wangari , Berkley James A , Tsofa Benjamin , Mwangangi Jospeh , Bejon Philip , Barasa Edwine , English Mike , Scott John Athony Gerard , Akech Samuel , Kagucia Eunice Wangeci , Agweyu Ambrose , Etyang Anthony Oliwa 
Published: November 2024

Abstract
Background
There are limited data from sub-Saharan Africa describing the demographic characteristics, clinical features and outcome of patients admitted to public hospitals with severe acute respiratory infections during the COVID-19 pandemic.

Methods
We conducted a prospective longitudinal hospital-based sentinel surveillance between May 2020 and December 2022 at 16 public hospitals in Kenya. All patients aged above 18 years admitted to adult medical wards in the participating hospitals were included. We collected data on demographic and clinical characteristics, SARS-CoV-2 infection and COVID-19 vaccination status and, admission episode outcomes. We determined COVID-19 vaccine effectiveness (VE) against admission with SARS-CoV-2 positive severe acute respiratory illness (SARI) (i.e., COVID-19) and progression to inpatient mortality among patients admitted with SARI, using a test-negative case control design.

Results
Of the 52,636 patients included in the study, 17,950 (34.1%) were admitted with SARI. The median age was 50 years. Patients were equally distributed across sexes. Pneumonia was the most common diagnosis at discharge. Hypertension, Human Immunodeficiency Virus (HIV) infection and Diabetes Mellitus were the most common chronic comorbidities. SARS-CoV-2 test results were positive in 2,364 (27.9%) of the 8,471 patients that underwent testing. After adjusting for age, sex and presence of a chronic comorbidity, SARI patients were more likely to progress to inpatient mortality compared to non-SARI patients regardless of their SARS-CoV-2 infection status (adjusted odds ratio (aOR) for SARI and SARS-CoV-2 negative patients 1.22, 95% CI 1.10–1.37; and aOR for SARI and SARS-CoV-2 positive patients 1.32, 95% CI 1.24–1.40). After adjusting for age, sex and presence of a chronic comorbidity, COVID-19 VE against progression to inpatient mortality following admission with SARI for those with a confirmed vaccination status was 0.59 (95% CI 0.27–0.77).

Conclusion
We have provided a comprehensive description of the demographic and clinical pattern of admissions with SARI in Kenyan hospitals during the COVID-19 pandemic period as well as the COVID-19 VE for these patients. These data were useful in providing situational awareness during the first three years of the pandemic in Kenya and informing national response measures.