INTRODUCTION
In late 2019 a cluster of pneumonia cases of unknown aetiology emerged in Wuhan, Hubei province, China. A novel coronavirus was reported to be the causative agent and officially named SARS-CoV-2 by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. Within a short period, it had spread to nearly all countries in the world, attaining pandemic status with an estimated global case count of 765 million and 6.9 million deaths as of 24th May 2023 . To date, Kenya has recorded 343,073 SARS-CoV-2 cases and 5688 case fatalities.
Acute respiratory infections (ARIs) are a significant public health concern due to their widespread morbidity and mortality and their potential to cause pandemics. ARIs are transmitted primarily via large respiratory droplets, contact with surfaces contaminated by respiratory droplets, and aerosolized small respiratory droplets. Most patients with SARS-CoV-2 exhibit fever, sore throat and dry cough, and the less common symptoms are joint aches, rhinorrhoea, myalgia, dizziness, difficulty breathing, diarrhoea, chest pains, and nausea.
Early detection and monitoring of ARIs are crucial for controlling outbreaks and preventing their spread. Limited diagnostic capabilities, limited access to health care, and economic constraints frustrate early public health interventions. There are over 25 known viral and bacterial ARI pathogens. Patients with ARIs frequently present with symptoms indicative of disease but not specific enough to distinguish what makes them ill clinically. The lack of clear diagnosis results in delayed interventions. Sentinel surveillance maps the evolution of epidemics and provides evidence to inform control approaches in advance since hospital admissions and mortality indicators lag community transmission. It is an effective tool for monitoring the incidence of ARIs in a population and has been effectively deployed to monitor syndromic illnesses.
Understanding epidemiology and transmission dynamics is vital in providing timely and accurate information for evidence-based public health interventions. There have been several studies on co-infection of SARS-CoV-2 with other ARIs worldwide, with most focusing on co-infection with influenzas A and B. There is limited data about SARS-CoV-2 co-infection with other ARI pathogens in Kenya. Viral respiratory infections have been shown to predispose patients to secondary bacterial infections and alter host immunopathology leading to increased morbidity and mortality. Identifying pathogens co-infecting with SARS-CoV-2 is critical in developing clinical and public health measures to improve patient outcomes.
We aimed to address these evidence gaps by conducting an active sentinel surveillance study among patients meeting the case definition of suspected SARS-CoV-2 cases. We investigated the incidence of SARS-CoV-2, RSV, influenza A and influenza B after which we subtyped influenza-A and RSV-positive samples. Finally, we investigated the co-infection of all the SARS-CoV-2-positive samples with 19 viral and bacterial respiratory pathogens. This manuscript presents the results of an active sentinel surveillance program conducted in four sentinel sites in the Rift Valley region, Kenya. We describe the methodology used for data collection, demographic characteristics of the population under surveillance, incidence rates and trends of different ARIs.