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.