Abstract:
Background: Endemic and seasonally recurring respiratory viruses are a major cause of
disease and death globally. The burden is particularly severe in developing countries.
Improved understanding of the source of infection, pathways of spread and persistence in
communities would be of benefit in devising intervention strategies. Methods: We report
epidemiological data obtained through surveillance of respiratory viruses at nine
outpatient health facilities within the Kilifi Health and Demographic Surveillance
System, Kilifi County, coastal Kenya, between January and December 2016.
Nasopharyngeal swabs were collected from individuals of all ages presenting with acute
respiratory infection (ARI) symptoms (up to 15 swabs per week per facility) and
screened for 15 respiratory viruses using real-time PCR. Paediatric inpatient surveillance
at Kilifi County Hospital for respiratory viruses provided comparative data. Results:
Over the year, 5,647 participants were sampled, of which 3,029 (53.7%) were aged <5
years. At least one target respiratory virus was detected in 2,380 (42.2%) of the samples;
the most common being rhinovirus 18.6% (1,050), influenza virus 6.9% (390),
coronavirus 6.8% (387), parainfluenza virus 6.6% (371), respiratory syncytial virus
(RSV) 3.9% (219) and adenovirus 2.7% (155). Virus detections were higher among <5-
year-olds compared to older children and adults (50.3% vs 32.7%, respectively; χ 2(1)
=177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ 2(8)
=13.38, P=0.072). However, prevalence was significantly higher among inpatients than
outpatients in <5-year-olds for RSV (22.1% vs 6.0%; χ 2(1) = 159.4, P=0.0001), and
adenovirus (12.4% vs 4.4%, χ 2(1) =56.6, P=0.0001). Conclusions: Respiratory virus
infections are common amongst ARI outpatients in this coastal Kenya setting,
particularly in young children. Rhinovirus predominance warrants further studies on the
health and socio-economic implications. RSV and adenovirus were more commonly
associated with severe disease. Further analysis will explore epidemiological
transmission patterns with the addition of virus sequence data.