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.
Highlights
Acute respiratory infection (ARI) is a major cause of morbidity and mortality globally, principally affecting young children and the elderly, and with majority of the burden occurring in lowresource settings[1,2]
Viruses are recognized as major cause of both mild acute respiratory infection (ARI) and of severe acute lower respiratory tract infection (LRTI)[3]
Respiratory syncytial virus (RSV), rhinovirus and influenza A are often identified as the most common viruses associated with ARI4,5, but a wide range of viruses are to be found in ARI presentations to the hospital and outpatient settings[5]
Summary
Acute respiratory infection (ARI) is a major cause of morbidity and mortality globally, principally affecting young children and the elderly, and with majority of the burden occurring in lowresource settings[1,2]. The changing landscape of ARI due to the widespread use of conjugated bacterial vaccines could lead to an increased prominence of viral causes of these illnesses[6,7]. Given this context, greater emphasis on the control of virusassociated ARI is likely. Vaccination as an intervention for the control of viral respiratory infections faces considerable hurdles These include continuous or rapid pathogen evolution (e.g. influenza)[8,9], high serotype diversity (e.g. rhinovirus)[10] or target populations not appropriate for current vaccines (e.g. RSV)[11]. Conclusions: Respiratory virus infections are common amongst ARI outpatients in this coastal Kenya setting, in young
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