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Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations
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Nyiro, Joyce Uchi, Munywoki, Patrick, Kamau, Everlyn, Agoti, Charles, Gichuki, Alex, Etyang, Timothy, Otieno, Grieven and Nokes, D. James (2018) Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations. Wellcome Open Research, 3 . 89. doi:10.12688/wellcomeopenres.14662.1 ISSN 2398-502X.
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Official URL: http://dx.doi.org/10.12688/wellcomeopenres.14662.1
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; χ2(1) =177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ2(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%; χ2(1) = 159.4, P=0.0001), and adenovirus (12.4% vs 4.4%, χ2(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.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology R Medicine > RC Internal medicine |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| Library of Congress Subject Headings (LCSH): | Respiratory organs -- Diseases -- Diagnosis -- Kenya, Viruses | |||||||||
| Journal or Publication Title: | Wellcome Open Research | |||||||||
| Publisher: | F1000Research | |||||||||
| ISSN: | 2398-502X | |||||||||
| Official Date: | 25 July 2018 | |||||||||
| Dates: |
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| Volume: | 3 | |||||||||
| Article Number: | 89 | |||||||||
| DOI: | 10.12688/wellcomeopenres.14662.1 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 3 August 2018 | |||||||||
| Date of first compliant Open Access: | 3 August 2018 | |||||||||
| RIOXX Funder/Project Grant: |
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