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Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission

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Kombe, Ivy K., Agoti, Charles N., Munywoki, Patrick K., Baguelin, Marc, Nokes, D. James and Medley, Graham (2021) Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission. Scientific Reports, 11 . 1463. doi:10.1038/s41598-021-81078-x

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Official URL: https://doi.org/10.1038/s41598-021-81078-x

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Abstract

Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group.

Item Type: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Epidemiology, Respiratory syncytial virus -- Kilifi District (Kenya), Respiratory syncytial virus -- Genetic aspects -- Kilifi District (Kenya)
Journal or Publication Title: Scientific Reports
Publisher: Nature Publishing Group
ISSN: 2045-2322
Official Date: 14 January 2021
Dates:
DateEvent
14 January 2021Published
4 January 2021Accepted
Date of first compliant deposit: 13 January 2021
Volume: 11
Article Number: 1463
DOI: 10.1038/s41598-021-81078-x
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
090853Wellcome Trusthttp://dx.doi.org/10.13039/100010269
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
203077/Z/16/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
107769/Z/10/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
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