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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
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 | |||||||||||||||
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| 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: |
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| 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: |
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