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Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
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Agoti, Charles N., Phan, My V. T., Munywoki, Patrick K., Githinji, George, Medley, Graham, Cane, Patricia A., Kellam, Paul, Cotton, Matthew and Nokes, D. James (2019) Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. Scientific Reports, 9 . 10076. doi:10.1038/s41598-019-46509-w
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Official URL: https://doi.org/10.1038/s41598-019-46509-w
Abstract
Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3–4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0–21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0–17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.
| Item Type: | Journal Article | |||||||||||||||||||||
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| Subjects: | Q Science > QR Microbiology R Medicine > RJ Pediatrics |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) | |||||||||||||||||||||
| Library of Congress Subject Headings (LCSH): | Respiratory syncytial virus , Respiratory syncytial virus -- Transmission -- Kenya, Communicable diseases in infants | |||||||||||||||||||||
| Journal or Publication Title: | Scientific Reports | |||||||||||||||||||||
| Publisher: | Nature Publishing Group | |||||||||||||||||||||
| ISSN: | 2045-2322 | |||||||||||||||||||||
| Official Date: | 11 July 2019 | |||||||||||||||||||||
| Dates: |
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| Date of first compliant deposit: | 2 July 2019 | |||||||||||||||||||||
| Volume: | 9 | |||||||||||||||||||||
| Article Number: | 10076 | |||||||||||||||||||||
| DOI: | 10.1038/s41598-019-46509-w | |||||||||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||||||||
| Publication Status: | Published | |||||||||||||||||||||
| Access rights to Published version: | Open Access | |||||||||||||||||||||
| RIOXX Funder/Project Grant: |
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