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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

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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
Subjects: Q Science > QR Microbiology
R Medicine > RJ Pediatrics
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:
DateEvent
11 July 2019Published
26 June 2019Accepted
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:
Project/Grant IDRIOXX Funder NameFunder ID
090853 Wellcome Trusthttp://dx.doi.org/10.13039/100010269
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
UNSPECIFIEDNew Partnership for Africa's Developmenthttp://dx.doi.org/10.13039/501100009250
UNSPECIFIEDAfrican Academy of SciencesUNSPECIFIED
107769/Z/10/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
UNSPECIFIEDGovernment of the United KingdomUNSPECIFIED
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