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Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant

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 in...

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Autores principales: Agoti, Charles N., Phan, My V. T., Munywoki, Patrick K., Githinji, George, Medley, Graham F., Cane, Patricia A., Kellam, Paul, Cotten, Matthew, Nokes, D. James
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624209/
https://www.ncbi.nlm.nih.gov/pubmed/31296922
http://dx.doi.org/10.1038/s41598-019-46509-w
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author Agoti, Charles N.
Phan, My V. T.
Munywoki, Patrick K.
Githinji, George
Medley, Graham F.
Cane, Patricia A.
Kellam, Paul
Cotten, Matthew
Nokes, D. James
author_facet Agoti, Charles N.
Phan, My V. T.
Munywoki, Patrick K.
Githinji, George
Medley, Graham F.
Cane, Patricia A.
Kellam, Paul
Cotten, Matthew
Nokes, D. James
author_sort Agoti, Charles N.
collection PubMed
description 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.
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spelling pubmed-66242092019-07-19 Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant Agoti, Charles N. Phan, My V. T. Munywoki, Patrick K. Githinji, George Medley, Graham F. Cane, Patricia A. Kellam, Paul Cotten, Matthew Nokes, D. James Sci Rep Article 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. Nature Publishing Group UK 2019-07-11 /pmc/articles/PMC6624209/ /pubmed/31296922 http://dx.doi.org/10.1038/s41598-019-46509-w Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Agoti, Charles N.
Phan, My V. T.
Munywoki, Patrick K.
Githinji, George
Medley, Graham F.
Cane, Patricia A.
Kellam, Paul
Cotten, Matthew
Nokes, D. James
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title_full Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title_fullStr Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title_full_unstemmed Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title_short Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
title_sort genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624209/
https://www.ncbi.nlm.nih.gov/pubmed/31296922
http://dx.doi.org/10.1038/s41598-019-46509-w
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