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Data for Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17
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Kamau, Everlyn, Otieno, James Richard, Murunga, Nickson, Oketch, John W., Ngoi, Joyce M., de Laurent, Zaydah R., Mwema, Anthony, Nyrio, Joyce U., Agoti, Charles N. and Nokes, D. James (2020) Data for Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. [Dataset]
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Official URL: https://doi.org/10.7910/DVN/RYISUE
Abstract
Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in 9 health facilities across a defined geographical area (∼890 km2), over 2 RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple virus introductions into the area and co-circulation of distinct genetic clusters, which transmitted and diversified locally with varying frequency. Increase in relative genetic diversity paralleled seasonal virus incidence. Importantly, we identified a cluster of viruses that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel non-synonymous change (K68Q) in antigenic site ∅ in the Fusion protein. RSVB diversity was additionally marked by signature non-synonymous substitutions that were unique to particular genomic clusters, some under diversifying selection. Our findings provide insights into recent evolutionary and epidemiological behaviors of RSV group B, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic strategies in development.
Item Type: | Dataset | ||||||||||||||||||
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Alternative Title: | Replication Data for : Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17 | ||||||||||||||||||
Subjects: | R Medicine > RC Internal medicine | ||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||||||||
Type of Data: | Observational data | ||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Respiratory organs -- Diseases -- Kenya -- Kilifi, Respiratory syncytial virus -- Transmission, Respiratory syncytial virus -- Transmission -- Kenya -- Kilifi | ||||||||||||||||||
Publisher: | University of Warwick, School of Life Sciences | ||||||||||||||||||
Official Date: | 9 March 2020 | ||||||||||||||||||
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Status: | Not Peer Reviewed | ||||||||||||||||||
Publication Status: | Published | ||||||||||||||||||
Media of Output (format): | .do .Rmd .txt | ||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||||||||
Copyright Holders: | University of Warwick | ||||||||||||||||||
Description: | Data record consists of two zip files, a STATA do file, an Rmd file and an accompanying README file. |
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