Abstract
In February 2012, the novel respiratory syncytial virus (RSV) group A, genotype ON1, was detected in Kilifi County, coastal Kenya. ON1 is characterized by a 72-nt duplication within the highly variable G gene (encoding the immunogenic attachment surface protein). Cases were diagnosed through surveillance of pneumonia in children at the county hospital. Analysis of epidemiologic, clinical, and sequence data of RSV-A viruses detected over 5 RSV seasons (2010/2011 to 2014/2015) indicated the following: 1) replacement of previously circulating genotype GA2 ON1, 2) an abrupt expansion in the number of ON1 variants detected in the 2014/2015 epidemic, 3) recently accumulation of amino acid substitutions within the ON1 duplicated sequence, and 4) no clear evidence of altered pathogenicity relative to GA2. The study demonstrates the public health importance of molecular surveillance in defining the spread, clinical effects, and evolution of novel respiratory virus variants.
Highlights
In February 2012, the novel respiratory syncytial virus (RSV) group A, genotype ON1, was detected in Kilifi County, coastal Kenya
Study Location and Population The study was undertaken in Kilifi County and is part of surveillance aimed at understanding the epidemiology and disease effects of Respiratory syncytial virus (RSV)-associated pneumonia cases in this region [22]
Over the 5 RSV epidemics examined (2010/2011 to 2014/2015), a total of 4,010 samples were collected from eligible children; 3,561 (88.8%) were tested for RSV and 881 (24.7%) RSV-positive samples were identified
Summary
In February 2012, the novel respiratory syncytial virus (RSV) group A, genotype ON1, was detected in Kilifi County, coastal Kenya. The temporal progression of RSV genotypes can be followed directly because of the unique tags (the duplications), which provides a rare opportunity to learn more about the introduction, spread, severity, and related selection processes (including immune evasion) for RSV and to obtain insights into the nature of emergence of novel virus variants. In this regard, we undertook an in-depth analysis of RSV-A genotype ON1 epidemiology in Kilifi, a county in coastal Kenya. We have analyzed sequence data collected over 5 RSV epidemic seasons in Kilifi (2010/2011 to 2014/2015), which includes the period after the initial detection of this novel genotype within Kilifi
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