Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

J R Otieno,A M Gichuki,P Lemey,Š Binter,P Kellam,E M Kamau,C N Agoti,G P Otieno,P A Cane,D J Nokes,J W Oketch,M Ngama,M Cotten,J M Ngoi

doi:10.1093/ve/vey027

Abstract

The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analysed 184 RSV-A whole-genome sequences (WGSs) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A circulation in this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identified signature amino acid substitutions between ON1 and GA2 viruses’ surface proteins (G and F), polymerase (L), and matrix M2-1 proteins, some of which were positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORFs) (G, F, L, N, and P) formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF also play a role in the adaptation of RSV to host populations, with the alternative possibility that some of the substitutions are neutral and provide no selective advantage. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies.

Highlights

Respiratory syncytial virus (RSV) is the leading viral cause of severe pneumonia and bronchiolitis among infants and children globally (Nokes et al 2008; Nair et al 2010; Shi et al 2017)
Two sets of samples were used in the current analysis: (1) samples collected from children admitted to the Kilifi County Hospital (KCH) presenting with syndromically defined severe or very severe pneumonia between September 2011 and August 2016 (Nokes et al 2009; Otieno et al 2017) and (2) samples collected from patients of all ages presenting at health facilities within the Kilifi Health and Demographic Surveillance System (KHDSS) (Scott et al 2012) with acute respiratory illnesses between January and December 2016 (Nyiro et al 2018)
Utilizing genomes from samples collected between 2010 and 2016, including 184 complete genomes from Kilifi alone, we obtained a finer resolution on the pattern of respiratory syncytial virus (RSV) introductions, persistence and evolution in a defined location, and the changes within the genome that might be important for the persistent circulation of the virus

Summary

Introduction

Respiratory syncytial virus (RSV) is the leading viral cause of severe pneumonia and bronchiolitis among infants and children globally (Nokes et al 2008; Nair et al 2010; Shi et al 2017). No licensed RSV vaccine exists, partly due to the antigenic variability in the virus (Cane 2001). A genotype can be further divided into (1) imported variants which show greater genetic difference than expected from in situ diversification (Agoti et al 2015b; Otieno et al 2016) and (2) local variants arising from recent introduction which subsequently diversify in situ (without time for purifying selection from, for example inter-epidemic bottlenecks) (Agoti et al 2017). We have previously shown that within RSV epidemics, there is co-circulation of RSV viruses belonging to different groups, genotypes, and variants both imported and local (Agoti et al 2015b, 2017; Otieno et al 2016), with the latter not clearly distinguished through partial G gene sequencing. Full genome sequencing offers the opportunity to differentiate introduced from persistent RSV viruses within a given location

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Conclusion