Molecular Characterization of Human Respirovirus Type 3 Isolated in Kenya between 2010 and 2013

Abstract

Human respirovirus type 3 (HRV3) is among the leading causative agents of lower respiratory tract infections such as pneumonia and bronchiolitis in young children, ranking only second to the human respiratory syncytial virus (RSV) in this respect. Despite their public health significance, there is scanty information on the molecular characteristics and diversity of HRV3 strains circulating in Kenya. The general objective of this study was therefore to determine the molecular characteristics of the HRV3 virus isolated in Kenya between 2010 and 2013, during a time when there was an increase of respiratory diseases in the country worsened by the influenza pandemic. To address this gap, 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013 were analysed. Viral RNA was extracted from the isolates and the entire HN gene amplified by RT-PCR followed by nucleotide Sanger sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates classified into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of strains grouped into sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence homology revealed a high similarity between the Kenyan isolates and the HRV3 prototype strain both at the nucleotide (94.3-95.6%) and amino acid (96.5 -97.9%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection analysis showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses showed that the mean TMRCA for the HN sequence dataset was estimated at 1942 (95% HPD: 1928 - 1957), while the mean evolutionary rate was 4.65x10-4 nucleotide substitutions/site/year (95% HPD: 2.99x10-4 to 6.35x10-4). Overall, the study demonstrates the introduction and co-circulation of multiple lineages of Cluster C HRV3 variants in Kenya during the study period. Furthermore, results obtained from this study provide more evidence of the conserved nature of the HRV3 HN glycoprotein. In conclusion, this study is the first to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene. Accordingly, there is a need to establish constant surveillance of these important pathogens in the country. This will contribute to a better understanding of circulation trends, disease associations, and outbreaks of HRV3 strains circulating in Kenya. It will also contribute to the future development of antivirals/therapeutics, leading to better patient management. Furthermore, whole genome sequencing of Kenyan HRV3 should be utilized in future to provide deeper insights into the genetic and evolutionary dynamics of these viruses.