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. 2020 Mar 10;15(3):e0229355.
doi: 10.1371/journal.pone.0229355. eCollection 2020.

Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene

Juliet Elusah  1 , Wallace Dimbuson Bulimo  2   3 , Silvanos Mukunzi Opanda  2 , Samwel Lifumo Symekher  4 , Fred Wamunyokoli  1
Affiliations

Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene

Juliet Elusah et al. PLoS One. .

Abstract

Human respirovirus type 3 (HRV3) is a leading etiology of lower respiratory tract infections in young children and ranks only second to the human respiratory syncytial virus (HRSV). Despite the public health importance of HRV3, there is limited information about the genetic characteristics and diversity of these viruses in Kenya. To begin to address this gap, we analyzed 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013. Viral RNA was extracted from the isolates, and the entire HN gene amplified by RT-PCR followed by nucleotide sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates grouped into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of isolates belonged to sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence analysis revealed high identities between the Kenyan isolates and the HRV3 prototype strain both at the amino acid (96.5-97.9%) and nucleotide (94.3-95.6%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection pressure analyses showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses revealed that the mean TMRCA for the HN sequence dataset was 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, our results demonstrate the co-circulation of strains of cluster C HRV3 variants in Kenya during the study period. This is the first study to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene.

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Conflict of interest statement

The authors have declared that no competing interests exist

Figures

Fig 1
Fig 1. Summary of % distribution of presenting symptoms of patients with human respirovirus 3 infections in Kenya from June 2010 to June 2013.
Fig 2
Fig 2. Bayesian phylogenetic tree based on nucleotide sequences of the complete HN gene of HRV3 strains.
The tree was constructed using MrBayes v3.2. The numbers at the nodes represent posterior probability values. The scale bar indicates the number of nucleotide substitutions per site. Kenyan isolates are shown in blue.
Fig 3
Fig 3. Maximum Clade Credibility (MCC) tree of HRV3 strains based on complete HN coding sequences, constructed using the BEAST program.
The Kenyan strains are shown in blue. The numbers at the nodes represent posterior probability values.
See this image and copyright information in PMC

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