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

PloS One
Juliet ElusahFred Wamunyokoli

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. Evolu...Continue Reading

References

Apr 1, 1994·Clinical Microbiology Reviews·R Vainionpää, T Hyypiä
Jul 24, 2001·The Pediatric Infectious Disease Journal·M E CounihanL J Anderson
Apr 15, 2003·Clinical Microbiology Reviews·Kelly J Henrickson
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Feb 17, 2005·Bioinformatics·Sergei L Kosakovsky Pond, Simon D W Frost
Apr 10, 2008·Molecular Biology and Evolution·David Posada
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Mar 1, 2012·Molecular Biology and Evolution·Alexei J DrummondAndrew Rambaut
May 17, 2012·Viruses·Andres Chang, Rebecca E Dutch
Jun 20, 2012·Current Opinion in Virology·Henrick SchomackerAlexander C Schmidt
Apr 16, 2013·The EMBO Journal·Catharina SteentoftHenrik Clausen
Sep 26, 2013·Frontiers in Microbiology·Hiroyuki TsukagoshiHirokazu Kimura
Nov 30, 2013·Influenza and Other Respiratory Viruses·Manuel V VillaranEric S Halsey
Dec 25, 2015·Molecular Phylogenetics and Evolution·Marcelo Reginato, Fabián A Michelangeli
Jan 19, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Stephanie GoyaMariana Viegas
May 4, 2017·Journal of Medical Microbiology·Tanja Košutić-GulijaDubravko Forčić
Feb 7, 2018·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Masaki TakahashiHirokazu Kimura
May 3, 2018·Systematic Biology·Andrew RambautMarc A Suchard

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Datasets Mentioned

BETA
MN116749
JN089924

Methods Mentioned

BETA
Assay
PCR
glycosylation

Software Mentioned

FUBAR
MrBayes
MEME
Tracer
REL
Muscle
jModelTest
BEAST
MEGA6
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