Open AccessSerotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008
Author(s) -
Milanoi Sylvia,
Ongus Juliette R.,
Gachara George,
Coldren Rodney,
Bulimo Wallace
Publication year - 2016
Publication title -
influenza and other respiratory viruses
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.743
H-Index - 57
eISSN - 1750-2659
pISSN - 1750-2640
DOI - 10.1111/irv.12373
Subject(s) - rhinovirus , serotype , biology , kenya , virology , amplicon , genetic diversity , phylogenetic tree , bronchiolitis , nucleotide diversity , virus , genotype , veterinary medicine , medicine , genetics , polymerase chain reaction , population , environmental health , gene , ecology , haplotype
Background Human rhinoviruses ( HRV s) are a well‐established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses ( SARI s) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized. Objectives This study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008. Methods A total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza‐like ( ILI ) symptoms. Real‐time RT ‐ PCR was employed for preliminary HRV detection. HRV ‐positive samples were amplified using RT ‐ PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis. Results Twenty‐five percent of the samples tested positive for HRV . Phylogenetic analysis revealed that the Kenyan HRV s clustered into three main species comprising HRV ‐A (54%), HRV ‐B (12%), and HRV ‐C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level. Conclusion These results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRV s contributed substantially to influenza‐like illness in Kenya in 2008.