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Spatial-temporal distribution and sequence diversity of Group A human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype
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Wangui, J., Nokes, D. James, Mobegi, V., Otieno, J. R., Agoit, C. N., Ngeranwa, J. N. and Bulimo, W. (2022) Spatial-temporal distribution and sequence diversity of Group A human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype. Influenza and Other Respiratory Viruses, 16 (3). pp. 501-510. doi:10.1111/irv.12948 ISSN 1750-2640.
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Official URL: https://doi.org/10.1111/irv.12948
Abstract
Background
Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity.
Methods
A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT-PCR (reverse transcriptase polymerase chain reaction). A segment of the G-gene was amplified using one-step RT-PCR and sequenced by Sanger di-deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction.
Results
Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes.
Conclusions
HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country.
Item Type: | Journal Article | ||||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
Journal or Publication Title: | Influenza and Other Respiratory Viruses | ||||||||
Publisher: | Wiley-Blackwell Publishing Ltd. | ||||||||
ISSN: | 1750-2640 | ||||||||
Official Date: | 5 April 2022 | ||||||||
Dates: |
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Volume: | 16 | ||||||||
Number: | 3 | ||||||||
Page Range: | pp. 501-510 | ||||||||
DOI: | 10.1111/irv.12948 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 8 December 2021 | ||||||||
Date of first compliant Open Access: | 10 January 2022 | ||||||||
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