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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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  • JULIA WANGUI,
  • David Nokes,
  • Victor Mobegi,
  • James Otieno,
  • Charles Agoti,
  • Joseph Ngeranwa,
  • Wallace Bulimo
JULIA WANGUI
Kenyatta University Graduate School
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David Nokes
KEMRI-Wellcome Trust Research Programme
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Victor Mobegi
University of Nairobi
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James Otieno
Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme
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Charles Agoti
Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme
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Joseph Ngeranwa
Kenyatta University Graduate School
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Wallace Bulimo
KEMRI
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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 towards the Western zones and decreasing towards the Eastern zones of the country.

Peer review status:Published

15 Nov 2021Submitted to Influenza and other respiratory viruses
16 Nov 2021Assigned to Editor
16 Nov 2021Submission Checks Completed
05 Dec 2021Editorial Decision: Accept
27 Dec 2021Published in Influenza and Other Respiratory Viruses. 10.1111/irv.12948