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Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018
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Luka, Martha M., Kamau, Everlyn, de Laurent, Zaydah R., Morobe, John Mwita, Alii, Leonard K., Nokes, D. James and Agoti, Charles N. (2021) Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Research, 6 . 178. doi:10.12688/wellcomeopenres.16911.1 ISSN 2398-502X.
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WRAP-Whole-genome-sequencing-two-human-rhinovirus-A-types-A101-A15-detected-Kenya-2016-2018-2021.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (3765Kb) | Preview |
Official URL: http://dx.doi.org/10.12688/wellcomeopenres.16911.1
Abstract
Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences.
Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya.
Results: We processed 73 samples collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. Improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies.
Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.
Keywords
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
Library of Congress Subject Headings (LCSH): | Human genome -- Analysis, Human gene mapping, Rhinoviruses -- Kenya, Phylogeny | ||||||||
Journal or Publication Title: | Wellcome Open Research | ||||||||
Publisher: | F1000Research | ||||||||
ISSN: | 2398-502X | ||||||||
Official Date: | 30 August 2021 | ||||||||
Dates: |
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Volume: | 6 | ||||||||
Article Number: | 178 | ||||||||
DOI: | 10.12688/wellcomeopenres.16911.1 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 21 September 2021 | ||||||||
Date of first compliant Open Access: | 22 September 2021 |
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