Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

Martha M Luka; Everlyn Kamau; Zaydah R de Laurent; John Mwita Morobe; Leonard K Alii; D James Nokes; Charles N Agoti

doi:10.12688/wellcomeopenres.16911.2

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

Wellcome Open Res. 2021 Sep 23:6:178. doi: 10.12688/wellcomeopenres.16911.2. eCollection 2021.

Authors

Martha M Luka^{1

2}, Everlyn Kamau¹, Zaydah R de Laurent¹, John Mwita Morobe¹, Leonard K Alii³, D James Nokes^{1

4}, Charles N Agoti^{1

5}

Affiliations

¹ Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.
² Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
³ Department of Mathematics and Computer Science, Pwani University, Kilifi, Kenya.
⁴ School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK.
⁵ Department of Public Health, Pwani University, Kilifi, Kenya.

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 nasopharyngeal swabs 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. An 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: human rhinovirus; phylogenetics; sequencing; whole-genome.

Grants and funding

This work was supported by the Wellcome Trust through a Wellcome Trust Senior Investigator Award to DJN (#102975). MML was supported by the Fogarty International Center (#U2RTW010677) of the National Institutes of Health (NIH) and DELTAS Africa Initiative (#DEL-15-003) of the African Academy of Sciences (AAS). The content is the authors’ responsibility and does not necessarily represent the official views of the Wellcome Trust, NIH, nor AAS.