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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [PMID: 34522789 PMCID: PMC8408540 DOI: 10.12688/wellcomeopenres.16911.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
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.
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Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Leonard K Alii
- Department of Mathematics and Computer Science, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [DOI: 10.12688/wellcomeopenres.16911.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 01/10/2023] Open
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.
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Wu D, Lu J, Sun Z, Cao L, Zeng Q, Liu Q, Wu T, Yang Z. Rhinovirus remains prevalent in school teenagers during fight against COVID-19 pandemic. IMMUNITY INFLAMMATION AND DISEASE 2020; 9:76-79. [PMID: 33247521 PMCID: PMC7753714 DOI: 10.1002/iid3.381] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/02/2022]
Affiliation(s)
- Di Wu
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Jianyun Lu
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zhangyu Sun
- Department of Respiratory Medicine, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Lan Cao
- Department of Virology and Immunology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Qing Zeng
- Department of Virology and Immunology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Qun Liu
- Pharmacology Laboratory, Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China
| | - Tiantian Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhicong Yang
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
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Luka MM, Kamau E, Adema I, Munywoki PK, Otieno GP, Gicheru E, Gichuki A, Kibinge N, Agoti CN, Nokes DJ. Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya. Open Forum Infect Dis 2020; 7:ofaa385. [PMID: 33094115 PMCID: PMC7568438 DOI: 10.1093/ofid/ofaa385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 01/12/2023] Open
Abstract
Background Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been previously described. The objective of this study was to characterize HRV molecular epidemiology in a primary school in a rural location of Kenya. Methods Between May 2017 and April 2018, over 3 school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time reverse transcription polymerase chain reaction. HRV-positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification. Results A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%; P < .001). HRV-A was the most common species (134/253; 53.0%), followed by HRV-C (73/253; 28.9%) and HRV-B (46/253; 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in 1 school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all 3 school terms. Conclusions HRV was frequently detected among school-going children with mild acute respiratory illness symptoms, particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed that were characterized by considerable genotype diversity.
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Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Irene Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Alex Gichuki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Nelson Kibinge
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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