Staff View: Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses

Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses

Enteroviruses (EVs) are a group of viruses that cause various human illnesses. While the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) method can generate VP1 gene fragments for enterovirus genotyping, it is unable to detect recombinant strains. Recent advances in viral genome sequenc...

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Main Authors:	Chien, Yeh Seng, Chen, Feng Jui, Wu, Han Chieh, Lin, Chieh Hua, Chang, Wen Chiung, David, Perera, Yang, Jyh Yuan, Lee, Min Shi, Liao, Yu Chieh
Format:	Article
Language:	English
Published:	American Society for Microbiology 2023
Subjects:	Q Science (General) QR355 Virology R Medicine (General)
Online Access:	http://ir.unimas.my/id/eprint/43592/3/Cost-effective.pdf http://ir.unimas.my/id/eprint/43592/ https://journals.asm.org/doi/10.1128/spectrum.02507-23
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spelling	my.unimas.ir.435922023-12-08T01:58:01Z http://ir.unimas.my/id/eprint/43592/ Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses Chien, Yeh Seng Chen, Feng Jui Wu, Han Chieh Lin, Chieh Hua Chang, Wen Chiung David, Perera Yang, Jyh Yuan Lee, Min Shi Liao, Yu Chieh Q Science (General) QR355 Virology R Medicine (General) Enteroviruses (EVs) are a group of viruses that cause various human illnesses. While the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) method can generate VP1 gene fragments for enterovirus genotyping, it is unable to detect recombinant strains. Recent advances in viral genome sequencing using next-generation sequencing technologies have enabled comprehensive analyses. However, the high cost poses a challenge for widespread adoption. To address this issue, this study proposes a cost-effective approach for generating complete enterovirus genome sequences using the Oxford Nanopore MinION sequencer. This protocol not only facilitates the generation of accurate genome sequences for various enterovirus strains but also allows for the differentiation of co-infections from viral isolates. In addition, the method can generate polyprotein sequences as well as peptide sequences of the upstream ORF (uORF) whose expression can impact virus infection. Through the analysis of complete enterovirus genomes, this study successfully identified seven enterovirus A71 isolates obtained during the 2018 enterovirus outbreak in Malaysia and Taiwan as recombinants between enterovirus A71 and coxsackievirus A2. Furthermore, our study has made a significant discovery by establishing a strong correlation between uORF trees and the epidemics of EVA71. This finding highlights the potential of uORF sequences as valuable indicators for monitoring and understanding the spread of EVA71 infections. We also identified notable amino acid changes in the transmembrane domain of the uORF protein within a newly identified lineage. These findings provide crucial insights into the molecular characteristics and evolutionary dynamics of EVA71, offering valuable information for future research and intervention strategies. American Society for Microbiology 2023-08-30 Article PeerReviewed text en http://ir.unimas.my/id/eprint/43592/3/Cost-effective.pdf Chien, Yeh Seng and Chen, Feng Jui and Wu, Han Chieh and Lin, Chieh Hua and Chang, Wen Chiung and David, Perera and Yang, Jyh Yuan and Lee, Min Shi and Liao, Yu Chieh (2023) Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses. Microbiology Spectrum, 11 (5). pp. 1-15. ISSN 2165-0497 https://journals.asm.org/doi/10.1128/spectrum.02507-23 DOI: https://doi.org/10.1128/spectrum.02507-23
institution	Universiti Malaysia Sarawak
building	Centre for Academic Information Services (CAIS)
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sarawak
content_source	UNIMAS Institutional Repository
url_provider	http://ir.unimas.my/
language	English
topic	Q Science (General) QR355 Virology R Medicine (General)
spellingShingle	Q Science (General) QR355 Virology R Medicine (General) Chien, Yeh Seng Chen, Feng Jui Wu, Han Chieh Lin, Chieh Hua Chang, Wen Chiung David, Perera Yang, Jyh Yuan Lee, Min Shi Liao, Yu Chieh Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
description	Enteroviruses (EVs) are a group of viruses that cause various human illnesses. While the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) method can generate VP1 gene fragments for enterovirus genotyping, it is unable to detect recombinant strains. Recent advances in viral genome sequencing using next-generation sequencing technologies have enabled comprehensive analyses. However, the high cost poses a challenge for widespread adoption. To address this issue, this study proposes a cost-effective approach for generating complete enterovirus genome sequences using the Oxford Nanopore MinION sequencer. This protocol not only facilitates the generation of accurate genome sequences for various enterovirus strains but also allows for the differentiation of co-infections from viral isolates. In addition, the method can generate polyprotein sequences as well as peptide sequences of the upstream ORF (uORF) whose expression can impact virus infection. Through the analysis of complete enterovirus genomes, this study successfully identified seven enterovirus A71 isolates obtained during the 2018 enterovirus outbreak in Malaysia and Taiwan as recombinants between enterovirus A71 and coxsackievirus A2. Furthermore, our study has made a significant discovery by establishing a strong correlation between uORF trees and the epidemics of EVA71. This finding highlights the potential of uORF sequences as valuable indicators for monitoring and understanding the spread of EVA71 infections. We also identified notable amino acid changes in the transmembrane domain of the uORF protein within a newly identified lineage. These findings provide crucial insights into the molecular characteristics and evolutionary dynamics of EVA71, offering valuable information for future research and intervention strategies.
format	Article
author	Chien, Yeh Seng Chen, Feng Jui Wu, Han Chieh Lin, Chieh Hua Chang, Wen Chiung David, Perera Yang, Jyh Yuan Lee, Min Shi Liao, Yu Chieh
author_facet	Chien, Yeh Seng Chen, Feng Jui Wu, Han Chieh Lin, Chieh Hua Chang, Wen Chiung David, Perera Yang, Jyh Yuan Lee, Min Shi Liao, Yu Chieh
author_sort	Chien, Yeh Seng
title	Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
title_short	Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
title_full	Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
title_fullStr	Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
title_full_unstemmed	Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses
title_sort	cost-effective complete genome sequencing using the minion platform for identification of recombinant enteroviruses
publisher	American Society for Microbiology
publishDate	2023
url	http://ir.unimas.my/id/eprint/43592/3/Cost-effective.pdf http://ir.unimas.my/id/eprint/43592/ https://journals.asm.org/doi/10.1128/spectrum.02507-23
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score	13.211869

Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses

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