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 sequ...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
AMER SOC MICROBIOLOGY
2023
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/43971/1/chien-et-al-2023-cost-effective-complete-genome-sequencing-using-the-minion-platform-for-identification-of-recombinant-1-2.pdf http://ir.unimas.my/id/eprint/43971/ https://journals.asm.org/doi/10.1128/spectrum.02507-23 https://doi.org/10.1128/spectrum.02507-23 |
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| Summary: | 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. |
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