ArticleVirology journal2016
Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens.
Article in Virology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Virological and epidemiological investigations of a severe hand foot and mouth disease outbreak, Vietnam, 2023.PLoS neglected tropical diseases · 2026Article
- Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.Wellcome open research · 2025Article
- Monkeypox Virus Infection in 2 Female Travelers Returning to Vietnam from Dubai, United Arab Emirates, 2022.Emerging infectious diseases · 2023Article
- Laboratory diagnosis of nonpolio enteroviruses: A review of the current literature.Biosafety and health · 2023Review
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Evaluation of the cross-neutralization activities elicited by Coxsackievirus A10 vaccine strains.Human vaccines & immunotherapeutics · 2021Article
- Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 2019.Virus evolution · 2021Article
- Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019.Microbiology resource announcements · 2021Article
- Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples.Wellcome open research · 2021Article
- Coxsackievirus A16 in Southern Vietnam.Frontiers in microbiology · 2021Article
- The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections.Viruses · 2020Article
- Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting.Open forum infectious diseases · 2020Article
- Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.Nature microbiology · 2020Article
- Illumina sequencing of clinical samples for virus detection in a public health laboratory.Scientific reports · 2019Article
- Detection and Characterization of Human Pegivirus 2, Vietnam.Emerging infectious diseases · 2018Observational
- Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples.Scientific reports · 2018Article
- Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam.Emerging infectious diseases · 2018Article
- The aetiologies of central nervous system infections in hospitalised Cambodian children.BMC infectious diseases · 2017Article
- Enterovirus D68 in Viet Nam (2009-2015).Wellcome open research · 2017Article
- Central Nervous System Infection Diagnosis by Next-Generation Sequencing: A Glimpse Into the Future?Open forum infectious diseases · 2017Article
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundHand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing. We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9-33.3) were used for assay evaluation.
resultsOur assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94-100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible.
conclusionsIn conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.
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