ArticleNature protocols2017
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07626073 (h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.), which is not on this map. Cited by 759 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.
Who cites it
759 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review.Epidemiology and infection · 2026Pooled it
- Protocol for Detecting and Sequencing Chikungunya Virus from Field-Collected Mosquitoes.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
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- Autochthonous chikungunya virus (CHIKV) outbreak in the province of Modena, Emilia-Romagna region, Italy, August to October 2025: epidemiology, clinical features and virological findings.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Detection and genomic characterization of a travel-associated ECSA lineage chikungunya virus infection in Mexico.ASM case reports · 2026Article
- Whole-genome sequencing of adenovirus 41 directly from wastewater using nested overlapping PCR and MinION.Microbiology spectrum · 2026Article
- Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses.iScience · 2026Article
- Zika virus positivity in Aedes aegypti mosquitoes and its genomic landscape from Pune, Western India.The Indian journal of medical research · 2026Article
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- Characterization and evolutionary history of novel SARS-CoV-2-related viruses in bats from Cambodia.Nature communications · 2026Article
- Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus.bioRxiv : the preprint server for biology · 2026Article
- A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus.Virology journal · 2026Article
- Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology.Nature communications · 2026Article
- Detection of and Early Genomic Insights into Chikungunya Virus, Bolivia, 2025.Emerging infectious diseases · 2026Article
- Machine-Learning Microfluidic Minute-Scale Microorganism Metrics Monitoring(M6).Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Geographic variability of severe fever with thrombocytopenia syndrome virus genomes in the Miyazaki Prefecture, Japan: a cross-sectional molecular epidemiological study.Parasites & vectors · 2026Article
- Review
- Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa.BMJ open · 2026Article
699 more citing papers are in PubMed but not listed here.
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Authors and funding
28 authors.
Funding
Abstract
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
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