ArticleBMC genomics2018
Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use.Reviews in medical virology · 2022Pooled it
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Clinical analysis of Mycoplasma pneumoniae pneumonia combined with adenovirus infection in children with lobar pneumonia.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- Low Prevalence of Middle East Respiratory Syndrome Coronavirus Infection in Camel-Exposed Patients Presenting with Respiratory Symptoms in Northern Kenya.The American journal of tropical medicine and hygiene · 2025Article
- Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak.Veterinary sciences · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.Frontiers in veterinary science · 2025Article
- Comprehensive Review on Viral RNA Extraction Strategies for Enhanced Molecular Diagnostics.Interdisciplinary perspectives on infectious diseases · 2025Review
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- Analysis of Suspected Measles Cases with Discrepant Measles-Specific IgM and rRT-PCR Test Results, Japan.Emerging infectious diseases · 2024Article
- RAPIDViruses · 2023Article
- Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.Journal of virological methods · 2023Article
- Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach.Viruses · 2023Review
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Article
- RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance.The Science of the total environment · 2022Review
- Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome.Frontiers in cellular and infection microbiology · 2022Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundNumerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly.
resultsIn this study, we performed qRT-PCR and viral metagenomic analysis of the extraction efficiency of four commonly used Qiagen extraction kits: QIAamp Viral RNA Mini Kit (VRMK), QIAamp MinElute Virus Spin Kit (MVSK), RNeasy Mini Kit (RMK), and RNeasy Plus Micro Kit (RPMK), using a mixed respiratory clinical sample without any pre-treatment. This sample contained an adenovirus (ADV), influenza virus A (Flu A), human parainfluenza virus 3 (PIV3), human coronavirus OC43 (OC43), and human metapneumovirus (HMPV). The quantity and quality of the viral extracts were significantly different among these kits. The highest threshold cycle(Ct)values for ADV and OC43 were obtained by using the RPMK. The MVSK had the lowest Ct values for ADV and PIV3. The RMK revealed the lowest detectability for HMPV and PIV3. The most effective rate of NGS data at 67.47% was observed with the RPMK. The other three kits ranged between 12.1-26.79% effectiveness rates for the NGS data. Most importantly, compared to the other three kits the highest proportion of non-host reads was obtained by the RPMK. The MVSK performed best with the lowest Ct value of 20.5 in the extraction of ADV, while the RMK revealed the best extraction efficiency by NGS analysis.
conclusionsThe evaluation of viral nucleic acid extraction efficiency is different between NGS and qRT-PCR analysis. The RPMK was most applicable for the metagenomic analysis of viral RNA and enabled more sensitive identification of the RNA virus genome in respiratory clinical samples. In addition, viral RNA extraction kits were also applicable for metagenomic analysis of the DNA virus. Our results highlighted the importance of nucleic acid extraction kit selection, which has a major impact on the yield and number of viral reads by NGS analysis. Therefore, the choice of extraction method for a given viral pathogen needs to be carefully considered.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.