ArticleNucleic acids research2013
Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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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.
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Who cites it
54 citing papers in PubMed, 82 citations in OpenAlex.
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- Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2023Article
- Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia.Microbial genomics · 2023Article
- RNA Sequencing Data Sets and Their Whole-Genome Sequence Assembly of Dengue Virus from Three Serial Passages in Vero Cells.Microbiology resource announcements · 2021Article
- The Single-Cell Transcriptomic Analysis of Prefrontal Pyramidal Cells and Interneurons Reveals the Neuronal Expression of Genes Encoding Antimicrobial Peptides and Immune Proteins.Frontiers in immunology · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics.PloS one · 2020Article
- Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage.Veterinary microbiology · 2019Article
- Contribution of Resident Memory CD8Pathogens (Basel, Switzerland) · 2019Review
- A Highly Pathogenic Strain of Porcine Deltacoronavirus Caused Watery Diarrhea in Newborn Piglets.Virologica Sinica · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates.PloS one · 2018Article
- Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.Virus evolution · 2018Article
- HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.AIDS research and human retroviruses · 2017Article
- Article
- Molecular detection of watermelon mosaic virus associated with a serious mosaic disease onVirusdisease · 2017Article
- Quasispecies evolution of the prototypical genotype 1 porcine reproductive and respiratory syndrome virus early during in vivo infection is rapid and tissue specific.Archives of virology · 2017Article
- Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
Abstract
RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and de novo assembly optimized for viral genomes. With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination.
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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.