ArticlemSystems
A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses.iScience · 2026Article
- Phylogenetic analysis and molecular genetic characteristics of West Nile virus lineage 2 isolates circulating in the Russian Federation.Virus genes · 2024Article
- The lncRNA ALPHA specifically targets chikungunya virus to control infection.Molecular cell · 2022Article
- Development and evaluation of a ligation-free sequence-independent, single-primer amplification (LF-SISPA) assay for whole genome characterization of viruses.Journal of virological methods · 2022Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- Presence of Segmented Flavivirus Infections in North AmericaEmerging infectious diseases · 2020Article
- High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine.Pathogens (Basel, Switzerland) · 2020Article
- Article
- Growth and adaptation of Zika virus in mammalian and mosquito cells.PLoS neglected tropical diseases · 2018Article
- Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains.Scientific reports · 2018Article
- Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.PLoS neglected tropical diseases · 2018Article
- Sequences of Zika Virus Genomes from a Pediatric Cohort in Nicaragua.Genome announcements · 2018Article
- A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences.Scientific reports · 2018Article
- Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.GigaScience · 2018Article
- Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells.Genome announcements · 2018Article
- Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts.PloS one · 2018Article
- Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice.PLoS neglected tropical diseases · 2017Article
- Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells.PLoS pathogens · 2017Article
- The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.PloS one · 2017Article
- Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus.Journal of virology · 2016Article
Corrections and comments
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Authors and funding
19 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA.
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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.