Back to Search
Start Over
Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping
- Source :
- Modern Pathology, bioRxiv, article-version (status) pre, article-version (number) 1
- Publication Year :
- 2020
-
Abstract
- The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq (“cRASL-seq”), which enables analysis of any targeted pathogen-(and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ∼1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ∼10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
- Subjects :
- 0301 basic medicine
Pathology
medicine.medical_specialty
Genotype
Polyadenylation
Computer science
Population
Virulence
Computational biology
Genome
DNA sequencing
Article
Pathology and Forensic Medicine
03 medical and health sciences
COVID-19 Testing
0302 clinical medicine
medicine
Humans
education
Genotyping
Messenger RNA
education.field_of_study
SARS-CoV-2
Oligonucleotide
Nucleic acid methods
COVID-19
High-Throughput Nucleotide Sequencing
RNA
Diagnostic markers
Reverse transcriptase
030104 developmental biology
Viral infection
030220 oncology & carcinogenesis
Nucleic acid
RNA, Viral
Oligonucleotide Probes
Ligation
Oligomer restriction
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- bioRxiv : the preprint server for biology
- Accession number :
- edsair.doi.dedup.....c10ff6ef9d654f0805db9a9a87f50300