ArticleViruses2020
Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism.
Article in Viruses, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 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
- SARS-CoV-2 resistance analyses from the Phase 3 PINETREE study of remdesivir treatment in nonhospitalized participants.Antimicrobial agents and chemotherapy · 2025Trial
- Genomic Surveillance of Endemic Human Coronaviruses in Côte d'Ivoire Using Targeted Hybrid-Capture Sequencing.Viruses · 2026Article
- Amplicon sequencing with Oxford nanopore technologies as a diagnostic alternative for small ruminant lentiviruses in sheep.Scientific reports · 2026Article
- The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19.Microbiology spectrum · 2025Article
- Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.Nucleic acids research · 2025Article
- Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever.Frontiers in cellular and infection microbiology · 2025Article
- Simultaneous and sensitive detection ofFrontiers in bioengineering and biotechnology · 2025Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Bioengineered small extracellular vesicles deliver multiple SARS-CoV-2 antigenic fragments and drive a broad immunological response.Journal of extracellular vesicles · 2024Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade.Nature communications · 2023Article
- Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery.Cells · 2023Review
- The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.Genome biology · 2023Article
- LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein.PLoS biology · 2023Article
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay.Gene reports · 2022Article
- XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection.Nature communications · 2022Article
- Intrinsic host susceptibility among multiple species to intranasal SARS-CoV-2 identifies diverse virological, biodistribution and pathological outcomes.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
46 authors at 9 institutions in 5 countries.
Funding
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.
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Registered trials
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