ArticleBMC genomics2020
A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
- 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
- Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus.bioRxiv : the preprint server for biology · 2026Article
- Development of a culture-independent whole-genome sequencing of Nipah virus using the MinION Oxford Nanopore platform.Microbiology spectrum · 2025Article
- varVAMP: degenerate primer design for tiled full genome sequencing and qPCR.Nature communications · 2025Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Low Prevalence of Nirmatrelvir-Ritonavir Resistance-Associated Mutations in SARS-CoV-2 Lineages From Botswana.Open forum infectious diseases · 2024Article
- A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition.mSystems · 2024Article
- Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing.Virologica Sinica · 2024Article
- High-performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks.Microbiology spectrum · 2024Article
- Article
- Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance.Animals : an open access journal from MDPI · 2023Article
- Early Detection of the Recombinant SARS-CoV-2 XAN Variant in Bulgaria: Initial Genomic Insights into Yet Another Piece of the Growing Puzzle of Recombinant Clades.Microorganisms · 2023Article
- COVID Variants, Villain and Victory: A Bioinformatics Perspective.Microorganisms · 2023Article
- Toward a global virus genomic surveillance network.Cell host & microbe · 2023Review
- Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.Scientific reports · 2023Article
- Article
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Early detection of variants of concern via funnel plots of regional reproduction numbers.Scientific reports · 2023Article
- Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron.FEMS microbes · 2023Article
- SARS-CoV-2 variant identification using a genome tiling array and genotyping probes.Personalized medicine · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries.
resultsHere we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach.
conclusionsThe tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.
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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.