ArticleScientific reports2022
Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- Medical software for precision diagnostics of infection with immunoprofiling and artificial intelligence.Journal of translational medicine · 2026Review
- Enabling global-scale nucleic acid repositories through versatile, scalable biochemical selection from room-temperature archives.Nature communications · 2026Article
- A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method.Frontiers in genetics · 2025Article
- ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.Bioinformatics (Oxford, England) · 2024Article
- Review
- Generation of quality-controlled SARS-CoV-2 variant stocks.Nature protocols · 2023Review
- COVID Variants, Villain and Victory: A Bioinformatics Perspective.Microorganisms · 2023Article
- Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons.Scientific reports · 2023Article
- The importance of equally accessible genomic surveillance in the age of pandemics.Biologia futura · 2023Review
- A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2023Article
- Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR.Frontiers in public health · 2023Article
- The origins of COVID-19 pandemic: A brief overview.Transboundary and emerging diseases · 2022Review
- Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays.Frontiers in cellular and infection microbiology · 2022Article
- Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19.Frontiers in bioengineering and biotechnology · 2022Review
- High-throughput and automated screening for COVID-19.Frontiers in medical technology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Monitoring new mutations in SARS-CoV-2 provides crucial information for identifying diagnostic and therapeutic targets and important insights to achieve a more effective COVID-19 control strategy. Next generation sequencing (NGS) technologies have been widely used for whole genome sequencing (WGS) of SARS-CoV-2. While various NGS methods have been reported, one chief limitation has been the complexity of the workflow, limiting the scalability. Here, we overcome this limitation by designing a laboratory workflow optimized for high-throughput studies. The workflow utilizes modified ARTIC network v3 primers for SARS-CoV-2 whole genome amplification. NGS libraries were prepared by a 2-step PCR method, similar to a previously reported tailed PCR method, with further optimizations to improve amplicon balance, to minimize amplicon dropout for viral genomes harboring primer-binding site mutation(s), and to integrate robotic liquid handlers. Validation studies demonstrated that the optimized workflow can process up to 2688 samples in a single sequencing run without compromising sensitivity and accuracy and with fewer amplicon dropout events compared to the standard ARTIC protocol. We additionally report results for over 65,000 SARS-CoV-2 whole genome sequences from clinical specimens collected in the United States between January and September of 2021, as part of an ongoing national genomics surveillance effort.
Indexed as
Identifiers
What OpenQuestion holds
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.