ArticleFrontiers in medicine2022
Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol.
Article in Frontiers in medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review of Methodological Approaches to SARS-CoV-2 Wastewater Surveillance.Viruses · 2026Pooled it
- From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens.Genes · 2026Article
- Longitudinal Epidemiology and Variant Dynamics of SARS-CoV-2 in Coastal Kenya (2020-2025): Clinical Features and Wave Patterns.Open forum infectious diseases · 2026Article
- Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.Microbiology spectrum · 2025Article
- Genomic and clinical epidemiology of SARS-CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave.BMC global and public health · 2025Article
- Monitoring SARS-CoV-2 Dissemination in Wastewater and Virus Isolation in Cell Cultures: An Integrated Approach for Pathogen Detection and Surveillance.Journal of cellular and molecular medicine · 2025Article
- Epidemiological dynamics of influenza B virus across multiple seasons in Kenya and Uganda inferred from sequence data, 2010-2021.BMC infectious diseases · 2025Article
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- varVAMP: degenerate primer design for tiled full genome sequencing and qPCR.Nature communications · 2025Article
- Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer.Wellcome open research · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM 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
- Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak.BMC genomics · 2024Article
- The first detection of SARS-CoV-2 RNA in the wastewater of Bucharest, Romania.Scientific reports · 2024Article
- Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment.PLoS pathogens · 2024Review
- Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification.Microorganisms · 2024Article
- Article
- A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.Virology journal · 2024Article
- Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.Environmental science & technology · 2024Review
- Targeted amplification-based whole genome sequencing ofMicrobiology spectrum · 2024Article
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Authors and funding
14 authors.
Funding
Abstract
introductionThe ARTIC Network's primer set and amplicon-based protocol is one of the most widely used SARS-CoV-2 sequencing protocol. An update to the V3 primer set was released on 18th June 2021 to address amplicon drop-off observed among the Delta variant of concern. Here, we report on an in-house optimization of a modified version of the ARTIC Network V4 protocol that improves SARS-CoV-2 genome recovery in instances where the original V4 pooling strategy was characterized by amplicon drop-offs.
methodsWe utilized a matched set of 43 clinical samples and serially diluted positive controls that were amplified by ARTIC V3, V4 and optimized V4 primers and sequenced using GridION from the Oxford Nanopore Technologies'.
resultsWe observed a 0.5% to 46% increase in genome recovery in 67% of the samples when using the original V4 pooling strategy compared to the V3 primers. Amplicon drop-offs at primer positions 23 and 90 were observed for all variants and positive controls. When using the optimized protocol, we observed a 60% improvement in genome recovery across all samples and an increase in the average depth in amplicon 23 and 90. Consequently, ≥95% of the genome was recovered in 72% (
conclusionUtilizing the ARTIC V4 primers, while increasing the primer concentrations for amplicons with drop-offs or low average read-depth, greatly improves genome recovery of Alpha, Beta, Delta, Eta and non-VOC/non-VOI SARS-CoV-2 variants.
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