ArticleMicrobial genomics2023
Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 21 citations in OpenAlex.
- Enriching Public Pathogen Genomic Records With Patient Metadata: Quantitative Study and Exploratory Case Analysis.JMIR bioinformatics and biotechnology · 2026Article
- Wastewater Metagenomic Virome Analysis of the 2026 World Cup in Texas.medRxiv : the preprint server for health sciences · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Review
- SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking of human read removal strategies for viral and microbial metagenomics.Cell reports methods · 2025Article
- Large-Scale Saliva-Based Clinical Surveillance Enables Real Time SARS-CoV-2 Outbreak Detection and Genomic Tracking (Arizona, 2020-2023).Diagnostics (Basel, Switzerland) · 2025Article
- Environmental Dissemination of SARS-CoV-2: An Analysis Employing Crassphage and Next-Generation Sequencing Protocols.Food and environmental virology · 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
- 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
- A Novel and Rapid Selective Viral Genome Amplification and Sequencing Method for African Swine Fever Virus.Viruses · 2024Article
- A novel isothermal whole genome sequencing approach for Monkeypox Virus.Scientific reports · 2024Article
- Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment.PLoS pathogens · 2024Review
- Testing for SARS-CoV-2: lessons learned and current use cases.Clinical microbiology reviews · 2024Review
- Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.Nature communications · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2.Genome biology and evolution · 2023Article
- Sequencing of SARS-CoV-2 RNA Fragments in Wastewater Detects the Spread of New Variants during Major Events.Microorganisms · 2023Article
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
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