ArticleMicrobiology spectrum2021
Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein.
Article in Microbiology spectrum, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 66 citations in OpenAlex.
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- Spatiotemporal structure of SARS-CoV-2 mutational frequencies in wastewater samples from Ontario.PloS one · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Therapeutic Potential of Neutralizing Monoclonal Antibodies (nMAbs) against SARS-CoV-2 Omicron Variant.Current pharmaceutical design · 2025Review
- 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
- Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Emergence of SARS-CoV-2 omicron variant JN.1 in Tamil Nadu, India - Clinical characteristics and novel mutations.Scientific reports · 2024Article
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.Nature communications · 2024Article
- Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics.PLoS computational biology · 2024Article
- Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations.medRxiv : the preprint server for health sciences · 2024Article
- Targeted amplification and genetic sequencing of the severe acute respiratory syndrome coronavirus 2 surface glycoprotein.Microbiology spectrum · 2024Article
- NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples.Pathogens (Basel, Switzerland) · 2024Article
- Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2.Wellcome open research · 2024Article
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- Genomic surveillance of SARS-CoV-2 using long-range PCR primers.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.
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