ArticleJournal of virological methods2023
SpikeSeq: A rapid, cost efficient and simple method to identify SARS-CoV-2 variants of concern by Sanger sequencing part of the spike protein gene.
Article in Journal of virological methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- 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
- Article
- SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay.Scientific reports · 2023Article
- Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing.Microbial genomics · 2023Article
- Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger.Enfermedades infecciosas y microbiologia clinica (English ed.) · 2023Article
- Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations.Microbiology spectrum · 2023Article
- Evaluating methodological approaches to assess the severity of infection with SARS-CoV-2 variants: scoping review and applications on Belgian COVID-19 data.BMC infectious diseases · 2022Article
- A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants.Diagnostics (Basel, Switzerland) · 2022Article
- Validation and advantages of using novel RT-qPCR melting curve analysis assays for the identification of SARS-CoV-2 variants.Scientific reports · 2022Article
- High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants.American journal of clinical pathology · 2022Article
- Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark.Genome medicine · 2022Article
- Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala.Frontiers in public health · 2022Article
- A metagenomics workflow for SARS-CoV-2 identification, co-pathogen detection, and overall diversity.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy.Genomics · 2021Article
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9 authors.
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Abstract
In 2020, the novel coronavirus, SARS-CoV-2, caused a pandemic, which is still raging at the time of writing this. Here, we present results from SpikeSeq, the first published Sanger sequencing-based method for the detection of Variants of Concern (VOC) and key mutations, using a 1 kb amplicon from the recognized ARTIC Network primers. The proposed setup relies entirely on materials and methods already in use in diagnostic RT-qPCR labs and on existing commercial infrastructure offering sequencing services. For data analysis, we provide an automated, open source, and browser-based mutation calling software (https://github.com/kblin/covid-spike-classification, https://ssi.biolib.com/covid-spike-classification). We validated the setup on 195 SARS-CoV-2 positive samples, and we were able to profile 85% of RT-qPCR positive samples, where the last 15% largely stemmed from samples with low viral count. We compared the SpikeSeq results to WGS results. SpikeSeq has been used as the primary variant identification tool on > 10.000 SARS-CoV-2 positive clinical samples during 2021. At approximately 4€ per sample in material cost, minimal hands-on time, little data handling, and a short turnaround time, the setup is simple enough to be implemented in any SARS-CoV-2 RT-qPCR diagnostic lab. Our protocol provides results that can be used to choose antibodies in a clinical setting and for the tracking and surveillance of all positive samples for new variants and known ones such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) Delta (B.1.617.2), Omicron BA.1(B.1.1.529), BA.2, BA.4/5, BA.2.75.x, and many more, as of October 2022.
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