ArticleMicrobiology spectrum2022
Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing.
Article in Microbiology spectrum, 2022. 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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Who cites it
14 citing papers in PubMed.
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in East Asia and the Pacific Region: Longitudinal Trend Analysis.JMIR public health and surveillance · 2025Article
- Novel method for the identification of circulating SARS-CoV-2 variants and clinical characteristics of patient infection with SARS-CoV-2 variants in Central China.Frontiers in cellular and infection microbiology · 2025Article
- Amplicon-based analyses of single-nucleotide polymorphisms reveal the genetic structure of a forest insect baculovirus.Virus evolution · 2025Article
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Canada: Longitudinal Trend Analysis.JMIR public health and surveillance · 2024Article
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Sub-Saharan Africa: Longitudinal Trend Analysis.JMIR public health and surveillance · 2024Article
- Surveillance Metrics and History of the COVID-19 Pandemic in Central Asia: Updated Epidemiological Assessment.JMIR public health and surveillance · 2024Article
- South Asia's COVID-19 History and Surveillance: Updated Epidemiological Assessment.JMIR public health and surveillance · 2024Article
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Europe: Longitudinal Trend Analysis.JMIR public health and surveillance · 2024Article
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in the Middle East and North Africa: Longitudinal Trend Analysis.JMIR public health and surveillance · 2024Article
- Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing.Briefings in bioinformatics · 2024Article
- Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Latin America and the Caribbean: Longitudinal Trend Analysis.JMIR public health and surveillance · 2024Article
- Article
- CRISPR techniques and potential for the detection and discrimination of SARS-CoV-2 variants of concern.Trends in analytical chemistry : TRAC · 2023Review
- Next-Generation Sequencing: A Promising Tool for Vaccines and Other Biological Products.Vaccines · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
COVID-19 is caused by SARS-CoV-2, several virulent variants of which have emerged since 2019. More than 529 million people have been infected, and at least 6 million have died. Our aim was to develop a fast, accurate, low-cost method for detecting and identifying newly emerging variants of concern (VOCs) that could pose a global threat. The 341-bp DNA sequence of a specific region of the SARS-CoV-2's spike protein was amplified by a one-step PCR on RNA samples from 46 patients. The product was sequenced using next-generation sequencing (NGS). DNA sequences from seven genomes, the original Wuhan isolate and six different representative variants obtained from the GISAID website, were used as references. Complete whole-genome sequences from local isolates were also obtained from the GISAID website, and their RNA was used for comparison. We used an amplicon-based NGS method (termed VOC-NGS) for genotyping and successfully identified all 46 samples. Fifteen (32.6%) were like the original isolate. Twenty-seven were VOCs: nine (19.5%) Alpha, eight (19%) Delta, six (14%) Beta, and four (8.7%) Omicron. Two were variants of interest (VOI): one (2%) Kappa and one (2%) Zeta. Two samples were mixtures of two variants, one of Alpha and Beta and one of Alpha and Delta. The Spearman correlation between whole-genome sequencing (WGS) and VOC-NGS was significant (
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