ArticleTransboundary and emerging diseases2022
Molecular detection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains.
Article in Transboundary and emerging diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- Article
- Article
- Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.Scientific reports · 2023Article
- The coming Omicron waves and factors affecting its spread after China reopening borders.BMC medical informatics and decision making · 2023Article
- Passive Surveillance of SARS-CoV-2 in Adult Blacklegged Ticks (Life (Basel, Switzerland) · 2023Article
- Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination.Micromachines · 2023Article
- Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2.Heliyon · 2023Article
- Assessment of the Risk and Symptoms of SARS-CoV-2 Infection Among Healthcare Workers During the Omicron Transmission Period: A Multicentric Study from Four Hospitals of Mainland China.Infection and drug resistance · 2023Article
- Molecular detection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains.Transboundary and emerging diseases · 2022Article
- Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2.Journal of virological methods · 2022Article
Corrections and comments
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Authors and funding
15 authors at 1 institution in 1 country.
Funding
Abstract
The SARS-CoV-2 virus is the causative agent of COVID-19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS-CoV-2 full- or near-full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31-33 aa deletion in the N-gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non-Delta/non-Omicron wild-type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild-type genotypes, respectively. The assay was designed to specifically detect SAR-CoV-2 strains. Selected samples with Omicron, Delta and wild-type genotypes identified by the RT-qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus-positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS-CoV-2 by the ThermoFisher TaqPath COVID-19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non-Omicron/non-Delta wild-type genotypes, respectively.
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