ArticleTransboundary and emerging diseases2022
Molecular detection of SARS-CoV-2 strains and differentiation of 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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Review
- Design, Synthesis and Biological Exploration of NovelInternational journal of molecular sciences · 2024Article
- Article
- Dynamics of water-mediated interaction effects on the stability and transmission of Omicron.Scientific reports · 2023Article
- Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination.Micromachines · 2023Article
- SARS-CoV-2 detection enabled by a portable and label-free photoelectrochemical genosensor using graphitic carbon nitride and gold nanoparticles.Electrochimica acta · 2023Article
- Competition of SARS-CoV-2 variants on the pandemic transmission dynamics.Chaos, solitons, and fractals · 2023Article
- Research progress of severe acute respiratory syndrome coronavirus 2 on aerosol collection and detection.Chinese chemical letters = Zhongguo hua xue kuai bao · 2023Review
- Identification of SARS CoV-2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq.Immunity, inflammation and disease · 2023Article
- A performance comparison of heterostructure surface plasmon resonance biosensor for the diagnosis of novel coronavirus SARS-CoV-2.Optical and quantum electronics · 2023Article
- SARS-CoV-2 Omicron and its current known unknowns: A narrative review.Reviews in medical virology · 2023Review
- In response to: Disease severity and efficacy of homologous vaccination among patients infected with SARS-CoV-2 Delta or Omicron VOCs, compared to unvaccinated using main biomarkers.Journal of medical virology · 2023Article
- Lateral Flow Immunoassays for Detecting Viral Infectious Antigens and Antibodies.Micromachines · 2022Review
- Review
- SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods.Pathogens (Basel, Switzerland) · 2022Review
- Molecular detection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains.Transboundary and emerging diseases · 2022Article
- Development of a real-time PCR assay for detection and differentiation of Mycoplasma ovipneumoniae and a novel respiratory-associated Mycoplasma species in domestic sheep and goats.Transboundary and emerging diseases · 2022Article
- The SARS-CoV-2 omicron wave is indicating the end of the pandemic phase but the COVID-19 will continue.Journal of medical virology · 2022Article
- Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.Journal of clinical microbiology · 2022Article
- Molecular Dynamics Studies on the Structural Stability Prediction of SARS-CoV-2 Variants Including Multiple Mutants.International journal of molecular sciences · 2022Article
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Authors and funding
14 authors.
Funding
Abstract
The Delta variant of SARS-CoV-2 has now become the predominant strain in the global COVID-19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have developed a real-time RT-PCR (RT-qPCR) for SARS-CoV-2 detection that provides nearly 100% strain coverage, and differentiation of highly transmissible Delta variant strains. All full or nearly full (≥28 kb) SARS-CoV-2 genomes (n = 403,812), including 6422 Delta and 280 Omicron variant strains, were collected from public databases at the time of analysis and used for assay design. The two amino acid deletions in the spike gene (S-gene, Δ156-157) that is characteristic of the Delta variant were targeted during the assay design. Although strain coverage for the Delta variant was very high (99.7%), detection coverage for non-Delta wild-type strains was 93.9%, mainly due to the confined region of design. To increase strain coverage of the assay, the design for CDC N1 target was added to the assay. In silico analysis of 403,812 genomes indicated a 95.4% strain coverage for the CDC N1 target, however, in combination with our new non-Delta S-gene target, total coverage for non-Delta wild-type strains increased to 99.8%. A human 18S rRNA gene was also analyzed and used as an internal control. The final four-plex RT-qPCR assay generated PCR amplification efficiencies between 95.4% and 102.0% with correlation coefficients (R
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