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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have received increasing attention globally because of their increased transmissibility and potential to escape immunity. Although whole-genome sequencing is the gold standard method for SARS-CoV-2 mutation detection and lineage determination, it is costly and time-consuming. However, SARS-CoV-2 variants can be identified based on select variant-specific single nucleotide polymorphisms (SNPs) in the spike protein-encoding gene (). This study validated and compared the limit of detection (LOD) of L452R, N501Y, HV69/70 del and E484K as variant-specific SNPs of the gene and as a SARS-CoV-2-specific gene, using the Novaplex SARS-CoV-2 variants assay kit series. For three SARS-CoV-2 lineages (B.1.617.2, B.1.1.7 and R.1), one strain per lineage was used. Variant-specific SNPs of the gene were analysed using the Novaplex SARS-CoV-2 variants I assay and Novaplex SARS-CoV-2 variants II assay kits. Validation confirmed the LODs of the variant kits. The LOD for each target variant-specific SNP and was five RNA copies per reaction. The Novaplex SARS-CoV-2 variants assay kit series performs well and the LOD for SARS-CoV-2 detection and variant-specific SNP detection are consistent. The kits are suitable for use as routine laboratory tests for SARS-CoV-2 and variant-specific SNP detection in a single step, saving time and labour.

Funding
This study was supported by the:
  • Seegene Technology
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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/content/journal/acmi/10.1099/acmi.0.000447
2022-10-27
2024-03-01
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References

  1. Volz E, Mishra S, Chand M, Barrett JC, Johnson R et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature 2021; 593:266–269 [View Article] [PubMed]
    [Google Scholar]
  2. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 2021; 19:409–424 [View Article] [PubMed]
    [Google Scholar]
  3. Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and delta variant of SARS-CoV-2: a comparative computational study of spike protein. J Med Virol 2022; 94:1641–1649 [View Article]
    [Google Scholar]
  4. La Rosa G, Mancini P, Bonanno Ferraro G, Veneri C, Iaconelli M et al. Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein. Water Res 2021; 197:117104 [View Article] [PubMed]
    [Google Scholar]
  5. Nörz D, Grunwald M, Olearo F, Fischer N, Aepfelbacher M et al. Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. J Clin Virol 2021; 141:104894 [View Article] [PubMed]
    [Google Scholar]
  6. Zhen W, Smith E, Manji R, Schron D, Berry GJ. Clinical evaluation of three sample-to-answer platforms for detection of SARS-CoV-2. J Clin Microbiol 2020; 58:e00783-20 [View Article]
    [Google Scholar]
  7. Kami W, Kinjo T, Arakaki W, Oki H, Motooka D et al. Rapid and simultaneous identification of three mutations by the Novaplex. J Clin Virol 2021; 141:104877 [View Article]
    [Google Scholar]
  8. Shirato K, Nao N, Katano H, Takayama I, Saito S et al. Development of genetic diagnostic methods for detection for novel coronavirus 2019(nCoV-2019) in Japan. Jpn J Infect Dis 2020; 73:304–307 [View Article]
    [Google Scholar]
  9. Nishiura H, Ito K, Anzai A, Kobayashi T, Piantham C et al. Relative reproduction number of SARS-CoV-2 omicron (B.1.1.529) compared with delta variant in South Africa. J Clin Med 2022; 11:30 [View Article]
    [Google Scholar]
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