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Bloemen, M., Rector, A., Swinnen, J., Ranst, M.V., Maes, P., Vanmechelen, B. and Wollants, E. (2022) Fast Detection of SARS-CoV-2 Variants Including Omicron Using One-Step RT-PCR and Sanger Sequencing. Journal of Virological Methods, 304, Article ID: 114512.
https://doi.org/10.1016/j.jviromet.2022.114512

has been cited by the following article:

• TITLE: Accurate Diagnosis of SARS-CoV-2 JN.1 by Sanger Sequencing of Receptor-Binding Domain Is Needed for Clinical Evaluation of Its Immune Evasion

  AUTHORS: Sin Hang Lee

  KEYWORDS: Omicron JN.1, SARS-CoV-2, Sanger Sequencing, RBD, L455S Mutation, Immune Evasion, Vaccination Policies, CDC

  JOURNAL NAME: Journal of Biosciences and Medicines, Vol.12 No.4, April 10, 2024

  ABSTRACT: Background: Omicron JN.1 has become the dominant SARS-CoV-2 variant in recent months. JN.1 has the highest number of amino acid mutations in its receptor binding domain (RBD) and has acquired a hallmark L455S mutation. The immune evasion capability of JN.1 is a subject of scientific investigation. The US CDC used SGTF of TaqPath COVID-19 Combo Kit RT-qPCR as proxy indicator of JN.1 infections for evaluation of the effectiveness of updated monovalent XBB.1.5 COVID-19 vaccines against JN.1 and recommended that all persons aged ≥ 6 months should receive an updated COVID-19 vaccine dose. Objective: Recommend Sanger sequencing instead of proxy indicator to diagnose JN.1 infections to generate the data based on which guidelines are made to direct vaccination policies. Methods: The RNA in nasopharyngeal swab specimens from patients with clinical respiratory infection was subjected to nested RT-PCR, targeting a 398-base segment of the N-gene and a 445-base segment of the RBD of SARS-CoV-2 for amplification. The nested PCR amplicons were sequenced. The DNA sequences were analyzed for amino acid mutations. Results: The N-gene sequence showed R203K, G204R and Q229K, the 3 mutations associated with Omicron BA.2.86 (+JN.1). The RBD sequence showed 24 of the 26 known amino acid mutations, including the hallmark L455S mutation for JN.1 and the V483del for BA.2.86 lineage. Conclusions: Sanger sequencing of a 445-base segment of the SARS-CoV-2 RBD is useful for accurate determination of emerging variants. The CDC may consider using Sanger sequencing of the RBD to diagnose JN.1 infections for statistical analysis in making vaccination policies.