Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Implementation of the eCDC/WHO Recommendation for Molecular Diagnosis of SARS-CoV-2 Omicron Subvariants and Its Challenges

Version 1 : Received: 12 June 2022 / Approved: 14 June 2022 / Online: 14 June 2022 (04:30:41 CEST)

How to cite: Lee, S.H. Implementation of the eCDC/WHO Recommendation for Molecular Diagnosis of SARS-CoV-2 Omicron Subvariants and Its Challenges . Preprints 2022, 2022060192 (doi: 10.20944/preprints202206.0192.v1). Lee, S.H. Implementation of the eCDC/WHO Recommendation for Molecular Diagnosis of SARS-CoV-2 Omicron Subvariants and Its Challenges . Preprints 2022, 2022060192 (doi: 10.20944/preprints202206.0192.v1).

Abstract

Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvariants have the highest number of mutations in the Spike (S) protein gene and these mutations mainly occur in the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the S gene. The eCDC and the WHO recommend partial Sanger sequencing of the SARS-CoV-2 S gene RBD and NTD on the PCR-positive samples in diagnostic laboratories as a practical means of determining the variants of concern to monitor a possible increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. The author’s diagnostic laboratory has implemented the eCDC/WHO recommendation by sequencing a 398-base segment of the N gene for the definitive detection of SARS-CoV-2 in clinical samples, and sequencing a 445-base segment of the RBD and a 490-509-base segment of the NTD for variant determination. This paper presents 5 selective cases to illustrate the challenges of using Sanger sequencing to diagnose Omicron subvariant when the samples harbor a high level of co-existing minor subvariant sequences with multi-allelic single nucleotide polymorphisms (SNPs) or possible recombinant Omicron subvariants containing a BA.1 NTD and a BA.2 RBD, which can only be detected by using specially designed PCR primers. The current large-scale surveillance programs using next-generation sequencing (NGS) do not face similar problems because NGS focuses on deriving consensus sequence.

Keywords

eCDC; WHO; Sanger sequencing; Omicron variant; minor subvariants; BA.4/BA.5; BA.2; mul-ti-allelic; SNPs; recombinant

Subject

MEDICINE & PHARMACOLOGY, General Medical Research

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