NDLI: Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data

Content Provider	Directory of Open Access Journals (DOAJ)
Author	Yosuke Hirotsu Makoto Maejima Masahiro Shibusawa Yume Natori Yuki Nagakubo Kazuhiro Hosaka Hitomi Sueki Hitoshi Mochizuki Toshiharu Tsutsui Yumiko Kakizaki Yoshihiro Miyashita Masao Omata
Abstract	Objectives: Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants. Methods: A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69–70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis. Results: A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69–70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69–70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169). Conclusion: TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.
ISSN	12019712
e-ISSN	18783511
DOI	10.1016/j.ijid.2022.06.039
Journal	International Journal of Infectious Diseases
Volume Number	122
Language	English
Publisher	Elsevier
Publisher Date	2022-01-01
Publisher Place	Netherlands
Access Restriction	Open
Subject Keyword	Infectious and Parasitic Diseases Sars-cov-2 Voc Omicron Ba.1 Ba.2
Content Type	Text
Resource Type	Article
Subject	Infectious Diseases Microbiology (medical)

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