Evidence map›Paper›PMID 35760380›Full record

ArticleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases2022

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

Yosuke Hirotsu, Makoto Maejima, Masahiro Shibusawa, Yume Natori, Yuki Nagakubo, Kazuhiro Hosaka, Hitomi Sueki, Hitoshi Mochizuki, Toshiharu Tsutsui, Yumiko Kakizaki and 2 more

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Article in International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Nanobodies targeting SARS-CoV-2 variants.Acta pharmaceutica Sinica. B · 2026
    Review
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  13. SARS-CoV-2 recombinant XN, Italy.Journal of clinical virology plus · 2022
    Article
  14. Article
  15. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Yosuke HirotsuGenome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan. Electronic address: hirotsu-bdyu@ych.pref.yamanashi.jp.
Makoto MaejimaDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Masahiro ShibusawaDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Yume NatoriDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Yuki NagakuboDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Kazuhiro HosakaDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Hitomi SuekiDivision of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Hitoshi MochizukiGenome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Central Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Toshiharu TsutsuiLung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Yumiko KakizakiLung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Yoshihiro MiyashitaLung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
Masao OmataDepartment of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectivesRecently, 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.

methodsA 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.

resultsA 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).

conclusionTaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.

Indexed as

COVID-19SARS-CoV-2HumansBA.1BA.2OmicronSARS-CoV-2VOC

Identifiers

PMID35760380
PMCPMC9233878

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.