Article ; Online: Rapid Detection of the Omicron (B.1.1.529) SARS-CoV-2 Variant Using a COVID-19 Diagnostic PCR Assay.
2022 Volume 10, Issue 4, Page(s) e0099022
Abstract: The Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is ...
| Abstract | The Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the last variant of concern (VOC) identified to date. Compared to whole-genome or gene-specific sequencing methods, reverse-transcription PCR assays may be a simpler approach to study VOCs. We used a point-of-care COVID-19 diagnostic PCR assay to detect the Omicron SARS-CoV-2 variant in the respiratory tract samples of COVID-19 patients who had tested positive for SARS-CoV-2 RNA between April 2021 and January 2022. Sequencing analyses had shown that 87 samples were positive for the Omicron variant and 43 samples were positive for a non-Omicron variant (Delta, 18 samples; Alpha, 13 samples; Gamma, 10 samples; Beta, 1 sample; or Epsilon, 1 sample). According to results by the PCR assay, whose primers anneal a nucleocapsid (N) gene region that comprises the E31/R32/S33 deletion (also termed the del31/33 mutation), we found that N gene target failure/dropout (i.e., a negative/low result) occurred in 86 (98.8%) of 87 Omicron variant-positive samples tested. These results were assessed in relation to those of the spike (S) gene, which expectedly, was detected in all (100%) 130 samples. A total of 43 (100%) of 43 Delta, Alpha, Gamma, Beta, or Epsilon variant-positive samples had a positive result with the N gene. Importantly, in 86 of 87 Omicron variant-positive samples, the del31/33 mutation was detected together with a P13L mutation, which was, instead, detected alone in the Omicron variant-positive sample that had a positive N-gene result. |
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| MeSH term(s) | COVID-19/diagnosis ; COVID-19 Testing ; Humans ; Mutation ; Polymerase Chain Reaction ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Sensitivity and Specificity |
| Chemical Substances | RNA, Viral |
| Language | English |
| Publishing date | 2022-07-05 |
| Publishing country | United States |
| Document type | Journal Article |
| ZDB-ID | 2807133-5 |
| ISSN | 2165-0497 ; 2165-0497 |
| ISSN (online) | 2165-0497 |
| ISSN | 2165-0497 |
| DOI | 10.1128/spectrum.00990-22 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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