Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1
- 18 May 2022
- journal article
- research article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 60 (6), e0060022
- https://doi.org/10.1128/jcm.00600-22
Abstract
Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a >= 2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.Keywords
Funding Information
- HHS | NIH | OSC | Common Fund (R61/33-HL137063)
- HHS | NIH | OSC | Common Fund (AI140442)
- Center for AIDS Research, University of Pennsylvania (P30-AI045008)
- HHS | Centers for Disease Control and Prevention (75D30120C09570)
- HHS | Centers for Disease Control and Prevention (CDC BAA 200-2021-10986)
- HHS | Centers for Disease Control and Prevention (75D30121C11102/000HCVL1-2021-55232)
- HHS | NIH | National Cancer Institute (P30 CA008748)
- HHS | NIH | National Institute of Allergy and Infectious Diseases (K23 AI121485)
- HHS | NIH | National Institute of Allergy and Infectious Diseases (U01 DA053949)
- HHS | NIH | National Institute of Allergy and Infectious Diseases (75N93021C00015)
This publication has 31 references indexed in Scilit:
- A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic AssayJournal of Clinical Microbiology, 2020
- A Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19Infectious Diseases and Therapy, 2020
- Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients With Coronavirus Disease 2019Clinical Infectious Diseases, 2020
- Can the Severe Acute Respiratory Syndrome Coronavirus 2 Polymerase Chain Reaction Cycle Threshold Value and Time From Symptom Onset to Testing Predict Infectivity?Clinical Infectious Diseases, 2020
- Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic SamplesClinical Infectious Diseases, 2020
- To Interpret the SARS-CoV-2 Test, Consider the Cycle Threshold ValueClinical Infectious Diseases, 2020
- Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease EpidemiologyJMIR Public Health and Surveillance, 2018
- brms: An R Package for Bayesian Multilevel Models Using StanJournal of Statistical Software, 2017
- Stan: A Probabilistic Programming LanguageJournal of Statistical Software, 2017