Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.

TitlePartial ORF1ab Gene Target Failure with Omicron BA.2.12.1.
Publication TypeJournal Article
Year of Publication2022
AuthorsRodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJin, Rolon RMarrero, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann A-C, Parikh BA, McMillen T, Jani K, N Babady E, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD
Corporate AuthorsYale SARS-CoV-2 Genomic Surveillance Initiative
Date Published2022 Apr 28

Mutations in the viral genome of SARS-CoV-2 can impact 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 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% 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 impact 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.

Alternate JournalmedRxiv
PubMed ID35547854
PubMed Central IDPMC9094110
Grant ListL30 AI120149 / AI / NIAID NIH HHS / United States
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