Title | Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. |
Publication Type | Journal Article |
Year of Publication | 2022 |
Authors | Rodino 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 Authors | Yale SARS-CoV-2 Genomic Surveillance Initiative |
Journal | medRxiv |
Date Published | 2022 Apr 28 |
Abstract | 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. |
DOI | 10.1101/2022.04.25.22274187 |
Alternate Journal | medRxiv |
PubMed ID | 35547854 |
PubMed Central ID | PMC9094110 |
Grant List | L30 AI120149 / AI / NIAID NIH HHS / United States |
Related Faculty:
Lars Westblade, Ph.D.