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Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Authors :
Kyle G, Rodino
David R, Peaper
Brendan J, Kelly
Frederic, Bushman
Andrew, Marques
Hriju, Adhikari
Zheng Jin, Tu
Rebecca Marrero, Rolon
Lars F, Westblade
Daniel A, Green
Gregory J, Berry
Fann, Wu
Medini K, Annavajhala
Anne-Catrin, Uhlemann
Bijal A, Parikh
Tracy, McMillen
Krupa, Jani
N Esther, Babady
Anne M, Hahn
Robert T, Koch
Nathan D, Grubaugh
Daniel D, Rhoads
Source :
medRxiv
Publication Year :
2022
Publisher :
American Society for Microbiology, 2022.

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.

Details

ISSN :
1098660X and 00951137
Volume :
60
Database :
OpenAIRE
Journal :
Journal of Clinical Microbiology
Accession number :
edsair.doi.dedup.....569c9e8f752f9e625a6f91146a7b915c