Clinical utility of SARS-CoV-2 subgenomic RT-PCR in a pediatric quaternary care setting.

Lucas J Osborn, Pei Ying Chen, Jessica Flores-Vazquez, Javier Mestas, Edahrline Salas, Marisa Glucoft, Michael A Smit, Cristina Costales, Jennifer Dien Bard

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2023 Jul

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During active transcription, SARS-CoV-2 generates subgenomic regions of viral RNA. While standard SARS-CoV-2 RT-PCR amplifies region(s) of genomic RNA, it cannot distinguish active infection from remnant viral genomic material. However, screening for subgenomic RNA (sgRNA) by RT-PCR may aid in the determination of actively transcribing virus. To evaluate the clinical utility of SARS-CoV-2 sgRNA RT-PCR testing in a pediatric population. Retrospective analysis was performed on inpatients from February-September 2022 positive for SARS-CoV-2 by RT-PCR with a concomitant order for sgRNA RT-PCR. Chart abstractions were conducted to determine clinical outcomes, management, and infection prevention and control (IPC) practices. Of 95 SARS-CoV-2 positive samples from 75 unique patients, 27 (28.4%) were positive by sgRNA RT-PCR. A negative sgRNA RT-PCR test allowed for de-isolation in 68 (71.6%) patient episodes. Regardless of age or sex, a positive sgRNA RT-PCR result significantly correlated with disease severity (P = 0.007), generalized COVID-19 symptoms (P = 0.012), hospitalization for COVID-19 (P = 0.019), and immune status (P = 0.024). Moreover, sgRNA RT-PCR results prompted changes in management in 28 patients (37.3%); specifically, therapeutic escalation in 13/27 (48.1%) positives and de-escalation in 15/68 (22.1%) negatives. Taken together, these findings underscore the clinical utility of sgRNA RT-PCR testing in a pediatric population as we report significant associations between sgRNA RT-PCR results and clinical parameters related to COVID-19. These findings align with the proposed use of sgRNA RT-PCR testing to guide patient management and IPC practices in the hospital setting. Copyright © 2023 Elsevier B.V. All rights reserved.

Citation

Lucas J Osborn, Pei Ying Chen, Jessica Flores-Vazquez, Javier Mestas, Edahrline Salas, Marisa Glucoft, Michael A Smit, Cristina Costales, Jennifer Dien Bard. Clinical utility of SARS-CoV-2 subgenomic RT-PCR in a pediatric quaternary care setting. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology. 2023 Jul;164:105494