Differentiating between infectious and non-infectious influenza A virus and coronavirus RNA levels using long-range RT-qPCR

Autor: Charlotte V. Rigby, Kalyan Dhanorkar, Vishalraj Hulle, Vijeta Jadhao, Hamid Jalal, Shraven Mutha, Aartjan J. W. te Velthuis, Pankaj Mathur, Ingrida Olendraite, Tejes Shah, Vikram Gopal, Dovile Juozapaite
Rok vydání: 2021
Předmět:
DOI: 10.1101/2021.11.11.21266219
Popis: During the Coronavirus Disease 2019 (COVID-19) pandemic, residual SARS-CoV-2 genome and subgenomic RNA fragments were observed in recovered COVID-19 patients. The presence of such RNAs in the absence of live virus leads to incorrectly positive RT-qPCR results, potentially delaying medical procedures and quarantine release. We here propose a simple modification to turn commercial COVID-19 RT-qPCR protocols into long-range RT-qPCR assays that can differentiate between infectious and non-infectious influenza and coronavirus RNA levels. We find that the long-range RT-qPCR method has a sensitivity that is indistinguishable from a commercial Taq-Path COVID-19 RT-qPCR assay when tested on clinical samples taken withing 5 days of the onset of symptoms. In clinical samples taken at least 15 days after the onset of symptoms when patients had recovered from COVID-19, the modified RT-qPCR protocol leads to significantly fewer positive diagnoses. These findings suggest that the long-range RT-qPCR method may improve test-to-release protocols and expand the tools available for clinical COVID-19 diagnosis.ImportanceVarious molecular tests can detect viral RNA in clinical samples. However, these molecular tests cannot differentiate between RNA from infectious viruses or residual viral genome fragments that are not infectious. In several percent of COVID-19 patients, such residual viral RNAs can be detected long after recovery and the disappearance of infectious SARS-CoV-2. These “persistently-positive” RT-qPCR results are different from false-positive RT-qPCR results, which can be generated due to in vitro cross-reactivity or contaminations. However, the detection of RNA fragments leads to incorrect conclusions about the status of a COVID-19 patient and an incorrect diagnosis. We here modified the commercial Taq-Path COVID-19 RT-qPCR kit to make this test less sensitive to residual viral RNA genome fragments, reducing the likelihood that incorrect RT-qPCR results affect the treatment or quarantine status of recovered COVID-19 patients.
Databáze: OpenAIRE