SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples

Area of Science:

• Virology
• Infectious Diseases
• Molecular Biology

Background:

• Viral RNA persistence in recovered COVID-19 patients raises questions about SARS-CoV-2 viability.
• Subgenomic RNAs (sgRNAs) are proposed as potential molecular markers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viability.
• Limited data exist on the longitudinal kinetics of sgRNAs compared to genomic RNA (gRNA) in clinical settings.

Purpose of the Study:

• To investigate the longitudinal kinetics of SARS-CoV-2 sgRNA and gRNA in clinical samples.
• To compare the decay patterns of sgRNA and gRNA in vitro.
• To evaluate the potential of sgRNA as a molecular viability marker for SARS-CoV-2.

Main Methods:

• Analysis of 536 samples from 205 COVID-19 patients in peginterferon Lambda-1a and favipiravir trials.
• Collection of nasal swabs at multiple time points (days 1, 4, 6 for Lambda; days 1, 5, 10 for favipiravir).
• Quantification of N-gene gRNA and sgRNA using quantitative reverse transcription polymerase chain reaction (RT-qPCR) and in vitro decay kinetics in infected cells treated with remdesivir.

Main Results:

• sgRNA remained detectable in approximately 50% of samples at later time points (day 6 and day 10).
• High linear correlation (R² = 0.83) was observed between gRNA and sgRNA cycle threshold (Ct) values.
• No significant difference in the rate of Ct increase was found between gRNA and sgRNA in clinical trials or in vitro remdesivir-treated cells.

Conclusions:

• sgRNA is highly correlated with gRNA in both clinical samples and in vitro experiments.
• sgRNA decay patterns do not differ significantly from gRNA.
• The findings do not support the application of sgRNA as a reliable viability marker for SARS-CoV-2.