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Total and subgenomic RNA viral load in patients infected with SARS-CoV-2 Alpha, Delta, and Omicron variants. The Journal of infectious diseases Dimcheff, D. E., Blair, C. N., Zhu, Y., Chappell, J. D., Gaglani, M., McNeal, T., Ghamande, S., Steingrub, J. S., Shapiro, N. I., Duggal, A., Busse, L. W., Frosch, A. E., Peltan, I. D., Hager, D. N., Gong, M. N., Exline, M. C., Khan, A., Wilson, J. G., Qadir, N., Ginde, A. A., Douin, D. J., Mohr, N. M., Mallow, C., Martin, E. T., Johnson, N. J., Casey, J. D., Stubblefield, W. B., Gibbs, K. W., Kwon, J. H., Talbot, H. K., Halasa, N., Grijalva, C. G., Baughman, A., Womack, K. N., Hart, K. W., Swan, S. A., Surie, D., Thornburg, N. J., McMorrow, M. L., Self, W. H., Lauring, A. S., Investigating Respiratory Viruses in the Acutely Ill (IVY) Network 2023

Abstract

BACKGROUND: SARS-CoV-2 genomic and subgenomic RNA levels are frequently used as a correlate of infectiousness. The impact of host factors and SARS-CoV-2 lineage on RNA viral load is unclear.METHODS: Total nucleocapsid (N) and subgenomic N (sgN) RNA levels were measured by RT-qPCR in specimens from 3,204 individuals hospitalized with COVID-19 at 21 hospitals. RT-qPCR cycle threshold (Ct) values were used to estimate RNA viral load. The impact of time of sampling, SARS-CoV-2 variant, age, comorbidities, vaccination, and immune status on N and sgN Ct values were evaluated using multiple linear regression.RESULTS: Ct values at presentation for N (mean ±standard deviation) were 24.14±4.53 for non-variants of concern, 25.15±4.33 for Alpha, 25.31±4.50 for Delta, and 26.26±4.42 for Omicron. N and sgN RNA levels varied with time since symptom onset and infecting variant but not with age, comorbidity, immune status, or vaccination. When normalized to total N RNA, sgN levels were similar across all variants.CONCLUSIONS: RNA viral loads were similar among hospitalized adults, irrespective of infecting variant and known risk factors for severe COVID-19. Total N and subgenomic RNA N viral loads were highly correlated, suggesting that subgenomic RNA measurements adds little information for the purposes of estimating infectivity.

View details for DOI 10.1093/infdis/jiad061

View details for PubMedID 36883903