ArticleThe Journal of infectious diseases2023
Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction.
Article in The Journal of infectious diseases, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed, 5 citations in OpenAlex.
- Mechanisms of sex differences in acute and long COVID sequelae in mice.bioRxiv : the preprint server for biology · 2025Article
- SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset.American journal of respiratory and critical care medicine · 2024Article
- Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.Microbiology spectrum · 2023Article
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Authors and funding
18 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundControl of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission requires understanding SARS-CoV-2 replication dynamics.
methodsWe developed a multiplexed droplet digital polymerase chain reaction (ddPCR) assay to quantify SARS-CoV-2 subgenomic RNAs (sgRNAs), which are only produced during active viral replication, and discriminate them from genomic RNAs (gRNAs). We applied the assay to specimens from 144 people with single nasopharyngeal samples and 27 people with >1 sample. Results were compared to quantitative PCR (qPCR) and viral culture.
resultssgRNAs were quantifiable across a range of qPCR cycle threshold (Ct) values and correlated with Ct values. The ratio sgRNA:gRNA was stable across a wide range of Ct values, whereas adjusted amounts of N sgRNA to a human housekeeping gene declined with higher Ct values. Adjusted sgRNA and gRNA amounts were quantifiable in culture-negative samples, although levels were significantly lower than in culture-positive samples. Daily testing of 6 persons revealed that sgRNA is concordant with culture results during the first week of infection but may be discordant with culture later in infection. sgRNA:gRNA is constant during infection despite changes in viral culture.
conclusionsCt values from qPCR correlate with active viral replication. More work is needed to understand why some cultures are negative despite presence of sgRNA.
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Registered trials
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