Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts.
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Authors
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Telwatte, Sushama1
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Martin, Holly Anne1
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Marczak, Ryan2
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Fozouni, Parinaz3
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Vallejo-Gracia, Albert3
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Kumar, G Renuka3
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Murray, Victoria4
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Lee, Sulggi4
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Ott, Melanie5
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Wong, Joseph K1
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Yukl, Steven A6
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1
Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States.
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(United States)
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2
University of California, Santa Barbara, CA, United States.
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(United States)
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3
Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States.
,
(United States)
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4
Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States.
,
(United States)
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5
Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States.
,
(United States)
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6
Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States. Electronic address: [email protected].
,
(United States)
- Type
- Published Article
- Journal
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Methods
- Publisher
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Elsevier
- Publication Date
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May 01, 2022
- Volume
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201
- Pages
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15–25
- Identifiers
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DOI: 10.1016/j.ymeth.2021.04.011
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PMID: 33882362
- Source
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Medline
- Keywords
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- Language
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English
- License
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Unknown
Abstract
The replication of SARS-CoV-2 and other coronaviruses depends on transcription of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and multiple different subgenomic mRNAs (sgRNAs) encompassing fragments arising from discontinuous transcription. Recent studies have aimed to characterize the expression of subgenomic SARS-CoV-2 transcripts in order to investigate their clinical significance. Here, we describe a novel panel of reverse transcription droplet digital PCR (RT-ddPCR) assays designed to specifically quantify multiple different subgenomic SARS-CoV-2 transcripts and distinguish them from transcripts that do not arise from discontinuous transcription at each locus. These assays can be applied to samples from SARS-CoV-2 infected patients to better understand the regulation of SARS-CoV-2 transcription and how different sgRNAs may contribute to viral pathogenesis and clinical disease severity. Published by Elsevier Inc.
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
This record was last updated on 07/07/2023 and may not reflect the most current and accurate biomedical/scientific data available from NLM.
The corresponding record at NLM can be accessed at
https://www.ncbi.nlm.nih.gov/pubmed/33882362
