ArticleMicrobiology spectrum2022
Profiling of SARS-CoV-2 Subgenomic RNAs in Clinical Specimens.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 32 citations in OpenAlex.
- Structure of the E3 ligase CRL2Cell reports · 2026Article
- Adaptation of the multiplexed CRISPR-Cas13 CARMEN RVP assay for longitudinal detection of respiratory pathogens from air samples.Applied and environmental microbiology · 2026Article
- Adaptation of the multiplexed CRISPR-Cas13 CARMEN RVP assay for longitudinal detection of respiratory pathogens from air samples.medRxiv : the preprint server for health sciences · 2025Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- Performance of Subgenomic RT-PCR for Predicting SARS-CoV-2 Infectivity Compared to Genomic RT-PCR and Culture Isolation.Journal of medical virology · 2025Article
- PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.Bioinformatics (Oxford, England) · 2025Article
- Reverse transcription-quantitative PCR assays for detecting SARS-CoV-2 using subgenomic RNA load.Heliyon · 2025Article
- Reduced Presence of SARS-CoV-2 microRNA-like Small RNA in the Serum of Patients with Post-Acute Sequelae SARS-CoV-2 Infection.Microorganisms · 2025Article
- SARS-CoV-2 ORF7 subgenomic RNA and Host IFN-β Expression in COVID-19 Hospitalized Patients with Different Prognosis.International journal of molecular and cellular medicine · 2025Article
- Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells.Access microbiology · 2025Article
- Patterns of Isoform Variation for N Gene Subgenomic mRNAs in Betacoronavirus Transcriptomes.Viruses · 2024Article
- Abortive infection of bat fibroblasts with SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Improved sub-genomic RNA prediction with the ARTIC protocol.Nucleic acids research · 2024Article
- Oral SARS-CoV-2 host responses predict the early COVID-19 disease course.Scientific reports · 2024Article
- Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: A comparison between Omicron BA.2 and non-VOC-D614G.Virologica Sinica · 2024Article
- Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2.International journal of molecular sciences · 2024Review
- One for all-human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses.Journal of virology · 2023Article
- Hospital-at-home care for immunodeficient patients with COVID-19: Approach to persistent COVID-19 infection.Clinical case reports · 2023Article
- Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture.Viruses · 2023Article
- Potential therapeutic applications of extracellular vesicles in the immunopathogenesis of COVID-19.Pathology, research and practice · 2023Review
Corrections and comments
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Authors and funding
12 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 transcribes a set of subgenomic RNAs (sgRNAs) essential for the translation of structural and accessory proteins to sustain its life cycle. We applied RNA-seq on 375 respiratory samples from individual COVID-19 patients and revealed that the majority of the sgRNAs were canonical transcripts with N being the most abundant (36.2%), followed by S (11.6%), open reading frame 7a (ORF7a; 10.3%), M (8.4%), ORF3a (7.9%), ORF8 (6.0%), E (4.6%), ORF6 (2.5%), and ORF7b (0.3%); but ORF10 was not detected. The profile of most sgRNAs, except N, showed an independent association with viral load, time of specimen collection after onset, age of the patient, and S-614D/G variant with ORF7b and then ORF6 being the most sensitive to changes in these characteristics. Monitoring of 124 serial samples from 10 patients using sgRNA-specific real-time RT-PCR revealed a potential of adopting sgRNA as a marker of viral activity. Respiratory samples harboring a full set of canonical sgRNAs were mainly collected early within 1 to 2 weeks from onset, and most of the stool samples (90%) were negative for sgRNAs despite testing positive by diagnostic PCR targeting genomic RNA. ORF7b was the first to become undetectable and again being the most sensitive surrogate marker for a full set of canonical sgRNAs in clinical samples. The potential of using sgRNA to monitor viral activity and progression of SARS-CoV-2 infection, and hence as one of the objective indicators to triage patients for isolation and treatment should be considered.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.