{"doi":"10.1016/j.ymeth.2021.04.011","title":"Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts","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.","journal":"Methods","year":2021,"id":164540,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":38,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9529,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":524690,"name":"Holly Anne Martin","orcid":null,"position":1,"is_corresponding":false},{"id":687248,"name":"Ryan Marczak","orcid":null,"position":2,"is_corresponding":false},{"id":107208,"name":"Parinaz Fozouni","orcid":"0000-0002-6710-1506","position":3,"is_corresponding":false},{"id":560691,"name":"Albert Vallejo-Gracia","orcid":"0000-0003-4815-5039","position":4,"is_corresponding":false},{"id":107216,"name":"G. Renuka Kumar","orcid":"0000-0001-6090-3285","position":5,"is_corresponding":false},{"id":636294,"name":"Victoria Murray","orcid":"0000-0002-4479-2359","position":6,"is_corresponding":false},{"id":75994,"name":"Sulggi A. Lee","orcid":"0000-0003-1560-2250","position":7,"is_corresponding":false},{"id":103701,"name":"Mélanie Ott","orcid":"0000-0002-5697-1274","position":8,"is_corresponding":false},{"id":28872,"name":"Joseph K. Wong","orcid":"0000-0001-9896-0605","position":9,"is_corresponding":false},{"id":28873,"name":"Steven A. Yukl","orcid":"0000-0002-4578-9872","position":10,"is_corresponding":false},{"id":28865,"name":"Sushama Telwatte","orcid":"0000-0003-4086-5212","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":null,"created_at":"2026-07-18T23:45:32.226038Z","pmid":"33882362","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}