Diagnostic usefulness of subgenomic RNA detection of viable SARS-CoV-2 in patients with COVID-19

Ji Yeun Kim, Joon Yong Bae, Seongman Bae, Hye Hee Cha, Ji Soo Kwon, Mi Hyun Suh, Hyun Jung Lee, Jiwon Jung, Min Jae Kim, Chunguang Cui, Heedo Park, Jungmin Lee, Man Seong Park, Sung Han Kim

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


Objectives: The development of a rapid diagnostic test for viable SARS-CoV-2 is important for infection control. Real-time RT-PCR assays detect non-viable virus, and cell culture differentiates viable virus but it takes several weeks and is labour-intensive. Subgenomic RNAs may reflect replication-competent virus. We therefore evaluated the usefulness of subgenomic RNAs for diagnosing viable SARS-CoV-2 in patients with COVID-19. Methods: Patients with various severities of confirmed COVID-19 were enrolled at a tertiary hospital between February and December 2020. RT-PCR assay results for genomic and subgenomic RNA of SARS-CoV-2 from nasopharyngeal swab, sputum and saliva specimens were compared with cell culture results. Results: A total 189 specimens from 20 COVID-19 patients were tested in genomic and subgenomic PCR assays and cultured on Vero cells. Of these 189 samples, 62 (33%) gave positive culture results, 93 (49%) negative results and the remaining 34 (18%) indeterminate results. Compared with cell culture results, the sensitivities of genomic RNA and subgenomic RNA of the N and S genes were comparable at 100%, but the specificity of subgenomic RNA (N, 65% and S, 68%) was higher than that of genomic RNA (N, 23% and S, 17%, p < 0.001). The mean durations of positive culture and subgenomic RNA were 11.39 ± 10.34 and 13.75 ± 11.22 days after symptom onset (p 0.437), respectively, while that of genomic RNA was 22.85 ± 11.83 days after symptom onset (p < 0.001). Discussion: Our comparison of subgenomic RNA detection with symptom duration and SARS-CoV-2 culture positivity provides a significant advancement on the transmissibility-based approach beyond the detection of SARS-CoV-2 genomic RNA, and warrants further studies on the development of better diagnostic strategy.

Original languageEnglish
Pages (from-to)101-106
Number of pages6
JournalClinical Microbiology and Infection
Issue number1
Publication statusPublished - 2022 Jan

Bibliographical note

Publisher Copyright:
© 2021 European Society of Clinical Microbiology and Infectious Diseases


  • COVID-19
  • Infective viral shedding
  • SARS CoV-2
  • Subgenomic RNA
  • Virus culture

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases


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