Abstract
The emergence of SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), represents a public health emergency of unprecedented proportion. The global containment efforts have been focused on testing, tracing of contacts and treatment (isolation) of those found COVID-19 positive. Since the whole genome sequences of a number of strains of this novel RNA virus were available in the public domain by early January 2020, a number of real-time polymerase chain reaction (RT-PCR) protocols were designed and used for diagnosis of this infection. Most RT-PCRs are designed for qualitative COVID-19 reporting (SARS-CoV-2 detected or not detected), but have been used for semi-quantitative estimation of viral load based on cycle threshold value. Our manuscript discusses the utility of quantitative PCR testing for COVID-19 and its patient management benefits.
Keywords: Coronavirus disease 2019, cycle threshold, patient management, quantitative RT-PCR, SARS-CoV-2
References
- 1.He Xi, Lau E, Wu P, Deng X, Wang J, Hao X. Temporal dynamics in viral shedding and transmissibility of Covid 19. Nat Med. 2020;26:672–675B. doi: 10.1038/s41591-020-0869-5. [DOI] [PubMed] [Google Scholar]
- 2.Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Variation in false-negative rate of reverse transcriptase polymerase chain reaction-based SARS-CoV-2 tests by time since exposure. Ann Intern Med. 2020;173:262–267. doi: 10.7326/M20-1495. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Muller MA. Virological assessment of hospitalized patients with Covid 19. Nature. 2020;581:465–469. doi: 10.1038/s41586-020-2196-x. [DOI] [PubMed] [Google Scholar]
- 4.Bullard J, Dust K, Funk D, Strong JE, Alexander D, Garnett L. Predicting infectious SARS-CoV-2 from diagnostic samples. Clin Infect Dis. 2020:ciaa638. doi: 10.1093/cid/ciaa638. May 22: doi: 10.1093/cid/ciaa638. Epub ahead of print. PMID: 32442256; PMCID: PMC7314198. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med. 2020;382:1177–1179. doi: 10.1056/NEJMc2001737. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.La Scola B, Le Bideau M, Andreani J, Hoang VT, Grimaldier C, Colson P. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur J Clin Microbiol Infect Dis. 2020;39:1059–1061. doi: 10.1007/s10096-020-03913-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Binnicker MJ. Can the SARS-CoV-2 PCR Cycle Threshold Value and Time from Symptom Onset to Testing Predict Infectivity? Clin Infect Dis. 2020:ciaa735. doi: 10.1093/cid/ciaa735. Jun 6: doi: 10.1093/cid/ciaa735. Epub ahead of print. PMID: 32504529; PMCID: PMC7314221. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Han MS, Byun JH, Cho Y, Rim JH. RT-PCR for SARS-CoV-2: quantitative versus qualitative. Lancet Infect Dis. 2020 doi: 10.1016/S1473-3099(20)30424-2. May 20; doi: 10.1016/S1473-3099(20)30424-2. Epub ahead of print. PMID: 32445709; PMCID: PMC7239624. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Poon LL, Chan KH, Wong OK, Cheung TK, Ng I, Zheng B. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays. Clin Chem. 2004;50:67–72. doi: 10.1373/clinchem.2003.023663. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Muenchhoff M, Helga M, Hans N, Natascha GK, Dieter H, Annemarie B, et al. Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020. Euro Surveill.2020;25(24) 10.2807/1560-7917.ES.2020.25.24.2001057. [DOI] [PMC free article] [PubMed]
- 11.Pujadas E, Chaudhry F, McBride R, Richter F, Zhao S, Wajnberg, et al. SARS-CoV-2 viral load predicts COVID-19 mortality. medRxiv preprint, June 2020 medRxiv 2020.06.11.20128934; doi: 10.1101/2020.06.11.20128934. [DOI] [PMC free article] [PubMed]
- 12.Alexandersen S, Chamings A and Bhatta TR. SARS-CoV-2 genomic and subgenomic RNA in diagnostic samples are not an indicator of active replication. medRxiv preprint doi: 10.1101/2020.06.01.20119750.2020. [DOI] [PMC free article] [PubMed]
- 13.World Health Organization . World Health Organization; 2020. Transmission of SARS-CoV-2: Implications for Infection Prevention Precautions. 9 July. [Google Scholar]
- 14.Centre for Disease Control . Centre for Disease Control; Atlanta: 2020. Duration of Isolation and Precautions for Adults with COVID-19. Available from: https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html. [Last accessed on 2020 Jun 22]. [Google Scholar]
- 15.Ministry of Health, Government of India. Revised Discharge policy for COVID-19. Available at: https://www.mohfw.gov.in/pdf/ReviseddischargePolicyforCOVID19.pd. [Last accessed on 2020 Aug 10].
- 16.Larremore DB, Wilder B, Lester E, Shehata S, Burke JM, Hay JA, et al. Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance. Medrxiv : the Preprint Server for Health Sciences. 2020 Jun. DOI: 10.1101/2020.06.22.20136309.
- 17.Lan L, Xu D, Ye G, Xia C, Wang S, Li Y. Positive RT-PCR test results in patients recovered from COVID-19. JAMA. 2020;323:1502–1503. doi: 10.1001/jama.2020.2783. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Guo L, Ren L, Yang S, Xiao M, Chang, Yang F. Profiling early humoral response to diagnose novel coronavirus disease (COVID-19) Clin Infect Dis. 2020;71:778–785. doi: 10.1093/cid/ciaa310. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Miller TE, Beltran W, Bard AZ, Gogakos T, Anahtar MN, Gerino M, et al. Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J. 2020 Aug 28:10.1096/fj.202001700RR. doi: 10.1096/fj.202001700RR. Epub ahead of print. PMID: 32856766; PMCID: PMC7461169. [DOI] [PMC free article] [PubMed]
- 20.Tan CW, Chia WN, Qin X, Liu P, Chen MI, Tiu C. A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction. Nat Biotechnol. 2020;38:1073–1078. doi: 10.1038/s41587-020-0631-z. [DOI] [PubMed] [Google Scholar]
- 21.Le Bert N, Tan AT, Kunasegaran K, Tham CY, Hafezi M, Chia A. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020;584:457–462. doi: 10.1038/s41586-020-2550-z. [DOI] [PubMed] [Google Scholar]
- 22.Odak I, Barros-Martins J, Bošnjak B, Stahl K, David S, Wiesner O. Reappearance of effector T cells is associated with recovery from COVID-19. EBioMedicine. 2020;57:102885. doi: 10.1016/j.ebiom.2020.102885. [DOI] [PMC free article] [PubMed] [Google Scholar]