Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds.
COVID-19
SARS-CoV-2
infectious virus
repeat testing
Journal
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
ISSN: 1537-6591
Titre abrégé: Clin Infect Dis
Pays: United States
ID NLM: 9203213
Informations de publication
Date de publication:
16 08 2021
16 08 2021
Historique:
received:
15
08
2020
pubmed:
27
10
2020
medline:
20
8
2021
entrez:
26
10
2020
Statut:
ppublish
Résumé
Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify. A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results. In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19. Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Sections du résumé
BACKGROUND
Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify.
METHODS
A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results.
RESULTS
In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19.
CONCLUSIONS
Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Identifiants
pubmed: 33104776
pii: 5940589
doi: 10.1093/cid/ciaa1616
pmc: PMC7665437
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e860-e869Subventions
Organisme : NIAID NIH HHS
ID : HHSN272201400007C
Pays : United States
Organisme : NIH HHS
ID : T32A1007417
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.
Références
JAMA Netw Open. 2020 Jul 1;3(7):e2016382
pubmed: 32697321
J Clin Virol. 2020 Sep;130:104578
pubmed: 32777761
J Virol Methods. 2015 Nov;224:58-66
pubmed: 26315318
Clin Infect Dis. 2020 Jul 28;71(15):778-785
pubmed: 32198501
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32317257
Ann Intern Med. 2020 Aug 18;173(4):262-267
pubmed: 32422057
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32404481
J Clin Virol. 2020 Jun;127:104383
pubmed: 32353760
Clin Infect Dis. 2020 Dec 31;71(11):2939-2946
pubmed: 32562544
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32381643
J Clin Virol. 2020 Jul;128:104416
pubmed: 32388470
Clin Infect Dis. 2020 Jul 28;71(15):793-798
pubmed: 32221523
Nat Med. 2020 Jun;26(6):861-868
pubmed: 32327757
Emerg Infect Dis. 2020 Jul;26(7):
pubmed: 32364890
N Engl J Med. 2020 Jul 30;383(5):494-496
pubmed: 32492294
J Virol. 2008 Oct;82(19):9477-91
pubmed: 18632859
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32341143
Lancet. 2003 May 24;361(9371):1767-72
pubmed: 12781535
Emerg Infect Dis. 2020 Jul;26(7):1633-1635
pubmed: 32294051
Clin Infect Dis. 2020 Dec 17;71(10):2663-2666
pubmed: 32442256
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32317256
Nature. 2020 May;581(7809):465-469
pubmed: 32235945
J Clin Virol. 2020 Sep;130:104583
pubmed: 32791382
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32327448
Clin Microbiol Infect. 2021 Feb;27(2):285.e1-285.e4
pubmed: 32422408
J Infect Dis. 2020 Aug 17;222(6):899-902
pubmed: 32594170
Clin Infect Dis. 2021 Jan 27;72(2):323-326
pubmed: 33501950
J Infect Dis. 2018 May 5;217(11):1708-1717
pubmed: 29648602
Lancet. 2020 Apr 25;395(10233):1339-1340
pubmed: 32304647
Emerg Infect Dis. 2020 Aug;26(8):1920-1922
pubmed: 32421494
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32461285
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32303565
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32332061
Emerg Infect Dis. 2004 Feb;10(2):294-9
pubmed: 15030700
J Clin Virol. 2020 Jul;128:104428
pubmed: 32434706
J Med Virol. 2020 Sep;92(9):1695-1698
pubmed: 32383179
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32461287
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32303564
Nat Methods. 2013 Oct;10(10):1003-5
pubmed: 23995387
Emerg Infect Dis. 2020 Nov;26(11):2701-2704
pubmed: 32749957
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Nat Med. 2020 May;26(5):672-675
pubmed: 32296168
Lancet Infect Dis. 2020 May;20(5):565-574
pubmed: 32213337
N Engl J Med. 2016 Sep 29;375(13):1303-5
pubmed: 27682053
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14989-94
pubmed: 22872860
Radiology. 2020 Aug;296(2):E32-E40
pubmed: 32101510
Nat Methods. 2015 Aug;12(8):733-5
pubmed: 26076426
Eur J Clin Microbiol Infect Dis. 2020 Jun;39(6):1059-1061
pubmed: 32342252
Int J Mol Med. 2020 Sep;46(3):957-964
pubmed: 32705153
J Infect. 2020 Aug;81(2):318-356
pubmed: 32283147
J Clin Virol. 2020 Jun;127:104384
pubmed: 32361285
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32471894
Radiology. 2020 Aug;296(2):E115-E117
pubmed: 32073353
J Clin Microbiol. 2020 May 26;58(6):
pubmed: 32245835
JAMA. 2020 May 12;323(18):1843-1844
pubmed: 32159775
Sci Transl Med. 2020 Jun 3;12(546):
pubmed: 32493791
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Clin Infect Dis. 2020 Jun 16;:
pubmed: 32556191
J Clin Microbiol. 2020 May 26;58(6):
pubmed: 32277022
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32518072
J Clin Microbiol. 2020 Jul 23;58(8):
pubmed: 32350048
Clin Infect Dis. 2021 Mar 15;72(6):1064-1066
pubmed: 32584972
J Virol. 2017 Dec 14;92(1):
pubmed: 29046451
Anal Chem. 2011 Nov 15;83(22):8604-10
pubmed: 22035192
Infect Control Hosp Epidemiol. 2020 Jul;41(7):859-861
pubmed: 32389155