Analytical and clinical evaluation of a heat shock SARS-CoV-2 detection method without RNA extraction for N and E genes RT-qPCR.
COVID-19
Heat shock
RNA extraction free
RT-qPCR
SARS-CoV-2
Journal
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
ISSN: 1878-3511
Titre abrégé: Int J Infect Dis
Pays: Canada
ID NLM: 9610933
Informations de publication
Date de publication:
Aug 2021
Aug 2021
Historique:
received:
04
11
2020
revised:
13
06
2021
accepted:
15
06
2021
pubmed:
25
6
2021
medline:
1
9
2021
entrez:
24
6
2021
Statut:
ppublish
Résumé
The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits. The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols. 1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68.8% (232/337) and 89.4% (202/226) of SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98.6%, 93.3% and 84.8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample. Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients at the time of testing. This affordable protocol can help overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.
Sections du résumé
BACKGROUND
BACKGROUND
The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits.
OBJECTIVE
OBJECTIVE
The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols.
RESULTS
RESULTS
1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68.8% (232/337) and 89.4% (202/226) of SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98.6%, 93.3% and 84.8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample.
CONCLUSIONS
CONCLUSIONS
Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients at the time of testing. This affordable protocol can help overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.
Identifiants
pubmed: 34166793
pii: S1201-9712(21)00526-9
doi: 10.1016/j.ijid.2021.06.038
pmc: PMC8215877
pii:
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
315-320Informations de copyright
Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest All authors have no conflict of interest to declare.
Références
J Clin Virol. 2020 Jul;128:104454
pubmed: 32485473
Emerg Infect Dis. 2020 Aug;26(8):
pubmed: 32396505
J Clin Virol. 2020 Nov;132:104587
pubmed: 32898817
Int J Infect Dis. 2021 Mar;104:303-305
pubmed: 33434671
Nature. 2020 Aug;584(7821):425-429
pubmed: 32604404
N Engl J Med. 2020 Jul 23;383(4):299-302
pubmed: 32412704
Int J Infect Dis. 2021 Jan;102:14-16
pubmed: 33115681
PLoS One. 2020 Jul 24;15(7):e0236564
pubmed: 32706827
Euro Surveill. 2020 Apr;25(14):
pubmed: 32290902
Virus Res. 2020 Dec;290:198173
pubmed: 32979475
Euro Surveill. 2020 Jan;25(3):
pubmed: 31992387
J Clin Virol. 2020 Aug;129:104519
pubmed: 32629187
PLoS Biol. 2020 Oct 2;18(10):e3000896
pubmed: 33006983
J Clin Microbiol. 2021 Jan 21;59(2):
pubmed: 33239378
Nature. 2020 May;581(7809):465-469
pubmed: 32235945
Cell. 2020 Dec 23;183(7):1901-1912.e9
pubmed: 33248470
Front Cell Infect Microbiol. 2020 Jun 23;10:356
pubmed: 32656101
Lancet. 2020 May 30;395(10238):1735-1738
pubmed: 32386564
One Health. 2020 Dec 20;11:100185
pubmed: 33102678
J Clin Virol. 2020 Aug;129:104439
pubmed: 32674034
J Virol Methods. 2004 Mar 15;116(2):181-7
pubmed: 14738986
J Clin Virol. 2020 Sep;130:104579
pubmed: 32795959