The Effect of Sample Site, Illness Duration, and the Presence of Pneumonia on the Detection of SARS-CoV-2 by Real-time Reverse Transcription PCR.
SARS-CoV-2
illness duration
pneumonia
rRT-PCR
sample site
Journal
Open forum infectious diseases
ISSN: 2328-8957
Titre abrégé: Open Forum Infect Dis
Pays: United States
ID NLM: 101637045
Informations de publication
Date de publication:
Sep 2020
Sep 2020
Historique:
received:
24
05
2020
accepted:
31
07
2020
entrez:
23
9
2020
pubmed:
24
9
2020
medline:
24
9
2020
Statut:
epublish
Résumé
The performance of real-time reverse transcription polymerase chain reaction (rRT-PCR) for SARS-CoV-2 varies with sampling site(s), illness stage, and infection site. Unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspected or confirmed cases of COVID-19. True positives were defined as patients with at least 1 SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, until discharge. Diagnostic performance was assessed and extrapolated for site combinations. We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, midturbinate, 62%, and saliva, 38%-52%. Clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 95%, 88%, 72%, and 44%-56%, respectively, if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28%-44% if >7 days of illness. Comparing patients with upper respiratory tract infection (URTI) vs pneumonia, clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43%-54% vs 26%-45%, respectively. A combination of nasopharyngeal plus throat or midturbinate plus throat specimen afforded overall clinical sensitivities of 89%-92%; this rose to 96% for persons with URTI and 98% for persons ≤7 days from illness onset. Nasopharyngeal specimens, followed by throat specimens, offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either midturbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.
Sections du résumé
BACKGROUND
BACKGROUND
The performance of real-time reverse transcription polymerase chain reaction (rRT-PCR) for SARS-CoV-2 varies with sampling site(s), illness stage, and infection site.
METHODS
METHODS
Unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspected or confirmed cases of COVID-19. True positives were defined as patients with at least 1 SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, until discharge. Diagnostic performance was assessed and extrapolated for site combinations.
RESULTS
RESULTS
We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, midturbinate, 62%, and saliva, 38%-52%. Clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 95%, 88%, 72%, and 44%-56%, respectively, if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28%-44% if >7 days of illness. Comparing patients with upper respiratory tract infection (URTI) vs pneumonia, clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43%-54% vs 26%-45%, respectively. A combination of nasopharyngeal plus throat or midturbinate plus throat specimen afforded overall clinical sensitivities of 89%-92%; this rose to 96% for persons with URTI and 98% for persons ≤7 days from illness onset.
CONCLUSIONS
CONCLUSIONS
Nasopharyngeal specimens, followed by throat specimens, offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either midturbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.
Identifiants
pubmed: 32964061
doi: 10.1093/ofid/ofaa335
pii: ofaa335
pmc: PMC7454916
doi:
Types de publication
Journal Article
Langues
eng
Pagination
ofaa335Investigateurs
Sean Wei Xiang Ong
(SWX)
Brenda Sze Peng Ang
(BSP)
David Chien Lye
(DC)
Poh Lian Lim
(PL)
Cheng Chuan Lee
(CC)
Li Min Ling
(LM)
Lawrence Lee
(L)
Barnaby Edward Young
(BE)
Tau Hong Lee
(TH)
Chen Seong Wong
(CS)
Sapna Sadarangani
(S)
Ray Lin
(R)
Deborah Hee Ling Ng
(DH)
Mucheli Sadasiv
(M)
Po Ying Chia
(PY)
Chiaw Yee Choy
(CY)
Glorijoy Shi En Tan
(GS)
Frederico Dimatatac
(F)
Isais Florante Santos
(IF)
Chi Jong Go
(CJ)
Yeo Tsin Wen
(YT)
Yu Kit Chan
(YK)
Pooja Rao
(P)
Jonathan W Z Chia
(JWZ)
Constance Yuan Yi Chen
(CYY)
Boon Kiat Toh
(BK)
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Infectious Diseases Society of America.
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