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
| Autor: | Sutjipto, Stephanie, Lee, Pei Hua, Tay, Jun Yang, Mendis, Shehara M, Abdad, Mohammad Yazid, Marimuthu, Kalisvar, Ng, Oon Tek, Cui, Lin, Chan, Monica, Soon, Margaret, Lin, Raymond T P, Leo, Yee-Sin, De, Partha P, Barkham, Timothy, Vasoo, Shawn, Ong, Sean Wei Xiang, Ang, Brenda Sze Peng, Lye, David Chien, Lim, Poh Lian, Lee, Cheng Chuan, Ling, Li Min, Lee, Lawrence, Young, Barnaby Edward, Lee, Tau Hong, Wong, Chen Seong, Sadarangani, Sapna, Lin, Ray, Ling Ng, Deborah Hee, Sadasiv, Mucheli, Chia, Po Ying, Choy, Chiaw Yee, En Tan, Glorijoy Shi, Dimatatac, Frederico, Santos, Isais Florante, Go, Chi Jong, Wen, Yeo Tsin, Chan, Yu Kit, Rao, Pooja, Chia, Jonathan W Z, Chen, Constance Yuan Yi, Toh, Boon Kiat |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
medicine.medical_specialty Saliva 030106 microbiology illness duration rRT-PCR Gastroenterology Major Articles 03 medical and health sciences 0302 clinical medicine stomatognathic system Internal medicine Throat medicine pneumonia 030212 general & internal medicine Respiratory system Nose business.industry SARS-CoV-2 Pharynx medicine.disease Reverse transcription polymerase chain reaction Pneumonia medicine.anatomical_structure Upper respiratory tract infection AcademicSubjects/MED00290 Infectious Diseases Oncology sample site business |
| Zdroj: | Open Forum Infectious Diseases |
| ISSN: | 2328-8957 |
| DOI: | 10.1093/ofid/ofaa335 |
| Popis: | 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 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 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 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. |
| Databáze: | OpenAIRE |
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