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

Abstract

Background The performance of rRT-PCR for SARS-CoV-2 varies with sampling site(s), illness stage and infection site. Methods Unilateral nasopharyngeal, nasal mid-turbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspect or confirmed cases of COVID-19.True positives were defined as patients with at least one SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, till 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%, mid-turbinate, 62%, and saliva, 38-52%. Clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 95%, 88%, 72%, and 44-56% if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28-44% if >7 days of illness. Comparing patients with URTI vs. pneumonia, clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43-54% vs 26-45%. A combination of nasopharyngeal plus throat or mid-turbinate 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. Conclusion Nasopharyngeal followed by throat specimens offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either mid-turbinate 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.

Low-Cost Polyester-Tipped Three-Dimensionally Printed Nasopharyngeal Swab for the Detection of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

“…Consequently, the patient specimens had high Ct values on average, as well as a higher than expected number of equivocal results. This is in keeping with observations by Sutjipto et al that nasopharyngeal swab clinical sensitivity decreased from 95.3% (95%CI 83-99.1) to 70% (95%CI 50.4-84.6) after day seven of illness (20). The findings of the current study may therefore be less broadly applicable to patients earlier in presentation, and with higher viral loads.…”

Self‐collected saliva for SARS‐CoV‐2 detection: A prospective study in the emergency room

“…10 Saliva collection and/or processing as well as sensitivity of the PCR assay may play a role in such lower performances. 10,11 In fact, the need of optimizing saliva collection and processing has been previously suggested. 12 In this study, saliva collection without any transport media or any nucleic acid stabilization proved to be adequate to achieve a high detection rate and sensitivity.…”

SARS-CoV-2-Diagnostik – was ist wirklich sinnvoll?

“…In der 2. Phase der Erkrankung (etwa 14 Tage nach Symptombeginn) findet sich häufig kein (replizierendes) Virus mehr in den oberen Atemwegen; hier sinkt die Sensitivität für die PCR aus dem Naso-/Oropharynx auf 43-54 % [8,9]. Proben aus den unteren Atemwegen sind dann für eine Diagnosestellung notwendig.…”