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

Sutjipto, Stephanie; Lee, Pei Hua; Tay, Jun Yang; Mendis, Shehara M; Abdad, Mohammad Yazid; Marimuthu, Kalisvar; Ng, Oon Tek; Lin, Cui; Chan, Monica; Soon, Margaret; Lin, Raymond T P; Leo, Yee-sin; De, Partha P; Barkham, Timothy; Vasoo, Shawn

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.