The Yield and Consistency of the Detection of SARS-CoV-2 in Multiple Respiratory Specimens

Haixia Zhang; Meiling Chen; Yanhua Zhang; Jing Wen; Yajie Wang; Liming Wang; Jinjin Guo; Chen Liu; Daijing Li; Ying Wang; Jing Bai; Guiju Gao; Sa Wang; Di Yang; Fengting Yu; Liting Yan; Gang Wan; Fujie Zhang

doi:10.1093/ofid/ofaa379

The Yield and Consistency of the Detection of SARS-CoV-2 in Multiple Respiratory Specimens

Open Forum Infect Dis. 2020 Aug 26;7(10):ofaa379. doi: 10.1093/ofid/ofaa379. eCollection 2020 Oct.

Authors

Haixia Zhang¹, Meiling Chen², Yanhua Zhang^{1

3}, Jing Wen^{1

3}, Yajie Wang⁴, Liming Wang^{3

5}, Jinjin Guo⁴, Chen Liu⁴, Daijing Li^{1

3}, Ying Wang^{1

3}, Jing Bai^{1

3}, Guiju Gao³, Sa Wang³, Di Yang³, Fengting Yu^{3

5}, Liting Yan^{3

5}, Gang Wan², Fujie Zhang^{3

5}

Affiliations

¹ The Nursing Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
² The Medical Statistic Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
³ Department of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
⁴ Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
⁵ Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China.

Abstract

Background: Few studies have compared the yield of reverse transcription polymerase chain reaction (RT-PCR) assays in nasopharyngeal swabs, oropharyngeal swabs, and sputum for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection.

Methods: We conducted an observational study in Beijing Ditan Hospital, China. Specimens including nasopharyngeal swabs, oropharyngeal swabs, and sputum from confirmed coronavirus 2019 patients were collected for RT-PCR testing. Disease duration was calculated from the date of symptom onset to the date of specimen collection and divided into 3 groups: ≤14 days, 14-21 days, and >21 days. We compared positive rates across the 3 specimens collected. The kappa coefficient was used to evaluate the consistency of RT-PCR results between different specimens.

Results: A total of 291 specimens were collected and tested from 43 confirmed patients. Among specimens collected with a disease duration of ≤14 days, the positive rate was highest in sputum (79.2%); this rate was significantly higher than that in nasopharyngeal swabs (37.5%; P = .003) and oropharyngeal swabs (20.8%; P < .001). Similar findings were observed with the disease durations of 14-21 days and >21 days. The consistency of testing results between nasopharyngeal swabs and oropharyngeal swabs was low with the disease durations of ≤14 days and >21 days. The consistency between the sputum and oropharyngeal swabs and between the sputum and nasopharyngeal swabs was very low across all 3 disease durations, with statistical significance.

Conclusions: Compared with nasopharyngeal swabs and oropharyngeal swabs, sputum had the highest yield of SARS-CoV-2 detection. Nasopharyngeal swabs and oropharyngeal swabs had a similar yield. If sputum is not feasible, a nasopharyngeal swab can be recommended for the detection of SARS-CoV-2, and early testing is needed.

Keywords: SARS-CoV-2; nasopharyngeal swabs; oropharyngeal swabs; positive rate; sputum.