Detection profile of SARS-CoV-2 using RT-PCR in different types of clinical specimens: A systematic review and meta-analysis

Abstract

Testing is one of the commendable measures for curbing the spread of coronavirus disease (COVID-19). But, it should be done using the most appropriate specimen and an accurate diagnostic test such as real-time reverse transcription-polymerase chain reaction (qRT-PCR). Therefore, a systematic review was conducted to determine the positive detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in different clinical specimens using qRT-PCR. A total of 8136 pooled clinical specimens were analyzed to detect SARS-CoV-2, the majority were nasopharyngeal swabs (69.6%). A lower respiratory tract (LRT) specimens had a positive rate (PR) of 71.3% (95% confidence interval [CI]: 60.3%-82.3%) while no virus was detected in the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95% CI: 79.9%-103.7%), followed by rectal swabs; 87.8% (95% CI: 78.6%-96.9%) then sputum; 68.1% (95% CI: 56.9%-79.4%). A low PR was observed in oropharyngeal swabs; 7.6% (95% CI: 5.7%-9.6%) and blood samples; 1.0% (95% CI: -0.1%-2.1%) whereas no SARS-CoV-2 was detected in urine samples. Feces had a PR of 32.8% (95% CI:1 5.8%-49.8%). Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95% CI: 31.2%-59.7%). In this study, SARS-CoV-2 was highly detected in LRT specimens while no virus was detected in urinogenital specimens. BLF had the highest PR followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had moderate PR. Low PR was recorded in oropharyngeal swab and blood samples while no virus was found in urine samples. Last, the virus was detected in feces, suggesting SARS-CoV-2 transmission by the fecal route.

Keywords: COVID-19; SARS-CoV-2; clinical sample; clinical specimen; polymerase chain reaction.

Figure 1

Prism flow chart showing study screening

Figure 2

The rate of detection based on type of clinical specimen. BLF specimen had the positivity rate of 91.8% (18/20; 95% CI: 79.9%‐103.7%), 87.8% (43/49; 95% CI: 78.6%‐96.9%) for rectal swab, 68.1% (261/370; 95% CI: 56.9%‐79.4%) for sputum specimen, 62.5% (5/8; 95% CI: 29.0%‐96.0%) for nasal swabs, 46.2% (6/13; 95% CI: 19.1%‐73.3%) for FBB specimen, 31.7% (126/398; 95% CI: 27.1%‐34.1%) for pharyngeal swabs, 32.8% (107/300; 95% CI: 15.8%‐49.8%) for feces, 1.0% (3/3017; 95%CI: −0.1%‐2.1%) for blood sample, 0.8% (0/126; 95% CI: −0.7%‐2.4%) for urine sample, 45.5% (2060/5662; 95% CI: 31.2%‐59.7%) for nasopharyngeal swab, 87.8% (43/49; 95% CI: 78.6%‐96.9%), 66.7% (2/3; 95% CI: 11.3%‐120.0%) for throat swab, 33.3% (1/3; 95% CI: −20.0%‐82.8%) for serum, 10.0% (0/4; 95% CI: −16.3%‐36.3%) for plasma sample, 38.9% (65/167; 95% CI: 31.5%‐46.3%) and 7.6% (54/706; 95% CI: 5.7%‐9.6%) for oropharyngeal swab. BLF, bronchoalveolar lavage fluid; CI, confidence interval; FBB, fibrobronchoscope brush biopsy

Figure 3

Positive detection rate based on sampling site. About 403 specimens were collected for detection of SARS‐CoV‐2 from LRT where 71.3% (285/403; 95% CI: 60.3%‐82.3%) tested positive. Specimens from URT had the positivity rate of 40.6% (2312/6944; 95% CI: 28.4%‐52.9%). Gastro intestinal tract (GIT) specimens recorded 43.2% positive SARS‐CoV‐2 (150/349; 95% CI: 16.6%‐69.9%). Blood fluids and UGT had the positivity rate of 1.0% (4/314; 95% CI: −0.1%‐2.1%) and 0.8% (0/126; 95% CI:−0.7%‐2.4%), respectively. CI, confidence interval; LRT, lower respiratory tract; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2; UGT, urinogenital tract