Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature

Abstract

Objective: The most widely used diagnostic technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is real-time reverse transcriptase-polymerase chain reaction (RT-PCR). It can be done on different samples: nasopharyngeal swabs (NPS) or oropharyngeal swabs (OPS), and self-collected saliva. However, negative findings do not rule out infection.

Methods: A review was conceived to discuss advantages and limitations of the available diagnostic modalities for nonserologic diagnosis of SARS-CoV-2 based on RT-PCR; the article also proposes some practical suggestions to improve diagnostic reliability.

Results: A total of 16 papers (corresponding to 452 patients) of the 56 initially identified were included. Most of the papers describe findings from different samples obtained in limited case series; comparative studies are missing.

Conclusions: Diagnostic accuracy of NPS and OPS is suboptimal and the risk of contaminated aerosol dispersal is not negligible. The SARS-CoV-2 RNA can be found in self-collected saliva specimens of many infected patients within 7 to 10 days after symptom onset. There is an urgent need for comparative trials to define the diagnostic modality of choice. Adequate education and training of health care personnel is mandatory.

Keywords: COVID-19; emergency; infection; nasopharynx; swab.

Figure 1.

Flowchart of article selection.

Figure 2.

Nasopharyngeal swab execution represented in a drawing (A) and performed in a patient (B); correct placement of the tip of the swab into the nasopharynx documented by means of transnasal videoendoscopy (C).

Figure 3.

Oropharyngeal swab execution represented in a drawing (A) and performed in a patient (B); correct placement of the tip of the swab at the posterior oropharyngeal wall documented by means of transnasal videoendoscopy (C).