Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study

Abstract

Introduction: Nasopharyngeal Swab (NPS) sample is considered as gold standard for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but is relatively invasive, and is perceived as uncomfortable by the patient while saliva sample collection is easy, non invasive, more acceptable and can be self-collected without requirement of any healthcare professional or expert. Aim: To validate the use of saliva as a biological sample for the diagnosis of SARS-CoV-2 in comparison to NPS for the detection of SARS-CoV-2 in clinically suspected patients. Materials and Methods: This was a cross-sectional study conducted at Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Andhra Pradesh, India from 28th January 2022 to 16th February 2022. Patients attending Medicine Outpatient Department (OPD) with signs and symptoms suggestive of SARS-CoV-2 infection were included in the study. Self-collected saliva sample and NPS collected by healthcare personnel from all patients were assigned separate identification numbers and sent to the laboratory for Reverse Transcription Polymerase Chain Reaction (RT-PCR). RT-PCR results of the two tests were compared in terms of percentage agreement and Cycle Threshold value (CT value). Statistical analysis was done using Jefferies Amazing Statistical Program 0.16.2 software (JASP). Results: A total of 352 patients were registered, of which 211 (59.94%) were male and 141 (40.05%) were female. Eight patients were excluded because of inconclusive results, hence a total of 344 patients were included in the study. Among the NPS samples , 88 (25.58%) samples tested positive for SARS-CoV-2 and 256 (74.41%) samples tested negative whereas with saliva samples, 54 samples (15.40%) tested positive and 290 samples (84.60%) were negative for SARS-CoV-2. Among NPS positive samples, only 46 were positive with saliva sample, while among the NPS negative samples, only 248 were negative and eight samples were positive for SARS-CoV-2 with saliva samples. Positive percent agreement, negative percent agreement and overall agreement of saliva sample with respect to NPS were 52.5%, 96.87% and 85.46%, respectively. Mean and standard deviation for CT value of E gene, Open Reading Frame (ORF) gene and Ribonucleic Acid (RNA) dependent RNA polymerase (RdRp) gene with saliva samples were 26.62±3.7, 27.07±3.9 and 27.05±4.0, respectively and that of NPS were 25.87±4.9, 24.78±5.3 and 24.50±5.2, respectively. Conclusion: Saliva sample is an easy, convenient, and economic alternative to NPS but because of its low positive percent agreement with that of NPS, it should be used only in resourcelimited settings involving a shortage of personal protective equipment and viral transport media during the pandemic.

Keywords

• cycle threshold value
• reverse transcription polymerase chain reaction
• severe acute respiratory syndrome coronavirus 2
• viral transport medium