Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), the prototype virus of the family Coronaviridae preferentially infects cells in respiratory tract (1, 2), but its organotropism including brain, conjunctiva, pharynx, lungs, heart, liver and kidneys remains poorly understood (3, 4). In late 2002, novel coronavirus (SARS-CoV) emerged as an epidemic in Asia, spread worldwide and became serious public health concern internationally (5, 6). According to World Health Organization (WHO) Emergencies Preparedness Response Report published in 2004, 8096 people around the world were diagnosed with 774 deaths (7). In December 2019, SARS-CoV-2, a novel coronavirus from same family of SARS-CoV and Middle East Respiratory Syndrome (MERS) coronavirus emerged causing coronavirus disease 2019 (COVID-19) pandemic (8, 9). The global number of SARS-CoV-2 positive cases were 43,820,929 and have been climbing vigorously. Untill the same period, number of deaths due to COVID-19 were 1,165,189, the worst affected being the United States of America and India (10).
The virus contains four major structural proteins including; matrix core protein (M), nucleocapsid (N), envelop (E), and glycoprotein spike surface (S). It employs spike surface glycoproteins to interact with receptor binding domain, angiotensin-converting enzyme 2 (ACE2), that is expressed on the epithelial AT2 cells of alveoli of lungs, in salivary glands, surface of artery, veins, heart and kidney tissues (11–13). SARS-CoV enters to host cell via clathrin- and caveolae- independent endocytic pathway (14). The SARS-CoV-2 generates proteolytically active fragments of RAS including Ang II and Ang 1–7 that may activate AT2 receptors to bind with ACE2 and via host cell directed network of G-protein-coupled receptors (GPCRs) ultimately activate c-Jun N-terminal Kinase (JNK) and Janus Tyrosine Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT) biochemical mechanism in host cells and for viral transmission (15).
Currently, there is no specific cure or vaccine available for COVID-19 (16). However more than 169 COVID-19 vaccine candidates are in pipeline, and 26 among them are in human trial phase (17). Early detection and isolation of infected cases is crucial factor to prevent viral pathogenesis (16). The nasopharyngeal swab (NPS) followed by real-time reverse-transcription polymerase chain reaction (RT-PCR) of extracted RNA, is recommended gold standard for diagnosis of SARS-CoV-2 and is applied commercially in accordance with WHO protocols (2, 18, 19). However, during the pandemic, detecting large number of patients via RT-PCR in limited time frame is challenging task and may also involve technical or financial burdens. Rapid, accurate and cost effective diagnosis of SARS-CoV-2 to meet national or international demands for resource limited countries, like Pakistan requires alternative public health containment strategies (19).
Rapid diagnostic tests (RDTs) are user-friendly, cost-effective and safe point-of-care testing; however there is potential concern regarding real-world performance and validation of these assays (20). The NPS procedure is invasive and may cause bleeding; there are increased chances of SARS-CoV-2 transmission to the healthcare workers (12). While, saliva specimen collection is non-invasive and can be safely handled outside hospitals (21). Also, self-collection of saliva samples can reduces risk of SARS-CoV-2 transmission to healthcare workers than NPS (22). Of note, there was no significant difference in SARS-CoV-2 viral load in NPS or saliva specimens (21).
In saliva or NPS based SARS-CoV-2 RDTs, the challenge is to determine most accurate diagnostic assay without compromising reliability of test results. Analyzing the sensitivity and specificity of most appropriate diagnostic assay or combination of diagnostic assays in comparison to gold standard RT-PCR based test might be helpful in formulating new testing strategy to curtail unprecedented COVID-19 pandemic. There is a dire need in Pakistan to timely develop suitable algorithm that accurately meets national demand for expanded SARS-CoV-2 screening, diagnosis, and treatment. We aimed to evaluate saliva or NPS RDTs based SARS-CoV-2 diagnostic kits with RT-PCR based test to formulate effective testing strategy for diagnosis of SARS-CoV-2 in Pakistani population.