Molecular testing as a tool to combat the COVID-19 pandemic

Abstract

Our tools in fighting the coronavirus disease 2019 (COVID-19) pandemic were initially limited. The first step was identifying who was infected by the virus. New molecular testing was quickly created to diagnose disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Now with over a year’s worth of experience, testing indications have changed and resources need to be considered. At the beginning of the pandemic, data was lacking on molecular test types, where to swab and who should swab. All these unknown variables were compounded by testing turnaround time. Molecular diagnostic laboratories were quickly expanded because the demand and intense focus was placed on which test and specimen types to use. Laboratories had to expand testing in a very brief period of time, bringing on board new assays, either as laboratory developed or emergency use authorized assays where instrumentation and reagents were difficult to be acquired. Nasopharyngeal (NP) samples are standard of care for influenza testing. Extrapolating this knowledge, we initially instituted NP specimens as the only option for SARSCoV-2 testing. Real life taught us the NP swabs can be harmful in fully anticoagulated patients, leading to the use of alternative specimen sites of combined anterior nares/oropharynx. Current Infectious Disease Society of America (IDSA) Guidelines recommend a SARS-CoV-2 nucleic acid amplification test (NAAT) obtained from NP swab, mid-turbinate swab, anterior nasal swab, saliva or a combined anterior nasal/oropharyngeal swab in symptomatic individuals[1]. NP specimens must be obtained by a trained healthcare worker (HCW) and are briefly uncomfortable, leading to a patient reluctance for testing. In addition, SARS-CoV-2 NAAT are qualitative, not quantitative. Unfortunately, viral loads are not reported routinely, but clinicians have access to cycle thresholds (CT). CTs are not uniform and can vary upon specimen type and collection technique. Recently published data compared NP swabs versus oropharyngeal (OP) swabs for SARS-CoV-2 in patients with ≤ 7 days of symptoms and reported 95.2% concordance[2]. Specimens were tested using the Centers for Disease Control (CDC) reverse transcription–polymerase chain(RT-PCR) detecting three genetic markers: N1, N2, and N3 nucleocapsid gene regions. The median cycle thresholds were lower for NP swabs, 24.3 vs 29.9 for N1 and 25.0 vs 31.4 for N2. This data is one reason why IDSA does not recommend oral swabs alone. The use of NP collection that may have higher viral load was the specimen of choice at our institution, but hesitance focused on the use of rapid transcription mediated amplification testing versus traditional RT-PCR, since these tests may show lower sensitivity. For this reason, our institution implemented the Abbott ID NOW COVID-19 assay only for inpatients that were symptomatic because the rapid turnaround time benefited patient care. In order to evaluate the Abbott ID NOW COVID-19 assay (NP collected in dry swab), we performed a performance comparison with the Simplexa COVID-19 Direct Kit (NP collected in viral transport media), if results were discrepant the laboratory developed CDC RT-PCR was used. The Abbott ID NOW COVID-19 showed a similar performance to the Simplexa COVID-19 Direct Kit. COVID-19 is indistinguishable from other respiratory viral syndromes by symptoms alone. Symptoms consistent with COVID-19 include cough, shortness of breath, fever, chills, fatigue, muscle pain, headache, sore throat, new loss of taste or smell, congestion, nausea, vomiting or diarrhea[3]. Anti-viral therapy cannot be prescribed until the diagnosis is confirmed via testing, hence the need for a rapid result. Patients, especially those with medical comorbidities and advanced age (>70 years old), acutely infected with SARS-CoV-2 were quickly recognized as having a higher post-operative mortality after major surgical procedures. [4]. Due to this early data and expert opinion, all patients were screened pre-operatively for SARS-CoV-2. In December 2020, the American Society of Anesthesiologists released guidelines postponing all elective procedures for COVID positive patients based off their illness severity [5]. Patients who were asymptomatic or had mild, non-respiratory symptoms should wait 4 weeks, while a patient requiring care in the intensive care unit should be postponed 3 months. Interestingly, they lump together diabetics, immunocompromised and otherwise hospitalized patients together and suggest an 8 to 10 week waiting time. Prior to this guidance, elective surgery timing was based on discontinuation of isolation. Early on in the United States, the CDC recommended 2 negative RT-PCRs prior to discontinuing isolation. RT-PCR positivity does not equate infectivity. We had anecdotal experience with this prior to COVID-19 in our chronic lymphocytic leukemic patients who would repeatedly test positive for Rhinovirus on respiratory viral PCR platform during consecutive hospital admissions. Patients persistently positive for SARS-CoV-2 were subject to continued