PCR to CRISPR: Role of Nucleic Acid Tests (NAT) in detection of COVID-19.

Sikandar Hayat Khan Sikandar Hayat Khan,Sabeen Khursheed Zaidi,Mehreen Gilani

doi:10.47391/jpma.2324

Abstract

COVID-19 infection has emerged as an unparalleled pandemic with morbidity and mortality tolls challenging diagnostic approaches and therapeutic interventions, and raising serious questions for healthcare policy-makers. From the diagnostic perspective, Reverse transcriptase polymerase chain reaction remains the gold standard. However, issues associated with gene primer variation in different countries, low analytical sensitivity, cross-reactivity with certain human coronaviruses have raised serious concerns within the scientific community. Alongside longer turnaround times, requirements of sophisticated equipment and trained technicians are the other challenges for conventional reverse transcriptase polymerase chain reaction testing. The recent biotechnological boom has now allowed newer nucleic acid testing options for diagnosing severe acute respiratory syndrome Coronovairus 2 (SARS-CoV2) with much better diagnostic efficiency, reduced turnaround times and possible benefit for use as a point-of-care test. Isothermal techniques with simple equipment requirements along with uniform temperature for analysis have emerged to be more sensitive and specific with turnaround times as low as 10-15 minutes. Similarly, Cluster Regularly Interspaced Short Palindromic Repeats have also been seen to play a very decisive role in COVID-19 diagnostics with much superior diagnostic efficiency and feasibility as a point-of-care test and its possible use for sequencing. The current narrative review was planned to consolidate data for all possible nucleic acid testing options under research/clinical use, and to provide a comparative assessment from the perspective of both the clinician and the laboratory.

Highlights

IntroductionSevere Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2), called the coronavirus disease-2019 (COVID-19), as people started to talk about the “New. Normal”
The world almost paralysed and reached a real-time “lock-down” by the newcomerSevere Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2), called the coronavirus disease-2019 (COVID-19), as people started to talk about the “NewNormal”
Literature review suggested few of the regions to be well-conserved across species and there remained specific gene region differentiating SARS-CoV-2 from other human coronaviruses (hCoVs) (Figure 1)

Summary

Introduction

Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2), called the coronavirus disease-2019 (COVID-19), as people started to talk about the “New. Normal”. At the time of writing, there have almost been over 15,945,330 people having already suffered from the virus, with more than 0.64 million deaths. [1] While the race for developing therapeutic agents and an efficacious vaccine is underway at an unprecedented pace, it will be some time before it becomes available in clinical settings. From the laboratory’s perspective, we are witnessing multiple dimensions emerging to diagnose the disease, including clinical criteria, serological biomarkers, nucleic acid tests (NATs) and sequencing technologies. Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) which allows the highest possible diagnostic sensitivity to detect SARS-CoV-2 in various specimen types and has been utilised for isolation strategies.

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Results

Conclusion