Diagnostic tests for COVID-19: An Evaluation of Current Methods, Practices and Future

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Laboratory tests for diagnosis of COVID-19 currently in practice as advised by the international bodies of experts are reviewed and evaluated.

Diagnostic tests

The COVID-19 disease, that originated in Wuhan China, has affected more than 208 countries till now. The scientific community in the entire world has been posed with a significant challenge in the past few months, to develop diagnostic tests for COVID-19 disease detection in order to screen patients and suspected individuals in order to effectively manage and control the pandemic.

Before we evaluate the current methods and practices used for detection of COVID-19, let us first understand what causes COVID-19 and how does one develop diagnostic tests to screen patients for this disease. COVID-19 disease is caused by a positively stranded RNA virus that are zoonotic, which means they can cross species barriers from animals to humans, and can cause, in humans, illness ranging from the common cold to more severe diseases such as MERS and SARS. The virus causing COVID-19 has now been named SARS-CoV-2 by the International Committee of Taxonomy of Viruses (ICTV), as it is very similar to the one that caused the SARS outbreak (SARS-CoVs). The diagnostic test for COVID-19 disease can be developed in number of ways.

The most popular and currently adopted method worldwide is to develop a diagnostic test that can detect the SARS-CoV-2 virus itself. This test is based on the detection of the viral genome in the patient sample by RT-real time PCR (reverse transcriptase-real time Polymerase Chain Reaction). This entails conversion of viral RNA to DNA using an enzyme called reverse transcriptase and then amplifying the DNA using specific set of primers and a fluorescent probe, that bind to a specific region on the viral DNA, using a Taq polymerase and detecting the fluorescent signal. These tests are referred to as NAATs (Nucleic Acid Amplification Tests). This technique can be very useful for very early detection of the presence of nucleic acid in patient sample, even in asymptomatic patients that do not show COVID-19 disease symptoms (especially in the incubation period of 14-28 days) and in the later part as well when disease is full-blown.

Various companies around the world have been working in a race against time during the past few months to develop NAAT based diagnostic test for the detection of SARS-CoV-2 based on CDC (Centre for Disease Control), Atlanta, USA and WHO guidelines (1, 2). The health authorities around the world have been approving these tests for emergency use for the detection of SARS-CoV-2. The viral genes targeted so far include the N, E, S and RdRP genes, along with appropriate positive and negative controls. The patient samples to be collected for such a test are from the upper respiratory tract (nasopharyngeal and oropharyngeal swab) and/or lower respiratory tract (sputum and/or endotracheal aspirate or bronchoalveolar lavage). However, it is also possible to detect virus in other samples, including stool and blood. The samples need to be collected rapidly in an appropriate manner taking all the necessary precautions and adhering to biosafety practices (as per guidelines laid down by WHO[1]), from patients meeting the suspected case definition for COVID-19, preserving and packaging it well if it requires to be transported to the diagnostic center and then processed (extracting RNA in a biosafety cabinet in a BSL-2 or equivalent facility) swiftly in a manner to ensure sample integrity. All this has to performed on a priority basis for better clinical management and outbreak control.

The detection time for various available NAAT based tests developed by major diagnostic companies around the world vary from 45 min to 3.5 hours. Various improvements are being made to these tests to convert them into point of care tests and achieve the desired results in as less time as possible without compromising the accuracy of result, to increase the number of tests that can be done in a day.

Other diagnostic test options are rapid diagnostic tests (RDTs) that either detect viral antigens/proteins that are expressed on the surface of the SARS-CoV-2 virus particles as they replicate in host cells and cause disease or host antibodies in response to infection; this test detects the presence of antibodies in the blood of people believed to have been infected with COVID-19 (3).

The accuracy and reproducibility of RDT to detect viral antigens depends on several factors including the time from onset of illness, the concentration of virus in the sample, the quality and processing of the sample, and the formulation of the reagents present in the test kits. Due to these variables, the sensitivity of these tests might vary from 34% to 80%. A major drawback of this option is that the virus needs to be in its replicative and infective stage in order to detect the viral proteins.

Similarly, tests detecting host antibodies are based on the strength of antibody response which depends on factors such as age, nutritional status, severity of disease, and certain medications or infections that suppress the immune system. A major drawback of this option is that antibodies are produced over days to weeks after infection with the SARS-CoV-2 virus and one has to wait that long to perform the test. This means that a diagnosis of COVID-19 infection based on host antibody response will often only be possible in the recovery phase, when many of the opportunities for clinical intervention or prevention of disease transmission have already passed.

Currently, the RDTs mentioned above have only been approved in a research setting and not for clinical diagnosis due to the lack of data (3, 4). As more and more epidemiological data becomes available for COVID-19, more RDTs will be developed and approved as point of care tests in a clinical setting as they can give results in 10-30 minutes as opposed to NAAT based tests that on an average takes few hours for detecting the disease.

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References:
1. WHO, 2020. Laboratory Testing Strategy Recommendations for COVID-19. Interim Guidance. 21 March 2020. Available online at https://apps.who.int/iris/bitstream/handle/10665/331509/WHO-COVID-19-lab_testing-2020.1-eng.pdf Accessed on 09 April 2020
2. CDC 2020. Information for laboratories. Interim Guidance for Laboratories Available online at https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html Accessed on 09 April 2020.
3. WHO, 2020. Advice on the Use of Point of Care Tests. Scientific Brief. 08 April 2020. Available online at https://www.who.int/news-room/commentaries/detail/advice-on-the-use-of-point-of-care-immunodiagnostic-tests-for-covid-19 Accessed on 09 April 2020.
4. ECDC, 2020. An Overview of the Rapid Test Situation for COVID-19 Diagnosis in the EU/EEA. 01 April 2020. European Center for disease prevention and control. Available online at https://www.ecdc.europa.eu/en/publications-data/overview-rapid-test-situation-covid-19-diagnosis-eueea Accessed on 09 April 2020

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