NIMS ​

NIMS Covid-19 RT-PCR Laboratory

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​RT-PCR for the Diagnosis of Covid 19:

The Wolrd Gold Standard

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COVID-19 testing involves analyzing samples to assess the current or past presence of SARS-CoV-2. The two main branches detect either the presence of the virus or of antibodies produced in response to infection. Molecular tests for viral presence through its molecular components are used to diagnose individual cases and to allow public health authorities to trace and contain outbreaks. Antibody tests (serology immunoassays) show whether someone once had the disease. They are less useful for diagnosing current infections because antibodies may not develop for weeks after infection. It is used to assess disease prevalence, which aids the estimation of the infection fatality rate.

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Individual jurisdictions have adopted varied testing protocols, including whom to test, how often to test, analysis protocols, sample collection and the uses of test results. This variation has likely significantly impacted reported statistics, including case and test numbers, case fatality rates and case demographics. Because SARS-CoV-2 transmission occurs days after exposure (and before the onset of symptoms) there is an urgent need for frequent surveillance and rapid availability of results.

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Test analysis is often performed in automated, high-throughput, medical laboratories by medical laboratory scientists. Alternatively, point-of-care testing can be done in physician's offices and parking lots, workplaces, institutional settings or transit hubs.

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Reverse transcription-polymerase chain reaction test

Polymerase chain reaction (PCR) is a process that amplifies (replicates) a small, well-defined segment of DNA many hundreds of thousands of times, creating enough of it for analysis. Test samples are treated with certain chemicals that allow DNA to be extracted. Reverse transcription converts RNA into DNA.

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Reverse transcription-polymerase chain reaction (RT-PCR) first uses reverse transcription to obtain DNA, followed by PCR to amplify that DNA, creating enough to be analyzed. RT-PCR can thereby detect SARS-CoV-2, which contains only RNA. The RT-PCR process generally requires a few hours. These tests are also referred to as molecular or genetic assays. Real-time PCR (qPCR) provides advantages including automation, higher-throughput and more reliable instrumentation. It has become the preferred method.

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The combined technique has been described as real-time RT-PCR or quantitative RT-PCR and is sometimes abbreviated qRT-PCR, rRT-PCR or RT-qPCR, although sometimes RT-PCR or PCR are used. The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines propose the term RT-qPCR, but not all authors adhere to this.

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Average sensitivity for rapid molecular tests depends on the brand. For ID NOW, the average sensitivity was 73.0% with an average specificity of 99.7%; for Xpert Xpress, the average sensitivity was 100% with an average specificity of 97.2%. The term sensitivity refers to the capacity of a test to identify all infected people, while specificity is the ability of a test to detect a particular virus.

Samples can be obtained by various methods, including a nasopharyngeal swab, sputum (coughed up material), throat swabs, deep airway material collected via a suction catheter or saliva. Drosten et al. remarked that for 2003 SARS, "from a diagnostic point of view, it is important to note that nasal and throat swabs seem less suitable for diagnosis, since these materials contain considerably less viral RNA than sputum, and the virus may escape detection if only these materials are tested."

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The sensitivity of clinical samples by RT-PCR is 63% for nasal swab, 32% for pharyngeal swab, 48% for faeces, 72–75% for sputum, and 93–95% for bronchoalveolar lavage.

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The likelihood of detecting the virus depends on the collection method and how much time has passed since infection. According to Drosten tests performed with the throat, swabs are reliable only in the first week. Thereafter the virus may abandon the throat and multiply in the lungs. In the second week, sputum or deep airways collection is preferred.

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Collecting saliva may be as effective as nasal and throat swabs, although this is not certain. Sampling saliva may reduce the risk for health care professionals by eliminating close physical interaction. It is also more comfortable for the patient. Quarantined people can collect their own samples. A saliva test's diagnostic value depends on the sample site (deep throat, oral cavity, or salivary glands). Some studies have found that saliva yielded greater sensitivity and consistency when compared with swab samples. On 15 August 2020, the US FDA granted an emergency use authorization for a saliva test developed at Yale University that gives results in hours. On 4 January 2021, the US FDA issued an alert about the risk of false results, particularly false-negative results, with the Curative SARS-Cov-2 Assay real-time RT-PCR test. Viral burden measured in upper respiratory specimens declines after symptom onset.