COVID-19 testing
COVID-19 testing involves analyzing samples to assess the current or past presence of SARS-CoV-2, the virus that causes COVID-19 and is responsible for the COVID-19 pandemic. The two main types of tests detect either the presence of the virus or 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 instead 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.
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, there is an urgent need for frequent surveillance and rapid availability of results.
Test analysis is often performed in automated, high-throughput, medical laboratories by medical laboratory scientists. Rapid self-tests and point-of-care testing are also available and can offer a faster and less expensive method to test for the virus although with a lower accuracy.
Methods
Positive viral tests indicate a current infection, while positive antibody tests indicate a prior infection. Other techniques include a CT scan, checking for elevated body temperature, checking for low blood oxygen level, and detection by trained dogs.Detection of the virus
Detection of the virus is usually done either by looking for the virus's inner RNA, or pieces of protein on the outside of the virus. Tests that look for the viral antigens are called antigen tests.There are multiple types of tests that look for the virus by detecting the presence of the virus's RNA. These are called nucleic acid or molecular tests, after molecular biology., the most common form of molecular test is the reverse transcription polymerase chain reaction test. Other methods used in molecular tests include CRISPR, isothermal nucleic acid amplification, digital polymerase chain reaction, microarray analysis, and next-generation sequencing.
Reverse transcription polymerase chain reaction (RT-PCR) test
is a process that amplifies 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.Reverse transcription polymerase chain reaction 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 provides advantages including automation, higher-throughput and more reliable instrumentation. It has become the preferred method.
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 guidelines propose the term RT-qPCR, but not all authors adhere to this.
Average sensitivity for rapid molecular tests depend 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%.
In a diagnostic test, sensitivity is a measure of how well a test can identify true positives and specificity is a measure of how well a test can identify true negatives. For all testing, both diagnostic and screening, there is usually a trade-off between sensitivity and specificity, such that higher sensitivities will mean lower specificities and vice versa. A 90% specific test will correctly identify 90% of those who are uninfected, leaving 10% with a false positive result.
Samples can be obtained by various methods, including a nasopharyngeal swab, sputum, throat swabs, deep airway material collected via 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."
Sensitivity of clinical samples by RT-PCR is 63% for nasal swab, 32% for pharyngeal swab, 48% for feces, 72–75% for sputum, and 93–95% for bronchoalveolar lavage.
The likelihood of detecting the virus depends on collection method and how much time has passed since infection. According to Drosten tests performed with 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.
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 sample site. 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. Following recovery, many patients no longer have detectable viral RNA in upper respiratory specimens. Among those who do, RNA concentrations three days following recovery are generally below the range in which replication-competent virus has been reliably isolated. No clear correlation has been described between length of illness and duration of post-recovery shedding of viral RNA in upper respiratory specimens.
Other molecular tests
tests also amplify the virus's genome. They are faster than PCR because they do not involve repeated heating and cooling cycles. These tests typically detect DNA using fluorescent tags, which are read out with specialized machines.CRISPR gene editing technology was modified to perform the detection: if the CRISPR enzyme attaches to the sequence, it colors a paper strip. The researchers expect the resulting test to be cheap and easy to use in point-of-care settings. The test amplifies RNA directly, without the RNA-to-DNA conversion step of RT-PCR.
Antigen tests
An antigen is the part of a pathogen that elicits an immune response. Antigen tests look for antigen proteins from the viral surface. In the case of a coronavirus, these are usually proteins from the surface spikes. SARS-CoV-2 antigens can be detected before onset of COVID-19 symptoms with more rapid test results, but with less sensitivity than PCR tests for the virus.COVID-19 rapid antigen tests are lateral flow immunoassays that detect the presence of a specific viral antigen, which indicates current viral infection. Antigen tests produce results quickly, and most can be used at the point-of-care or as self-tests. Self-tests are rapid tests that can be taken at home or anywhere, are easy to use, and produce rapid results. Antigen tests can be performed on nasopharyngeal, nasal swab, or saliva specimens.
Antigen tests that can identify SARS-CoV-2 offer a faster and less expensive method to test for the virus. Antigen tests are generally less sensitive than real-time reverse transcription polymerase chain reaction and other nucleic acid amplification tests.
Antigen tests may be one way to scale up testing to much greater levels. Isothermal nucleic acid amplification tests can process only one sample at a time per machine. RT-PCR tests are accurate but require too much time, energy and trained personnel to run the tests. "There will never be the ability on a test to do 300 million tests a day or to test everybody before they go to work or to school," Deborah Birx, head of the White House Coronavirus Task Force, said on 17 April 2020. "But there might be with the antigen test."
Samples may be collected via nasopharyngeal swab, a swab of the anterior nares, or from saliva. The sample is then exposed to paper strips containing artificial antibodies designed to bind to coronavirus antigens. Antigens bind to the strips and give a visual readout. The process takes less than 30 minutes, can deliver results at point of care, and does not require expensive equipment or extensive training.
Swabs of respiratory viruses often lack enough antigen material to be detectable. This is especially true for asymptomatic patients who have little if any nasal discharge. Viral proteins are not amplified in an antigen test. A Cochrane review based on 64 studies investigating the efficacy of 16 different antigen tests determined that they correctly identified COVID-19 infection in an average of 72% of people with symptoms, compared to 58% of people without symptoms. Tests were most accurate when used in the first week after symptoms first developed, likely because people have the most virus in their system in the first days after they are infected. While some scientists doubt whether an antigen test can be useful against COVID-19, others have argued that antigen tests are highly sensitive when viral load is high and people are contagious, making them suitable for public health screening. Routine antigen tests can quickly identify when asymptomatic people are contagious, while follow-up PCR can be used if confirmatory diagnosis is needed.