Types of COVID-19 tests: Which one works better?

Several approaches to diagnosing the novel coronavirus have developed since the coronavirus pandemic swept the world in January. New alternatives to existing tests for COVID-19 are still emerging.

Timely diagnosis of the novel coronavirus is vital for saving patients’ lives and slowing the spread of the disease, which has infected over 2.6 million people around the globe.

The novel coronavirus, or SARS-CoV-2, can potentially show no symptoms in infected people. This means people who are not aware of their exposure can pass the disease to others. Mass testing can limit this possibility.

Ukraine has performed 72,296 tests, through which doctors were able to identify 7,170 cases as of April 23. That is a relatively low rate in comparison to other countries.

The United States, for instance, has performed around 4.5 million tests and identified 849,092 cases as of April 23. Italy did 1.5 million tests, 183,957 of which proved positive, and Turkey did 713,000 tests that revealed 95,591 cases as of April 22.

The Kyiv Post delved into the types of tests and algorithms of their usage to explain how they are applied now and how can be used most effectively.

What are COVID-19 tests?

Two main approaches to testing exist at the moment.

The first one identifies the presence of the virus in a cell and establishes whether the patient is currently infected with COVID-19. Such a test is carried out in a laboratory on a sample of the patient’s nasal or throat swab. It can say whether the person is infected at an early stage.

“A person can have no symptoms, no antibodies yet, but he already has nucleic acid of the virus. Laboratory tests will show you this,” said Oksana Piven, a senior research fellow at the Institute of Molecular Biology and Genetics.

The other kind of test identifies the presence of antibodies to the coronavirus in a patient’s blood. This test exposes whether the patient used to be infected in the past or possibly is still fighting the disease. Such tests are widely known as rapid tests or blood tests.

“Such tests are absolutely useless in the situation we have…Rapid tests start working on the tenth day or even later,” said Alla Mironenko, professor and head of the Viral Infections Department at the Gromashevsky Institute of Epidemiology and Infectious Diseases.

How does the lab test work?

The general principle of the laboratory test is to look into the patient’s cell and to search there for viral RNA of SARS-CoV-2, the causative agent of coronavirus. Such laboratory tests are more reliable than antibody tests.

Currently, two types of lab tests that can diagnose COVID-19 exist.

The first one is called a polymerase chain reaction or PCR test. It is recommended by the World Health Organization (WHO) and is the only one that is used to officially confirm a coronavirus infection. These confirmed cases are used to form a statistical basis.

The other method is based on Clustered Regularly Interspaced Palindromic Repeats (CRISPR). Primarily discovered as a gene-editing tool, CRISPR has proved effective in searching for viral RNA and DNA in patient’s cells. A few independent laboratories have adjusted this tool for COVID-19 diagnostics. They claim this method to be quicker, cheaper, and more accurate than the PCR test. However, it is not yet approved for mass use.

How does the PCR test diagnose COVID-19?

First, a healthcare worker takes a patient’s sample by conducting a nasopharyngeal swab, which is then delivered to the laboratory for analysis.

There, the researchers extract the nucleic acid from the patient’s samples, synthesize it into DNA (the PCR method works only with DNA), enlarge it until it is suitable for further analysis and then search for SARS-CoV-2 genes.

Such a PCR test takes around 5-6 hours.

“PCR method is the gold standard of laboratory diagnostics,” said Piven.

The PCR method was such a breakthrough that its invention won the 1993 Nobel Prize in Chemistry.

However, the procedure of taking the swab is painful for the patient and dangerous for the healthcare worker because he or she comes into close contact with an infected person.

Researchers at Rutgers University have come up with a solution, a saliva test.

On April 13, the U.S. Food and Drug Administration approved an emergency use authorization for a COVID-19 test using a patient’s saliva.

This test also relies on PCR to detect viral genes, but instead of swabbing the back of a patient’s throat, it requires a patient just to spit into a tube.

The test’s creators believe it will protect health care workers from getting infected because the patient can give the sample him or herself. 

How does CRISPR search for coronavirus?

This method is based on Clustered Regularly Interspaced Palindromic Repeats (CRISPR), best known for its potential to fix genetic mistakes.

CRISPR is something nature came up with itself and scientists noticed at some point in the 1980s.

It is based on the quirky way the immune systems of bacteria work in response to viruses. The scientists later managed to exploit it to edit genes in other organisms, including humans. Lately, it has emerged that this method can be useful not only for genetic engineering but also for diagnostics of diseases.

It was applied to detect the Zika virus and now is proposed as a tool for COVID-19 diagnostics.

There are a few different CRISPR systems. The ones suggested for COVID-19 detection are either CRISPR-Cas12 or CRISPR-Cas13. The difference is in the protein of bacteria used and what it looks into. Cas12 looks into DNA, while Cas13 looks into RNA.

This method works by using a synthetically made guide RNA that is programmed to help the protein find matching sequencing of the nucleic acid of SARS-CoV-2 in the patient’s cell.

After RNA points to the target, the protein starts acting like a paper shredder and chops whatever it sees on its way.

A few groups of scientists independently created their own versions of CRISPR-based tests. One is by Mammoth Biosciences and the University of California and the other is by the Massachusetts Institute of Technology (MIT). Both test systems have yet to be validated for clinical use.

MIT’s test is called SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing). It has been recently adapted to SARS-CoV-2 detection.

The test by Mammoth Biosciences is called DETECTR (Endonuclease-Targeted CRISPR Trans Reporter).

So, what is better: PCR or CRISPR tests?

Both CRISPR-based tests can generate results in under than 40 minutes in comparison to PCR tests, which take around 6 hours, according to the tests’ creators.

Even though faster PCR tests that give results within 2.5 hours have recently appeared, they are believed to be more expensive than ordinary PCR tests.

CRISPR tests are cheaper, faster and even better or comparably accurate, according to their producers.

“In comparison to PCR, here with CRISPR we do not need to extract nucleic acid from the swab and we do not need to synthesize RNA into DNA. This means two fewer steps for a reaction. Hence it is quicker, requires less equipment and is cheaper…because we would not need reagents for transforming RNA into DNA,” said Piven.

“The fact that it requires less time than a PCR test and identifies the virus is huge progress and possibly this is the future, but we have to understand whether this method is as specific and as sensitive as a PCR test,” Mironenko said.

Research from China published in February suggests that the PCR test may give false-negative results about 30% of the time. DETECTR’s producers say their method gives 95% accurately positive results and 100% accurately negative results.

Any use for rapid tests?

Rapid tests are still in the research stage of development and the WHO does not recommend using them for patient care. However, the Ukrainian authorities have purchased and received as donations hundreds of thousands of rapid tests to use.

Two types of rapid tests exist – antigen and antibody tests.

The antigen test aims at detecting viral proteins called antigens in sufficient quantities in the patient’s sample. It is normally designed as a paper strip and shows the result within 30 minutes.

The antibody test searches for antibodies in the patient’s blood. This diagnostic approach also takes about half an hour.

Scientists question the effectiveness of both rapid tests, as they are notably less accurate than PCR ones.

“Rapid tests are designed to show a different thing. They diagnose the presence of antibodies, if there are enough of them, to show that a person is currently in an active phase of fighting the disease and the antibodies have developed,” said Piven.

“A person can be infected, but antibodies have not appeared yet. In such a case, the test will tell you that the person is healthy,” she continued.

Mironenko also believes that rapid tests cannot be used for COVID-19 diagnostics.

“Antibodies to COVID-19 develop starting from the tenth day after infection, but it is very individual and some patient can have them on the 15th day, while another patient can get them on the 20th. It all depends on the state of the body, age, individual factors of the immune system, many factors,” Mironenko said.

Such tests can be used for research purposes only to study how people’s immune system responds to COVID-19, the scientists believe.