In January 2020, a few weeks after the first Covid-19 cases occurred in China, the complete genome of the new coronavirus was published online. Using this genomic sequence, scientists scrambled to design a wide variety of diagnostic tests for the virus.
But the virus has since mutated. And as the coronavirus evolved, so did the landscape. The emergence of new variants has sparked a wave of interest in the development of tests for specific viral mutations, raising concerns about the accuracy of some existing tests.
“With this Covid diagnosis, we were on a time crunch, we had to get something out there,” said Lorraine Lillis, the scientific program officer of PATH, a global health organization that monitors coronavirus tests. “Diagnosis usually takes a long, long time, and we usually challenge them with several variants.” She added: “And we do it, but we do it in real time.”
The Food and Drug Administration has warned that new mutations in the coronavirus could make some tests less effective. Last week, PATH launched two online dashboards to monitor how certain variants can affect the performance of existing diagnostic tests.
So far, according to scientists, there is no evidence that the known variants cause tests to fail completely. “The tests today work very, very well,” said Mara Aspinall, an expert in biomedical diagnostics at Arizona State University.
But scientists say manufacturers and regulators need to be vigilant to ensure they keep up with a virus that is constantly changing. If variations begin to be detected, this could result not only for individual patients who may not receive the necessary treatment, but also for public health.
If a test misses someone infected by a variant, the person may not realize that he or she needs to isolate. “And then that person may not be quarantined, circulate in the community, and possibly spread the variant to others,” said Gary Schoolnik, a physician and communicator of infectious diseases at Stanford University and chief medical officer of Visby Medical, a diagnostic enterprise, said. it makes a coronavirus test. “And so a diagnostic test can actually promote the spread of the variant if it does not have variants.”
The risk of false negatives
Molecular tests, such as the multiple polymerase chain reaction, or PCR test, are designed to detect specific sequences of the coronavirus genome. If mutations occur in these “target” sequences, the virus may no longer be able to detect the virus, resulting in false negatives.
“You could end up in a situation where you just had an accident choosing your test, and something came up that made your test less effective,” said Nathan Grubaugh, a virologist at Yale University. said.
The gene for the characteristic vein protein of the virus, known as the S gene, is particularly prone to mutation, and tests targeting this gene may miss certain variants. The Thermo Fisher-TaqPath test, for example, could not detect the mutated S gene of the B.1.1.7 variant, which was first identified in Britain and is now rapidly spreading throughout the United States.
But the test is not just based on the S gene; it has three targets and can still produce accurate results by detecting two other parts of the coronavirus genome.
Only 1.3 percent of molecular tests rely solely on an S target, according to calculations by Rachel West, a fellow physician at the Johns Hopkins Center for Health Safety. The rest focus on more stable regions of the genome, which are less likely to mutate, or have multiple targets, making them less prone to failure. “It is very unlikely that you will get mutations in everyone,” said Dr. Lillis said.
The FDA has listed four different molecular tests “whose performance may be affected by the variants”, but notes that the tests still need to work. Three of the tests have multiple targets; a fourth may be slightly less sensitive if the virus has one specific mutation and occurs at very low levels. (The four tests are the TaqPath Covid-19 Combo Kit, the Linea Covid-19 Assay Kit, the Xpert Xpress and Xpert Omni SARS-CoV-2, and the Accula SARS-CoV-2 test.)
“We do not think the four tests will be significantly affected,” said Dr. Tim Stenzel, who heads the FDA’s office for in vitro diagnostics and radiological health. “It was more out of the abundance of caution and transparency that we made the information public.”
Antigen tests are less sensitive than molecular tests, but they are usually cheaper and faster and are widely used in coronavirus screening programs. These tests detect specific proteins on the outside of the virus. Some genetic mutations can alter the structure of these proteins so that they can escape detection.
Most antigen tests focus on the nucleocapsid protein. The gene encoding this protein, known as the N gene, is more stable and less likely to mutate than the S gene, and the FDA has not listed any antigen tests as of concern. “We did not find one waving a red flag, nor did we have such reports,” said Dr. Stenzel said.
Still, according to experts, not every test manufacturer reveals the specific series their tests are aimed at, and the virus will continue to mutate. “There was no evidence to suggest that a specific molecular test or even an antigen test completely misses the boat when it detects it,” says Neha Agarwal, co-director of diagnostics at PATH. “But things are going to change.”
The FDA continues to monitor the situation and weekly checks coronavirus sequencing databases to see if the virus is developing so that it can evade diagnostic tests. “We are very vigilant,” Dr Stenzel said. “And we will remain vigilant.”
Screening for specific variants
As the variants spread, researchers are also working to develop and improve tests to detect them. At present, identifying a variant is usually a two-step process. First, a standard coronavirus test, such as a PCR test, is used to determine if the virus is present. If the test returns positive, a sample is sent for genomic sequencing.
Juan Carlos Izpisua Belmonte, developmental biologist at the Salk Institute in La Jolla, California, said these two tasks are currently being done. “It means more time, labor and resources.”
Many researchers are now working to create integrated solutions – tests that can determine if someone is infected with the virus and if they have a specific variant.
In a recent article, dr. Izpisua Belmonte and his colleague, Mo Li, a stem cell biologist at King Abdullah University of Science and Technology in Saudi Arabia, for example, describe a new test method that can identify. mutations in up to five different regions of the coronavirus genome.
And dr. Grubaugh and his colleagues developed a PCR test that could detect specific combinations of mutations that characterize three worrying variants: B.1.1.7; B.1.351, first detected in South Africa; and P.1, first found in Brazil. (The work has not yet been published in a scientific journal.)
Dr Grubaugh said researchers in Brazil, South Africa and elsewhere used all the tests to screen through a mountain of coronavirus samples, identifying those that should be preferred for complete genomic sequencing. “Our group’s primary interest is to improve genomic monitoring through sequencing, especially in areas limited to resources,” said Dr. Grubaugh said. “If you want to know if there are variants circulating, you need a way to try.”
A number of companies are also starting to release coronavirus tests that they say can differentiate between certain variants, even though they are intended for research purposes only. Setting up a test that can definitively diagnose someone with a specific variant is ‘infinitely more difficult’, said dr. Grubaugh said.
Similar mutations arise in different variants, which complicates the distinction between them. The mutations of interest will change as the virus changes, and sequencing is the best way to get a complete picture of the virus.
But tests that could test for certain mutations could be an important tool for public health, Ms. Agarwal said: ‘This newer diagnosis looking at the variants will, in my opinion, be the key to understanding the epidemiology of the virus and to planning our next generation. of attempts against it. ”