In January 2020, just weeks after the first cases of Covid-19 appeared in China, the complete genome of the novel coronavirus was Posted on the Internet. Using this genetic sequence, scientists have scrambled to design a wide range of diagnostic tests for the virus.
But the virus has since mutated. And as the Coronavirus has evolved, so has the testing landscape. The New variants emerge It sparked a flurry of interest in developing tests for specific virus mutations and raised concerns about the accuracy of some of the existing tests.
“With these Covid diagnoses, we were in a time crisis, and we had to get something out there,” said Lauren Lyles, science program officer at PATH, a global non-profit health organization that tracks coronavirus tests. “Normally, diagnostics take a long time, and we usually challenge them in multiple ways.” She added, “We do it, but we do it in real time.”
Food and Drug Administration Cautious That new mutations in the Coronavirus could make some tests less effective. And last week, PATH was launched Two online dashboards to observe How some variables might affect the performance of current diagnostic tests.
So far, scientists agree that there is no evidence that known variants of concern cause tests to fail completely. “Today, the tests work very well,” said Mara Espinal, an expert in biomedical diagnostics at Arizona State University.
But Scientists say manufacturers and regulators will need to be vigilant to ensure it keeps up with the ever-changing virus. If the variables begin to avoid detection, it could be a consequence of not only individual patients, who may not be receiving the treatment they need, but also of overall health.
If a person with the variant misses the test, that person may not realize that they need to be isolated. “This person is then allowed to not be quarantined, to circulate in the community and perhaps spread that alternative to others,” said Gary Skolnick, a physician and infectious disease expert at Stanford University and lead medical director for Visby Medical, a diagnostic company. That is conducting a corona virus test. “This is how a diagnostic test, if it is missing the variants, can enhance the prevalence of that variant.”
The risk of false negatives
Molecular tests, such as the widely used polymerase chain reaction test, or PCR test, are designed to detect specific sequences of the coronavirus genome. If mutations appear in these “target” sequences, the tests may not be able to detect the virus, resulting in false negative results.
“You could run into a situation where you just got unlucky, where you chose to target your test, and something came out there that made your test less effective,” said Nathan Grupo, a virologist at Yale University.
The gene for the virus’s characteristic spike protein, known as the S gene, was particularly susceptible to mutation, and tests targeting this gene may miss some variants. For example, Thermo Fisher’s TaqPath assay failed to detect the mutated S gene of variant B.1.1.7, which was first identified in Britain and is now spreading rapidly across the United States.
But the test is not based on the S gene alone; It has three goals and can still provide accurate results by discovering two more stretches of the coronavirus genome.
Only 1.3 percent of molecular tests depend on the target of the S gene, according to calculations by Rachel West, a postdoctoral fellow at the Johns Hopkins Center for Health Security. The rest either target more stable regions of the genome that are less likely to mutate, or have multiple target sequences, making them less likely to fail. “It is very unlikely that you will have mutations in all of them,” said Dr. Lillis.
FDA Has been included Four different molecular tests “could be affected” by variables, but they indicate that the tests must continue to work. Three of the exams have multiple objectives; Fourth It may be slightly less sensitive when the virus has a specific mutation and is present at very low levels. (The four tests are the TaqPath Covid-19 Combo Kit, Linea Covid-19 Assay Kit, Xpert Xpress, Xpert Omni SARS-CoV-2, and the Accula SARS-CoV-2 test.)
“We don’t think these four tests are significantly affected,” said Dr. Tim Stenzel, who directs the FDA’s Office of Laboratory Diagnostics and Radiation Health. “It was because of the abundance of caution and transparency that we made this information public.”
Antigen tests are less sensitive than molecular tests, but they are usually cheaper and faster, and are widely deployed in coronavirus screening programs. These tests detect specific proteins on the outside of the virus. Certain gene mutations can change the structure of these proteins, allowing them to escape detection.
Most antigen tests target the nucleoprotein. The gene that codes for this protein, known as the N gene, is more stable and less susceptible to mutation than the S gene, and the FDA has not listed any antigen tests as a concern. “We did not find one with the red flag, nor did we receive any reports of that,” said Dr. Stenzel.
However, experts note that not every test manufacturer detects the specific sequences their tests target, and the virus will continue to mutate. “There was no evidence to prove that a particular molecular test or even an antigen test completely missed detection,” Neha Agarwal, associate director of diagnostics at PATH, said. “But things will change.”
The US Food and Drug Administration continues to monitor the situation, checking the Coronavirus sequence databases weekly to see if the virus is developing in ways that may help it evade diagnostic tests. “We’re very vigilant,” said Dr. Stenzel. “We will remain vigil.”
Examine the selected variables
As the variants proliferate, researchers are also working to develop and improve tests to detect them. Currently, setting a variable is usually a two-step process. First, a standard coronavirus test, such as a PCR test, is used to determine whether or not the virus is present. If the test is positive, a sample is sent for genetic sequencing.
“These two tasks are currently being performed in two separate workflow paths. That means more time, labor and resources,” said Juan Carlos Ispissoa Belmonte, a developmental biologist at the Salk Institute in La Jolla, California.
Several researchers are now working to create integrated solutions – tests that can determine whether someone has the virus and whether they might have a particular variant.
For example, In a recent paperDr. Izbiswa Belmonte and his colleague Mu Li, a stem cell biologist at King Abdullah University of Science and Technology in Saudi Arabia, described a new test method that can identify Mutations in up to five different regions of the coronavirus genome.
Dr. Grupo and colleagues They developed a PCR test It can detect specific sets of mutations that characterize three variants of concern: B 188.8.131.52; B.1.351, which was first discovered in South Africa; And P.1, it is first found in Brazil. (The work has not yet been published in a scientific journal.)
Dr. Grupo said that researchers in Brazil, South Africa and elsewhere are already using the tests to screen a mountain of coronavirus samples, determining which ones should prioritize complete genetic sequences. “The primary concern of our group is to enhance genetic surveillance through sequencing, especially in resource-constrained areas,” said Dr. Grupo. “If you want to know if there are variables that are traded, you need a way to sort.”
A number of companies have also started launching coronavirus tests that they say can differentiate certain variants, although they are only intended for research purposes. Dr. Grupo said creating a test that can definitively diagnose someone with a particular variable is “infinitely more difficult”.
Similar mutations appear in different variants, which makes distinguishing between them more difficult. The mutations of interest will change as the virus does, and sequencing remains the best way to obtain a complete picture of the virus.
Ms Agarwal said that tests that can screen for certain mutations could be an important public health tool: “These newer diagnostics that look across variables, I think will be really essential in understanding the epidemiology of the virus and planning our next generation of efforts against it.”