In January 2020, just weeks after the first Covid-19 cases emerged in China, the full genome of the new coronavirus was published online. Using this genomic sequence, scientists scrambled to design a large assortment of diagnostic tests for the virus.
But the virus has mutated since then. And as the coronavirus has evolved, so has the landscape of testing. The emergence of new variants has sparked a flurry of interest in developing tests for specific viral mutations and prompted concerns about the accuracy of some existing tests.
“With these Covid diagnostics, we were on a time crunch, we had to get something out there,” said Lorraine Lillis, the scientific program officer at PATH, a global health nonprofit that has been tracking coronavirus tests. “Normally, diagnostics take a long, long time, and we’d normally challenge them with multiple variants.” She added: “And we’re doing that, but we’re doing it in real time.”
The Food and Drug Administration has warned that new mutations in the coronavirus could render some tests less effective. And last week, PATH launched two online dashboards to monitor how certain variants might affect the performance of existing diagnostic tests.
has listed four different molecular tests “whose performance could be impacted” by the variants, but notes that the tests should still work. Three of the tests have multiple targets; a fourth may be slightly less sensitive when the virus has one particular mutation and is present 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 don’t think that those four assays are significantly impacted,” said Dr. Tim Stenzel, who directs the F.D.A.’s office of in vitro diagnostics and radiological health. “It was more out of an abundance of caution and transparency that we made that information public.”
Antigen tests are less sensitive than molecular tests, but they are typically cheaper and faster, and they are being deployed widely in coronavirus screening programs. These tests detect specific proteins on the outside of the virus. Some genetic mutations could change the structure of these proteins, allowing them to escape detection.
in a recent paper, Dr. Izpisua Belmonte and his colleague, Mo Li, a stem cell biologist at King Abdullah University of Science and Technology in Saudi Arabia, described a new testing method that can identify mutations in up to five different regions of the coronavirus genome.
And Dr. Grubaugh and his colleagues have developed a P.C.R. test that can detect specific combinations of mutations that characterize three variants of concern: B.1.1.7; B.1.351, which was 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 that researchers in Brazil, South Africa and elsewhere are already using the tests to sift through a mountain of coronavirus samples, identifying those that should be prioritized for full genomic sequencing. “Our group’s primary interest is enhancing genomic surveillance through sequencing, especially in resource-limited areas,” Dr. Grubaugh said. “If you want to know if there’s variants that are circulating, you need a way to triage.”
A number of companies are also beginning to release coronavirus tests that they say can differentiate between certain variants, although these are intended for research purposes only. Creating a test that can definitively diagnose someone with a particular variant is “infinitely harder,” Dr. Grubaugh said.
Similar mutations are springing up in different variants, which makes distinguishing among them more difficult. The mutations of interest will change as the virus does, and sequencing remains the best way to get a complete picture of the virus.
But tests that can screen for certain mutations could be an important public health tool, Ms. Agarwal said: “These newer diagnostics that are looking across the variants, I think will be really key in understanding the epidemiology of the virus and planning our next generation of efforts against it.”