Coronavirus tests can spot most variants
Most tests used to diagnose coronavirus infections are able to detect all currently circulating forms of the virus, including variants that have developed concerning mutations.
The tests are designed to look for the presence of genetic material at multiple locations on the virus’s genome. So it’s conceivable that the virus could develop mutations that make it undetectable to the tests if the genome has changed in those locations.
But most of the tests look at locations that are stable and do not change much. In fact, the tests were designed that way, so that they could continue to detect the virus even as it evolved.
Some of most common locations that the tests target, for example, are the envelope or E gene and the nucleocapsid or N gene, which are generally stable, said Dr. Ben Pinsky, medical director of Stanford’s Clinical Virology Lab, which is sequencing coronavirus specimens to look for variants.
All of the variants of concern, such as the United Kingdom variant B.1.1.7, the South
African variant B.1.351 and the California variant B.1.429, have mutations on the S or spike gene — not at the locations that most tests look for. Those variants have other mutations, but none that allow them to fully evade most diagnostic tests.
There are two types of coronavirus diagnostic tests. Molecular diagnostic tests — which include the PCR, or polymerase chain reaction, tests — are typically done with a nasal swab and look for the presence of viral genetic material; PCR tests are the preferred and most common type. The other type is an antigen test, which is usually also a nasal swab and looks for the presence of viral proteins. Antigen tests are less involved and timeconsuming to perform — and also less sensitive — than PCR tests, which is why some can report results in as little as 15 minutes.
About 85% of the 246 molecular diagnostic tests — including PCR tests — authorized by the Food and Drug Administration have targets other than the spike gene, so they should still be effective for the variants, according to a February analysis by the Johns Hopkins Bloomberg School of Public Health.
Of the remaining 15% of tests, half have multiple targets in addition to the spike gene, “so they should continue to yield accurate results,” the researchers found.
Similarly, most antigen tests target the nucleocapsid protein — not the spike protein — and should still be reliable at diagnosing the variants.
Still, test manufacturers and scientists are monitoring the variants and stand ready to modify the tests if the need arises. The FDA this week urged test manufacturers to closely track variants and to be prepared to adjust their test targets accordingly.
Modifying tests should be relatively straightforward and quick, testing experts said. It would involve selecting other locations on the SARSCoV2 genome the test will target.
“We don’t really need to be extremely concerned, but we do need to be vigilant,” said Stacia Wyman, senior genomics scientist who leads coronavirus genome sequencing efforts at UC Berkeley’s Innovative Genomics Institute.