Whether older COVID-19 tests can detect newer viral strains is a key public health concern as the SARS-CoV-2 virus continues to change. Generally, the tests authorized early in the pandemic still work against newer variants, but with a significant caveat. Their ability to successfully identify an infection, known as sensitivity, can be reduced depending on the specific test design and the variant’s mutations. This reduced sensitivity is particularly noticeable in certain types of at-home tests. Therefore, a negative result might not be as definitive as it once was, emphasizing that diagnostic tools rely on the specific parts of the virus they target.
The Molecular Targets of COVID-19 Tests
COVID-19 diagnostic tests function by seeking out specific molecular targets from the SARS-CoV-2 virus. These targets fall into two main categories: the virus’s genetic material and its structural proteins.
Molecular Tests (PCR)
Molecular tests, such as Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) assays, look for unique segments of the viral RNA genome. PCR tests often target highly conserved genes like the Nucleocapsid (N), Envelope (E), and RNA-dependent RNA-polymerase (RdRP) genes. Targeting multiple genes is a strategy to ensure the test remains accurate even if the virus mutates in one region.
Rapid Antigen Tests (RATs)
Rapid Antigen Tests (RATs) are designed to detect the presence of specific viral proteins. The primary target for nearly all RATs is the Nucleocapsid (N) protein, which is highly abundant within the virus particle. The N protein is favored because it is generally more conserved than the Spike (S) protein and is present in high concentrations early in the infection. The test uses antibodies bound to a strip to capture the N protein from a nasal swab sample, producing a visible line for a positive result.
How Viral Mutation Affects Test Accuracy
The constant evolution of the SARS-CoV-2 virus means its genetic code and proteins are constantly changing, a process known as antigenic drift. If a mutation occurs in the specific region a test is designed to detect, the test’s ability to bind to its target can be compromised. This reduces the test’s sensitivity, potentially leading to a false negative result.
PCR Safeguards
The strategy of targeting multiple genes in PCR testing provides a built-in safeguard against single-point mutations. If a mutation causes one target region to fail—a phenomenon known as a “gene drop-out”—the test can still successfully detect the virus using its other targets. This redundancy makes PCR assays inherently robust against the single or double mutations often found in new variants.
Antigen Test Vulnerability
Rapid Antigen Tests typically rely on a single or dual target for the Nucleocapsid protein, making them more susceptible to mutations in that specific protein structure. Changes in the N protein can reduce the binding efficiency of the antibodies used in the test, lowering the sensitivity threshold. Because the Omicron variant and its sublineages carry numerous mutations, including some in the N protein, concerns have arisen about the sustained performance of some antigen tests.
Practical Performance: PCR Versus Rapid Tests
The emergence of highly transmissible variants, such as the Omicron sublineages, has provided real-world data on how the different test types perform. Laboratory-based PCR tests generally maintain their high sensitivity, confirming their status as the gold standard for detecting active infection. Their multi-target approach means they are rarely completely neutralized by a variant’s mutations, though a gene drop-out may occur, which can serve as a marker for a specific variant.
Rapid Antigen Tests (RATs) have shown a clear pattern of reduced sensitivity, particularly during the early phase of an Omicron infection. Studies indicate that RATs may take a couple of days longer to turn positive compared to a PCR test. This delay is significant because an infected person can be highly infectious before their RAT registers a positive result.
The reduced sensitivity of RATs is most pronounced in samples with lower viral loads. If symptoms are present but the at-home antigen test is negative, public health recommendations advise repeating the test after 48 hours. Alternatively, a follow-up molecular test, such as a PCR, is recommended to confirm the infection. While RATs remain highly specific—meaning a positive result is almost certainly accurate—their limitations emphasize the need for serial testing or confirmatory molecular testing to avoid false negatives.