The continuous evolution of SARS-CoV-2 raises questions about the ability of existing diagnostic tools to keep pace with new variants. Generally, tests authorized early in the pandemic remain effective, but viral mutations can affect test performance. The primary concern is whether changes in the viral structure prevent the test from recognizing the virus, potentially leading to an inaccurate negative result. Understanding how these tests are designed and what they target is the first step in assessing their ongoing utility.
Understanding Test Mechanisms
The two most common types of tests available to the public, Rapid Antigen Tests (RATs) and Polymerase Chain Reaction (PCR) tests, operate on fundamentally different scientific principles. Rapid antigen tests are designed to detect specific proteins, or antigens, found on the surface or within the SARS-CoV-2 virus. The vast majority of these at-home tests target the Nucleocapsid (N) protein, which encases the viral genetic material. This protein is often chosen because it is abundant and generally considered more structurally stable, or conserved, across different strains compared to the Spike (S) protein.
In contrast, laboratory-based molecular tests, such as PCR, detect the virus’s genetic material (RNA). These tests are significantly more sensitive because they amplify target RNA sequences, allowing them to detect very low levels of the virus. To minimize the risk of a variant escaping detection, many PCR tests employ a multi-target approach, looking for several different, highly conserved regions of the viral genome. While PCR tests are highly sensitive, antigen tests provide a fast, convenient result and are adept at identifying people when the viral load is highest.
How Variants Affect Test Sensitivity
The emergence of new variants, particularly Omicron and its sub-lineages, has led to documented instances of reduced test sensitivity, especially with certain rapid antigen tests. This reduction is primarily tied to the concept of analytical sensitivity—the lowest amount of virus a test can reliably detect. Mutations in the N-protein, the primary target of most RATs, can slightly alter the shape of the protein. This change may prevent the antibodies embedded in the test strip from binding effectively to the viral protein, making it harder to register a positive result.
Specific amino acid substitutions observed in variants like Beta and Delta have been shown to impair the analytical sensitivity of certain RATs. For a person infected with such a variant, the test requires a slightly higher concentration of virus to turn positive compared to the original strain. The clinical sensitivity of RATs (their ability to correctly identify an infected person) dropped during the Omicron surge, partly because the variant often presented with lower viral loads early in the infection.
For molecular tests, the risk is different, often involving a phenomenon known as “gene dropout.” If a mutation occurs precisely in one of the highly specific genetic regions targeted by the PCR test’s primers, the test may fail to amplify that specific target. For example, some PCR tests that target the S-gene showed a dropout with the Omicron variant due to multiple mutations in that region. However, the multi-target design of most modern PCR assays acts as a built-in safeguard, ensuring that if one target is missed due to a mutation, the virus is still detected by the other, unaffected targets.
Ensuring Test Reliability
Regulatory bodies play an active role in ensuring that authorized tests maintain their ability to detect circulating variants. Agencies like the Food and Drug Administration (FDA) continuously monitor the performance of diagnostic tests through a process known as post-market surveillance. This oversight includes requiring test manufacturers to evaluate the impact of new SARS-CoV-2 strains on their products.
Agencies employ sophisticated bioinformatics analysis, using computational modeling to compare the genetic sequences of new variants with the target regions of authorized tests. If a mismatch is predicted, laboratory “wet testing” is performed using actual variant samples to confirm if sensitivity has been compromised. If a test fails against a predominant variant, the regulatory body may issue public safety communications or revoke the test’s authorization. This continuous monitoring and verification ensures that diagnostic tools are appropriate for the current viral landscape.
Practical Guidance for Testing
Given the possibility of reduced sensitivity with some variants, especially for rapid antigen tests, using the tests correctly is important for obtaining reliable results. The timing of testing is a major factor, as testing too early in the course of the infection, when the viral load is still low, is a frequent cause of an inaccurate negative result. If you have symptoms, it is advisable to test immediately, but a single negative rapid test does not rule out infection.
Repeat, or serial, testing is a standard recommendation for at-home antigen tests. If you are symptomatic and receive a negative result, test again 48 hours later, for a minimum of two tests. If you have been exposed but are asymptomatic, wait at least five full days after exposure, and then test at least three times over five days, with 48 hours between each test. If you have strong symptoms but continue to receive negative antigen test results, seek a laboratory-based molecular test to confirm or rule out infection.